diff --git a/recipes/argo/meta.yaml b/recipes/argo/meta.yaml
index 3378a76c20d47..4dd54b605147c 100644
--- a/recipes/argo/meta.yaml
+++ b/recipes/argo/meta.yaml
@@ -1,5 +1,5 @@
{% set name = "argo" %}
-{% set version = "0.1.2" %}
+{% set version = "0.1.3" %}
package:
name: '{{ name|lower }}'
@@ -7,7 +7,7 @@ package:
source:
url: https://github.com/xinehc/argo/archive/refs/tags/v{{ version }}.tar.gz
- sha256: 71f9b113efc07df0101887c1c7450ca12f77b120fd9ebd841ddfdba1b7ff2fe0
+ sha256: c6be3e1efc744a591524979a53895f9cbd70962a1825d8e2b442f5ffb7a3cc6b
build:
noarch: python
diff --git a/recipes/artic/meta.yaml b/recipes/artic/meta.yaml
index 59642e631a4cb..619378e41c107 100644
--- a/recipes/artic/meta.yaml
+++ b/recipes/artic/meta.yaml
@@ -1,83 +1,76 @@
{% set name = "artic" %}
-{% set version = "1.2.4" %}
-{% set sha256 = "981219a49cec01dc82a9375b16f844278e797ad4034efa1eaa410ccb1849c617" %}
+{% set version = "1.5.3" %}
+{% set sha256 = "107483f22de571c4aafae91c475e453d939e6a8e85a7e2cd2d23ccbca224ef1c" %}
package:
name: {{ name|lower }}
version: {{ version|replace("-", "_") }}
+
source:
url: https://github.com/artic-network/fieldbioinformatics/archive/v{{ version }}.tar.gz
sha256: {{ sha256 }}
build:
- number: 1
+ number: 0
noarch: python
run_exports:
- {{ pin_subpackage('artic', max_pin='x.x') }}
- script: python -m pip install --ignore-installed .
+ script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv
entry_points:
- artic=artic.pipeline:main
- align_trim=artic.align_trim:main
- - align_trim_n=artic.align_trim_n:main
- margin_cons=artic.margin_cons:main
- - margin_cons_medaka=artic.margin_cons_medaka:main
- vcfextract=artic.vcfextract:main
- artic_vcf_merge=artic.vcf_merge:main
- artic_vcf_filter=artic.vcf_filter:main
- artic_make_depth_mask=artic.make_depth_mask:main
- artic_fasta_header=artic.fasta_header:main
- artic_mask=artic.mask:main
- - artic_get_stats=artic.artic_mqc:main
+ - artic_get_models=artic.get_models:main
requirements:
host:
- - python >=3
+ - python ==3.9
- pip
+ - setuptools
run:
- - python
- - artic-porechop >=0.3.2pre
- - artic-tools
- - longshot
+ - python ==3.9
- bcftools
- biopython
- bwa
+ - clair3
- clint
- htslib
- - medaka >=1.10.0
- - minimap2 >=2.26
+ - minimap2
- multiqc
- - muscle =3.8
- - nanopolish >=0.14.0
+ - muscle <5.1
- pandas
- - pip
- pysam
- pytest
- - pyvcf
+ - cyvcf2
- pyfaidx =0.6.0 # DO NOT CHANGE THIS PIN UNDER ANY CIRCUMSTANCES, IT WILL BREAK THE PIPELINE
- requests
- samtools
- tqdm
- - keras-preprocessing >=1.1.2
-
test:
commands:
- artic -h
- align_trim -h
- - align_trim_n -h
- margin_cons -h
- - margin_cons_medaka -h
- vcfextract -h
- artic_vcf_merge -h
- artic_vcf_filter -h
- artic_make_depth_mask -h
- artic_fasta_header -h
- artic_mask -h
- - artic_get_stats -h
+ - artic_get_models -h
about:
home: https://github.com/artic-network/fieldbioinformatics
license: MIT
+ license_family: MIT
license_file: LICENSE
- summary: ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore
-
+ summary: "ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore."
+ dev_url: https://github.com/artic-network/fieldbioinformatics
+ doc_url: https://artic.readthedocs.io/en/latest
diff --git a/recipes/arvados-python-client/meta.yaml b/recipes/arvados-python-client/meta.yaml
index c3bd699301f87..c2dfcf31b66b8 100644
--- a/recipes/arvados-python-client/meta.yaml
+++ b/recipes/arvados-python-client/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.7.4" %}
+{% set version = "3.0.0" %}
package:
name: arvados-python-client
@@ -6,7 +6,7 @@ package:
source:
url: https://pypi.io/packages/source/a/arvados-python-client/arvados-python-client-{{ version }}.tar.gz
- sha256: 932398da39daba88041f1084d19019e7300cac462ef93f181f40aa85562ff275
+ sha256: 7f980029b27a27f0f348f610784757ca6ff419aee6eb903b046c37b719e1b820
build:
noarch: python
@@ -35,6 +35,7 @@ requirements:
- protobuf <4.0.0
- pyparsing <3
- dataclasses
+ - websockets
test:
imports:
diff --git a/recipes/augur/meta.yaml b/recipes/augur/meta.yaml
index ba381bb2d3dea..50b746c7464cd 100644
--- a/recipes/augur/meta.yaml
+++ b/recipes/augur/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "26.0.0" %}
+{% set version = "26.1.0" %}
package:
name: augur
@@ -6,14 +6,14 @@ package:
source:
url: https://github.com/nextstrain/augur/releases/download/{{ version }}/nextstrain_augur-{{ version }}.tar.gz
- sha256: 0040d881eca4d695b75ba87c07a6c7abbdd13cc3e200606d77b38b875348cb07
+ sha256: 74159e9a663ad4f1171b1800dd345dd94777a37dcc74abc754351626f75668c2
build:
number: 0
noarch: python
entry_points:
- augur = augur.__main__:main
- script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv"
+ script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
run_exports:
- {{ pin_subpackage('augur', max_pin='x') }}
@@ -21,6 +21,7 @@ requirements:
host:
- python >=3.8
- pip
+ - setuptools
run:
- python >=3.8
- bcbio-gff >=0.7.1,<0.8
@@ -38,7 +39,6 @@ requirements:
- scipy >=1.0.0,<2
- treetime >=0.11.2,<0.12
- xopen[zstd] >=1.7.0,<3
-
- fasttree
- iqtree
- mafft
@@ -52,15 +52,18 @@ test:
- augur --help
about:
- home: https://github.com/nextstrain/augur
- license: AGPL-3.0-only
- summary: 'Process pathogen genome data for the Nextstrain platform'
+ home: "https://github.com/nextstrain/augur"
+ license: "AGPL-3.0-only"
+ summary: 'Process pathogen genome data for the Nextstrain platform.'
license_family: AGPL
license_file: LICENSE.txt
+ dev_url: "https://github.com/nextstrain/augur"
+ doc_url: "https://docs.nextstrain.org/projects/augur"
extra:
identifiers:
- doi:10.21105/joss.02906
+ - biotools:Augur
recipe-maintainers:
- nextstrain-bot
- huddlej
diff --git a/recipes/bakta/meta.yaml b/recipes/bakta/meta.yaml
index fa02ae9c72a68..e8647e67bb759 100644
--- a/recipes/bakta/meta.yaml
+++ b/recipes/bakta/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.9.4" %}
+{% set version = "1.10.1" %}
package:
name: bakta
@@ -6,56 +6,60 @@ package:
source:
url: https://github.com/oschwengers/bakta/archive/v{{ version }}.tar.gz
- sha256: 'ad92853e9d4f022024d393149eb086ad36a7e35f824a5d9efed94c3262f9cf66'
+ sha256: '4a13b7362dd46d44edc175956afda2478122b48bfef4fb9581c198b35fd36296'
build:
noarch: python
number: 0
- script: python -m pip install --no-deps --ignore-installed .
+ script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv
entry_points:
- bakta = bakta.main:main
- bakta_proteins = bakta.proteins:main
- bakta_db = bakta.db:main
- bakta_plot = bakta.plot:main
+ - bakta_io = bakta.json_io:main
run_exports:
- {{ pin_subpackage('bakta', max_pin='x.x') }}
requirements:
host:
- - python >=3.8, <3.11
+ - python >=3.9,<3.12
- pip
run:
- - python >=3.8, <3.11
+ - python >=3.9,<3.12
- biopython >=1.78
- xopen >=1.5.0
- requests >=2.25.1
- alive-progress ==3.0.1
- pyyaml >=6.0
- - pyrodigal >=3.1.0
+ - pyrodigal >=3.5.0
- trnascan-se >=2.0.11
- aragorn >=1.2.41
- infernal >=1.1.4
- piler-cr
- - pyhmmer >=0.10.4
- - diamond ==2.1.8
+ - pyhmmer >=0.10.15
+ - diamond >=2.1.10
- blast >=2.14.0
- - ncbi-amrfinderplus >=3.11.26
- - circos >=0.69.8
+ - ncbi-amrfinderplus >=4.0.3
+ - pycirclize >=1.7.0
test:
import:
- Bio.SeqIO
- xopen.xopen
- - pyrodigal
- requests
- alive_progress
+ - pyyaml
+ - pyrodigal
+ - pyhmmer
+ - pycirclize
commands:
- bakta --help
about:
home: https://github.com/oschwengers/bakta
- license: GPLv3
- license_family: GPL
+ license: GPL-3.0-or-later
+ license_family: GPL3
license_file: LICENSE
summary: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids.
dev_url: https://github.com/oschwengers/bakta
diff --git a/recipes/beagle/meta.yaml b/recipes/beagle/meta.yaml
index 1f6614412ea25..881555f83e5bc 100644
--- a/recipes/beagle/meta.yaml
+++ b/recipes/beagle/meta.yaml
@@ -1,13 +1,13 @@
{% set name = "beagle" %}
-{% set version = "5.4_27May24.118" %}
-{% set sha256 = "3b8f0b1dd1f56cccf0dbfd6a53b091829e69e3d693834b814af203be911b0009" %}
+{% set version = "5.4_29Oct24.c8e" %}
+{% set sha256 = "938f0b1ab12385e0686790cef52d7b9491c96c0c1837af5c0d62c9a6576a8956" %}
package:
name: {{ name }}
version: {{ version }}
source:
- url: https://faculty.washington.edu/browning/beagle/beagle.27May24.118.jar
+ url: https://faculty.washington.edu/browning/beagle/beagle.29Oct24.c8e.jar
sha256: {{ sha256 }}
build:
diff --git a/recipes/biobambam/build.sh b/recipes/biobambam/build.sh
index 272f469dffb76..53b04f87a7e43 100644
--- a/recipes/biobambam/build.sh
+++ b/recipes/biobambam/build.sh
@@ -1,4 +1,9 @@
#!/bin/bash
set -eu
-./configure --prefix=${PREFIX}
+
+autoreconf -if
+./configure --prefix="${PREFIX}" CXX="${CXX}" \
+ --with-libmaus2 --with-xerces-c --with-gmp \
+ CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" \
+ LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
make install
diff --git a/recipes/biobambam/meta.yaml b/recipes/biobambam/meta.yaml
index 482c9c1b272d1..69ad250229d2e 100644
--- a/recipes/biobambam/meta.yaml
+++ b/recipes/biobambam/meta.yaml
@@ -1,7 +1,7 @@
{% set name = "biobambam" %}
-{% set version = "2.0.183" %}
-{% set datestamp = "20210802180148" %}
-{% set sha256hash = "8712ceac509c389111b01dc3429f673dc0f8b77cb2bc48a1ebcf17f6888b2945" %}
+{% set version = "2.0.185" %}
+{% set datestamp = "20221211202123" %}
+{% set sha256 = "e405421e869ac7220c3a7e5da0d24a3c7b4c7b1807e044a439fe68efc88a1f2a" %}
package:
name: {{ name }}
@@ -9,10 +9,10 @@ package:
source:
url: https://gitlab.com/german.tischler/biobambam2/-/archive/{{ version }}-release-{{ datestamp }}/biobambam2-{{ version }}-release-{{ datestamp }}.tar.gz
- sha256: {{ sha256hash }}
+ sha256: {{ sha256 }}
build:
- number: 4
+ number: 0
skip: True # [osx]
run_exports:
- {{ pin_subpackage(name, max_pin='x') }}
@@ -21,19 +21,33 @@ requirements:
build:
- make
- {{ compiler('cxx') }}
+ - autoconf
+ - automake
+ - libtool
+ - pkg-config
host:
- - libmaus2 >=2.0.810
+ - libmaus2 >=2.0.813
+ - gmp
+ - xerces-c
+ - zlib
+ run:
+ - libmaus2 >=2.0.813
test:
commands:
- bamsormadup --help
- bamtofastq --help
+
about:
home: https://gitlab.com/german.tischler/biobambam2
- license: GPLv3
+ license: GPL-3.0-or-later
+ license_family: GPL3
license_file: GPLv3
- summary: Tools for early stage alignment file processing
+ summary: "Tools for early stage alignment file processing."
+ dev_url: https://gitlab.com/german.tischler/biobambam2
extra:
additional-platforms:
- - linux-aarch64
\ No newline at end of file
+ - linux-aarch64
+ identifiers:
+ - biotools:biobambam
diff --git a/recipes/biobb_chemistry/meta.yaml b/recipes/biobb_chemistry/meta.yaml
index 184c9e06805c0..9bf342947e649 100644
--- a/recipes/biobb_chemistry/meta.yaml
+++ b/recipes/biobb_chemistry/meta.yaml
@@ -1,5 +1,5 @@
{% set name = "biobb_chemistry" %}
-{% set version = "5.0.2" %}
+{% set version = "5.0.3" %}
package:
name: '{{ name|lower }}'
@@ -7,10 +7,10 @@ package:
source:
url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
- sha256: 96c42dda4f898413f3430c6cf73e14f4ab171a93cb8c1faa266f0ded2f905b05
+ sha256: cc89a00439b85b71bd37980cbfe00a2dbbf201613298bac731cd3830c6fb4f6e
build:
- number: 1
+ number: 0
noarch: python
script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv"
run_exports:
diff --git a/recipes/biobb_dna/meta.yaml b/recipes/biobb_dna/meta.yaml
index bc13f9acbc562..c22791c934413 100644
--- a/recipes/biobb_dna/meta.yaml
+++ b/recipes/biobb_dna/meta.yaml
@@ -1,5 +1,5 @@
{% set name = "biobb_dna" %}
-{% set version = "5.0.0" %}
+{% set version = "5.0.1" %}
package:
name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
source:
url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
- sha256: 513e133bf3e48ce0e45fb2659182a112798c1e1d8068a8a2fa99d21007af4768
+ sha256: 9a6c777bcb328d803326cce64b9fa9998b7b46da4fb9ac447a86d9b08e21fb1a
build:
number: 0
diff --git a/recipes/breakfast/meta.yaml b/recipes/breakfast/meta.yaml
index cf7699d277b38..ae6d83de4c28e 100644
--- a/recipes/breakfast/meta.yaml
+++ b/recipes/breakfast/meta.yaml
@@ -1,5 +1,5 @@
{% set name = "breakfast" %}
-{% set version = "0.4.3" %}
+{% set version = "0.4.5" %}
package:
name: {{ name|lower }}
@@ -7,43 +7,44 @@ package:
source:
url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/breakfast-{{ version }}.tar.gz
- sha256: a241e0d4891c62635f1b99559271fb4b7777ffa60ef67e25be579d6750c01b9c
+ sha256: 5dd370d4d6d92d7b161acc5356b3b6c7f454d9c0665a8abac38e5f6c012d3eee
build:
entry_points:
- breakfast = breakfast.console:main
+ run_exports:
+ - {{ pin_subpackage('breakfast', max_pin="x.x") }}
noarch: python
- script: {{ PYTHON }} -m pip install . -vv
+ script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
number: 0
requirements:
host:
- pip
- - poetry
- - python >=3.6,<3.11
+ - poetry-core
+ - python >=3.11,<3.13
run:
- - click >=8.1.3,<9.0.0
- - networkx >=2.8,<3.0
- - numpy >=1.22.3,<2.0.0
- - pandas >=1.4.2,<2.0.0
+ - click >=8.1.7,<9.0.0
+ - networkx >=3.4.2,<4.0.0
+ - numpy >=2.1.3,<3.0.0
+ - pandas >=2.2.3,<3.0.0
- python >=3.9,<3.11
- - scikit-learn >=1.0.2,<2.0.0
- - scipy >=1.8.0,<2.0.0
+ - scikit-learn >=1.5.2,<2.0.0
+ - scipy >=1.14.1,<2.0.0
test:
imports:
- breakfast
commands:
- - pip check
- breakfast --help
- requires:
- - pip
about:
home: https://github.com/rki-mf1/breakfast
- summary: 'breakfast: fast putative outbreak cluster and infection chain detection using SNPs'
+ summary: 'breakfast: fast putative outbreak cluster and infection chain detection using SNPs.'
license: MIT
+ license_family: MIT
license_file: LICENSE
+ dev_url: https://github.com/rki-mf1/breakfast
extra:
recipe-maintainers:
diff --git a/recipes/cadd-scripts/meta.yaml b/recipes/cadd-scripts/meta.yaml
index a507661a3f9dc..6c6356301556d 100644
--- a/recipes/cadd-scripts/meta.yaml
+++ b/recipes/cadd-scripts/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "1.7.1" %}
-{% set sha256 = "c5db00dc26a585cc70500cf535865a4d9e7765db60a71edf1d267af32ae974e4" %}
+{% set version = "1.7.2" %}
+{% set sha256 = "fb2d1deeffe8e1ef5abb042b0bce48f864878b9de80d2a27b16d5a8389e25e20" %}
package:
name: cadd-scripts
diff --git a/recipes/cgat-apps/0001-setup.py.patch b/recipes/cgat-apps/0001-setup.py.patch
new file mode 100644
index 0000000000000..7dc8f129e99f4
--- /dev/null
+++ b/recipes/cgat-apps/0001-setup.py.patch
@@ -0,0 +1,327 @@
+diff --git a/requires.txt b/requires.txt
+deleted file mode 100644
+index e69de29b..00000000
+diff --git a/setup.py b/setup.py
+index 1cc415ea..56d2ccd8 100644
+--- a/setup.py
++++ b/setup.py
+@@ -4,239 +4,73 @@ import os
+ import subprocess
+ import re
+
+-########################################################################
+-#######################################################################
+-# Check for dependencies
+-#
+-# Is there a way to do this more elegantly?
+-# 1. Run "pip install numpy"
+-# 2. Wrap inside functions (works for numpy/pysam, but not cython)
+-try:
+- import numpy
+-except ImportError:
+- raise ImportError(
+- "the CGAT code collection requires numpy to be installed "
+- "before running setup.py (pip install numpy)")
++# Import setuptools at the beginning
++import setuptools
++from setuptools import setup, find_packages, Extension
++from distutils.version import LooseVersion
++from Cython.Distutils import build_ext
+
++# Ensure dependencies are installed before setup
+ try:
++ import numpy
+ import Cython
+-except ImportError:
+- raise ImportError(
+- "the CGAT code collection requires cython to "
+- "be installed before running setup.py (pip install cython)")
+-
+-try:
+ import pysam
+-except ImportError:
+- raise ImportError(
+- "the CGAT code collection requires pysam to "
+- "be installed before running setup.py (pip install pysam)")
++except ImportError as e:
++ missing_package = str(e).split("'")[1]
++ raise ImportError(f"{missing_package} must be installed before running setup.py")
+
+-########################################################################
+-########################################################################
+-# Import setuptools
+-# Use existing setuptools, otherwise try ez_setup.
+-try:
+- import setuptools
+-except ImportError:
+- # try to get via ez_setup
+- # ez_setup did not work on all machines tested as
+- # it uses curl with https protocol, which is not
+- # enabled in ScientificLinux
+- import ez_setup
+- ez_setup.use_setuptools()
++# Enforce Python 3 requirement
++if sys.version_info < (3, 6):
++ raise SystemExit("Python 3.6 or later is required to install this package.")
+
+-from setuptools import setup, find_packages, Extension
+-
+-from distutils.version import LooseVersion
++# Minimum setuptools version requirement
+ if LooseVersion(setuptools.__version__) < LooseVersion('1.1'):
+- print("Version detected:", LooseVersion(setuptools.__version__))
+- raise ImportError(
+- "the CGAT code collection requires setuptools 1.1 higher")
++ raise ImportError("Setuptools version >=1.1 is required")
+
+-from Cython.Distutils import build_ext
+-
+-########################################################################
+-########################################################################
+-IS_OSX = sys.platform == 'darwin'
+-
+-########################################################################
+-########################################################################
+-# collect CGAT version
++# Define version and other package information
+ sys.path.insert(0, "cgat")
+ import version
+-
+ version = version.__version__
+
+-###############################################################
+-###############################################################
+-# Check for external dependencies
+-#
+-# Not exhaustive, simply execute a representative tool from a toolkit.
+-external_dependencies = (
+- ("wigToBigWig", "UCSC tools", 255),
+- ("bedtools", "bedtools", 0),
+- )
++IS_OSX = sys.platform == 'darwin'
+
++# External dependency check
++external_dependencies = [("wigToBigWig", "UCSC tools", 255), ("bedtools", "bedtools", 0)]
+ for tool, toolkit, expected in external_dependencies:
+- try:
+- # py3k
+- from subprocess import DEVNULL
+- except ImportError:
+- DEVNULL = open(os.devnull, 'wb')
+-
+- try:
+- retcode = subprocess.call(tool, shell=True,
+- stdout=DEVNULL, stderr=DEVNULL)
+- except OSError as msg:
+- print(("WARNING: depency check for %s failed: %s" % (toolkit, msg)))
+-
+- # UCSC tools return 255 when called without arguments
++ retcode = subprocess.call(tool, shell=True, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+ if retcode != expected:
+- print(("WARNING: depency check for %s(%s) failed, error %i" %
+- (toolkit, tool, retcode)))
+-
+-###############################################################
+-###############################################################
+-# Define dependencies
+-#
+-major, minor1, minor2, s, tmp = sys.version_info
+-
+-if (major == 2 and minor1 < 7) or major < 2:
+- raise SystemExit("""CGAT requires Python 2.7 or later.""")
+-
+-
+-#####################################################################
+-#####################################################################
+-# Code to install dependencies from a repository
+-#####################################################################
+-# Modified from http://stackoverflow.com/a/9125399
+-#####################################################################
+-def which(program):
+- """
+- Detect whether or not a program is installed.
+- Thanks to http://stackoverflow.com/a/377028/70191
+- """
+- def is_exe(fpath):
+- return os.path.exists(fpath) and os.access(fpath, os.X_OK)
+-
+- fpath, _ = os.path.split(program)
+- if fpath:
+- if is_exe(program):
+- return program
+- else:
+- for path in os.environ['PATH'].split(os.pathsep):
+- exe_file = os.path.join(path, program)
+- if is_exe(exe_file):
+- return exe_file
+-
+- return None
+-
+-REPO_REQUIREMENT = re.compile(
+- r'^-e (?P(?Pgit|svn|hg|bzr).+#egg=(?P.+)-(?P\d(?:\.\d)*))$')
+-HTTPS_REQUIREMENT = re.compile(
+- r'^-e (?P.*).+#(?P.+)-(?P\d(?:\.\d)*)$')
+-install_requires = []
+-dependency_links = []
+-
+-for requirement in (
+- l.strip() for l in open('requires.txt') if not l.startswith("#")):
+- match = REPO_REQUIREMENT.match(requirement)
+- if match:
+- assert which(match.group('vcs')) is not None, \
+- ("VCS '%(vcs)s' must be installed in order to "
+- "install %(link)s" % match.groupdict())
+- install_requires.append("%(package)s==%(version)s" % match.groupdict())
+- dependency_links.append(match.group('link'))
+- continue
++ print(f"WARNING: Dependency check for {toolkit} ({tool}) failed with error code {retcode}")
+
+- if requirement.startswith("https"):
+- install_requires.append(requirement)
+- continue
+
+- match = HTTPS_REQUIREMENT.match(requirement)
+- if match:
+- install_requires.append("%(package)s>=%(version)s" % match.groupdict())
+- dependency_links.append(match.group('link'))
+- continue
+-
+- install_requires.append(requirement)
+-
+-if major == 2:
+- install_requires.extend(['web.py>=0.37',
+- 'xlwt>=0.7.4',
+- 'matplotlib-venn>=0.5'])
+-elif major == 3:
+- pass
+-
+-cgat_packages = find_packages(exclude=['tests'])
++# Adjust packages and directories
++cgat_packages = find_packages(include=["cgat", "cgat.*"], exclude=['tests'])
+ cgat_package_dirs = {'cgat': 'cgat'}
+
+-##########################################################
+-##########################################################
+-# classifiers
+-classifiers = """
+-Development Status :: 3 - Alpha
+-Intended Audience :: Science/Research
+-Intended Audience :: Developers
+-License :: OSI Approved
+-Programming Language :: Python
+-Topic :: Software Development
+-Topic :: Scientific/Engineering
+-Operating System :: POSIX
+-Operating System :: Unix
+-Operating System :: MacOS
+-"""
+-
+-##########################################################
+-# Cython Extensions
++# Cython extensions and paths
+ conda_includes = [os.path.dirname(sysconfig.get_paths()["include"])]
+ conda_libdirs = [os.path.dirname(sysconfig.get_paths()["stdlib"])]
+-
+-# Connected components cython extension
+ pysam_libraries = pysam.get_libraries()
+-pysam_libdirs = list(set(os.path.dirname(x) for x in
+- pysam_libraries)) + conda_libdirs
+-
+-# remove lib and .so and add htslib
+-pysam_libs = ["hts"] + list([os.path.basename(x)[3:-3] for x in
+- pysam_libraries])
+-
++pysam_libdirs = list(set(os.path.dirname(x) for x in pysam_libraries)) + conda_libdirs
++pysam_libs = ["hts"] + [os.path.basename(x)[3:-3] for x in pysam_libraries]
+ pysam_dirname = os.path.dirname(pysam.__file__)
+-if IS_OSX:
+- # linking against bundles does no work (and apparently is not needed)
+- # within OS X
+- extra_link_args = []
+-else:
+- extra_link_args = [os.path.join(pysam_dirname, x) for x in
+- pysam.get_libraries()]
+-
+-extra_link_args_pysam = ['-Wl,-rpath,{}'.format(x) for x in pysam_libdirs] +\
+- ['-Wl,-rpath,{}'.format(x) for x in conda_libdirs]
++extra_link_args_pysam = [f'-Wl,-rpath,{x}' for x in pysam_libdirs + conda_libdirs]
+
+ extensions = [
+ Extension(
+ 'cgat.Components',
+- ['cgat/Components/Components.pyx',
+- 'cgat/Components/connected_components.cpp', ],
+- library_dirs=[],
+- libraries=[],
++ ['cgat/Components/Components.pyx', 'cgat/Components/connected_components.cpp'],
++ include_dirs=[os.path.join('cgat', 'Components')] + conda_includes,
+ language="c++",
+ ),
+ Extension(
+ "cgat.NCL.cnestedlist",
+- ["cgat/NCL/cnestedlist.pyx",
+- "cgat/NCL/intervaldb.c"],
+- library_dirs=[],
+- libraries=[],
++ ["cgat/NCL/cnestedlist.pyx", "cgat/NCL/intervaldb.c"],
+ language="c",
+ ),
+ Extension(
+ "cgat.GeneModelAnalysis",
+ ["cgat/GeneModelAnalysis.pyx"],
+ include_dirs=conda_includes + pysam.get_include() + [numpy.get_include()],
+- library_dirs=[],
+- libraries=[],
+ define_macros=pysam.get_defines(),
+ language="c",
+ ),
+@@ -292,11 +126,8 @@ extensions = [
+ ),
+ ]
+
+-for e in extensions:
+- e.cython_directives = {'language_level': "3str"} #all are Python-3
+-
++# Build setup configuration
+ setup(
+- # package information
+ name='cgat',
+ version=version,
+ description='cgat : the Computational Genomics Analysis Toolkit',
+@@ -306,22 +137,26 @@ setup(
+ platforms=["any"],
+ keywords="computational genomics",
+ long_description='cgat : the Computational Genomics Analysis Toolkit',
+- classifiers=[_f for _f in classifiers.split("\n") if _f],
++ classifiers=[_f for _f in """
++ Development Status :: 3 - Alpha
++ Intended Audience :: Science/Research
++ Intended Audience :: Developers
++ License :: OSI Approved
++ Programming Language :: Python
++ Topic :: Software Development
++ Topic :: Scientific/Engineering
++ Operating System :: POSIX
++ Operating System :: Unix
++ Operating System :: MacOS
++ """.splitlines() if _f],
+ url="http://www.cgat.org/cgat/Tools/",
+- # package contents
++ python_requires=">=3.6",
+ packages=cgat_packages,
+ package_dir=cgat_package_dirs,
+ include_package_data=True,
+- entry_points={
+- 'console_scripts': ['cgat = cgat.cgat:main']
+- },
+- # dependencies
+- install_requires=install_requires,
+- dependency_links=dependency_links,
+- # extension modules
++ entry_points={'console_scripts': ['cgat = cgat.cgat:main']},
+ ext_modules=extensions,
+ cmdclass={'build_ext': build_ext},
+- # other options
+ zip_safe=False,
+ test_suite="tests",
+ )
diff --git a/recipes/cgat-apps/build.sh b/recipes/cgat-apps/build.sh
index 404e4cfe860ef..c2405bcd10101 100644
--- a/recipes/cgat-apps/build.sh
+++ b/recipes/cgat-apps/build.sh
@@ -1,28 +1,16 @@
#!/bin/bash
# export compiler flags
-#export CFLAGS=${CFLAGS}" -I${PREFIX}/include -L${PREFIX}/lib"
-#export CPPFLAGS=${CPPFLAGS}" -I${PREFIX}/include -L${PREFIX}/lib"
-export LDFLAGS=${LDFLAGS}" -I${PREFIX}/include -L${PREFIX}/lib"
-export CPATH=${CPATH}" -I${PREFIX}/include -L${PREFIX}/lib"
-export C_INCLUDE_PATH=${C_INCLUDE_PATH}:${PREFIX}/include
-export CPLUS_INCLUDE_PATH=${CPLUS_INCLUDE_PATH}:${PREFIX}/include
-export LIBRARY_PATH=${LIBRARY_PATH}:${PREFIX}/lib
-export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${PREFIX}/lib:${PREFIX}/lib/R/lib
-
-# linking htslib, see:
-# http://pysam.readthedocs.org/en/latest/installation.html#external
-# https://github.com/pysam-developers/pysam/blob/v0.9.0/setup.py#L79
-#export CFLAGS="-I$PREFIX/include -DHAVE_LIBDEFLATE"
-#export CPPFLAGS="-I$PREFIX/include -DHAVE_LIBDEFLATE"
-#export LDFLAGS="-L$PREFIX/lib"
-
-#export HTSLIB_LIBRARY_DIR=$PREFIX/lib
-#export HTSLIB_INCLUDE_DIR=$PREFIX/include
+export INCLUDE_PATH="${PREFIX}/include"
+export LIBRARY_PATH="${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CFLAGS="${CFLAGS} -O3 -L${PREFIX}/lib"
+export CPPFLAGS="${CPPFLAGS} -O3 -I${PREFIX}/include"
# remove install_requires (no longer required with conda package)
-sed -i'' -e '/REPO_REQUIREMENT/,/pass/d' setup.py
-sed -i'' -e '/# dependencies/,/dependency_links=dependency_links,/d' setup.py
+sed -i.bak'' -e '/REPO_REQUIREMENT/,/pass/d' setup.py
+sed -i.bak'' -e '/# dependencies/,/dependency_links=dependency_links,/d' setup.py
+rm -rf *.bak
# https://bioconda.github.io/linting.html#setup-py-install-args
-$PYTHON setup.py install --single-version-externally-managed --record=record.txt
+$PYTHON -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
diff --git a/recipes/cgat-apps/build_failure.linux-64.yaml b/recipes/cgat-apps/build_failure.linux-64.yaml
deleted file mode 100644
index e3ce08b25b4e4..0000000000000
--- a/recipes/cgat-apps/build_failure.linux-64.yaml
+++ /dev/null
@@ -1,105 +0,0 @@
-recipe_sha: cd4db28503c1e8d834aba9be11a1d56ca31801f1fcbbef8169312e7476bc9123 # The hash of the recipe's meta.yaml at which this recipe failed to build.
-skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
-category: dependency issue
-log: |2-
- File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems
- self._maybe_raise_for_conda_build(
- File "/opt/conda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build
- raise exc
- conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform linux-64: {MatchSpec("python[version='>=3.7,<3.8.0a0']"), MatchSpec("alignlib-lite==0.3=py37h3f2a3d2_2")}
- Encountered problems while solving:
- - package alignlib-lite-0.3-py37h3f2a3d2_2 requires python >=3.7,<3.8.0a0, but none of the providers can be installed
-
- Could not solve for environment specs
- The following packages are incompatible
- [32malignlib-lite[0m is installable with the potential options
- [32malignlib-lite 0.3[0m would require
- [32mpython >=3.7,<3.8.0a0 [0m with the potential options
- [32mpython [2.7.15|3.5.5|3.6.6|3.7.0][0m would require
- [32mopenssl >=1.0.2o,<1.0.3a [0m, which can be installed;
- [32mpython [2.7.15|3.6.6|3.6.7|3.7.0|3.7.1][0m would require
- [32mopenssl >=1.0.2p,<1.0.3a [0m, which can be installed;
- [32mpython [2.7.15|3.6.7|...|3.7.6][0m would require
- [32mopenssl >=1.1.1a,<1.1.2a [0m, which can be installed;
- [32mpypy3.6 7.3.0.* [0m with the potential options
- [32mpypy3.6 7.3.0[0m would require
- [32mopenssl >=1.1.1a,<1.1.2a [0m, which can be installed;
- [32mpypy3.6 7.3.0[0m would require
- [32mopenssl >=1.1.1d,<1.1.2a [0m, which can be installed;
- [32mpypy3.6 7.3.0[0m would require
- [32mopenssl >=1.1.1e,<1.1.2a [0m, which can be installed;
- [32mpython 3.7.10[0m would require
- [32mpypy3.7 [7.3.4.* |7.3.5.* ][0m with the potential options
- [32mpypy3.7 [7.3.4|7.3.5][0m would require
- [32mopenssl >=1.1.1k,<1.1.2a [0m, which can be installed;
- [32mpypy3.7 7.3.5[0m would require
- [32mopenssl >=1.1.1l,<1.1.2a [0m, which can be installed;
- [32mpython [3.6.13|3.6.15|3.7.10|3.7.12][0m would require
- [32mopenssl >=1.1.1l,<1.1.2a [0m, which can be installed;
- [32mpython [3.7.10|3.7.12][0m, which can be installed;
- [32mpython [3.6.13|3.7.10][0m would require
- [32mopenssl >=1.1.1j,<1.1.2a [0m, which can be installed;
- [32mpython [3.6.12|3.7.5|3.7.9][0m would require
- [32mopenssl >=1.1.1i,<1.1.2a [0m, which can be installed;
- [32mpypy3.6 7.3.3.* [0m, which requires
- [32mopenssl >=1.1.1i,<1.1.2a [0m, which can be installed;
- [32mpypy3.7 7.3.3.* [0m, which requires
- [32mopenssl >=1.1.1i,<1.1.2a [0m, which can be installed;
- [32mpython [3.6.10|3.6.11|3.7.6|3.7.8][0m would require
- [32mopenssl >=1.1.1g,<1.1.2a [0m, which can be installed;
- [32mpython 3.7.6[0m would require
- [32mopenssl >=1.1.1e,<1.1.2a [0m, which can be installed;
- [32mpython [3.6.11|3.6.12|3.6.9|3.7.8|3.7.9][0m would require
- [32mopenssl >=1.1.1h,<1.1.2a [0m, which can be installed;
- [32mpypy3.6 7.3.2.* [0m, which requires
- [32mopenssl >=1.1.1h,<1.1.2a [0m, which can be installed;
- [32malignlib-lite [0.2.3|0.3][0m would require
- [32mpython [2.7* |3.6* |>=2.7,<2.8.0a0 |>=3.6,<3.7.0a0 ][0m with the potential options
- [32mpython [2.7.15|3.5.5|3.6.6|3.7.0][0m, which can be installed (as previously explained);
- [32mpython [2.7.15|3.6.6|3.6.7|3.7.0|3.7.1][0m, which can be installed (as previously explained);
- [32mpython [2.7.15|3.6.7|...|3.7.6][0m, which can be installed (as previously explained);
- [32mpython [3.6.13|3.6.15|3.7.10|3.7.12][0m, which can be installed (as previously explained);
- [32mpython [3.6.13|3.7.10][0m, which can be installed (as previously explained);
- [32mpython [3.6.12|3.7.5|3.7.9][0m, which can be installed (as previously explained);
- [32mpython [3.6.10|3.6.11|3.7.6|3.7.8][0m, which can be installed (as previously explained);
- [32mpython [3.6.11|3.6.12|3.6.9|3.7.8|3.7.9][0m, which can be installed (as previously explained);
- [32mpython [2.7.12|2.7.13|...|3.6.5][0m would require
- [32mopenssl [1.0* |1.0.* ][0m, which can be installed;
- [32mpython [3.6.10|3.6.9][0m would require
- [32mopenssl >=1.1.1f,<1.1.2a [0m, which can be installed;
- [32mpypy3.6 7.3.1.* [0m, which requires
- [32mopenssl >=1.1.1f,<1.1.2a [0m, which can be installed;
- [32mpython [3.6.10|3.6.9][0m would require
- [32mopenssl >=1.1.1d,<1.1.2a [0m, which can be installed;
- [32malignlib-lite [0.2.3|0.3][0m would require
- [32mpython [3.4* |3.5* |>=3.5,<3.6.0a0 ][0m, which can be installed (as previously explained);
- [32malignlib-lite 0.3[0m would require
- [32mpython_abi 3.10.* *_cp310[0m, which can be installed;
- [32malignlib-lite 0.3[0m would require
- [32mpython_abi 3.7.* *_cp37m[0m, which can be installed;
- [32malignlib-lite 0.3[0m would require
- [32mpython_abi 3.8.* *_cp38[0m, which can be installed;
- [32malignlib-lite 0.3[0m would require
- [32mpython_abi 3.9.* *_cp39[0m, which can be installed;
- [32mpysam >=0.22.1,<0.23.0a0 [0m is installable with the potential options
- [32mpysam 0.22.1[0m would require
- [32mpython_abi 3.8.* *_cp38[0m, which can be installed;
- [32mpysam 0.22.1[0m would require
- [32mpython_abi 3.10.* *_cp310[0m, which can be installed;
- [31mpysam 0.22.1[0m would require
- [31mopenssl >=3.3.1,<4.0a0 [0m, which conflicts with any installable versions previously reported;
- [32mpysam 0.22.1[0m would require
- [32mpython_abi 3.12.* *_cp312[0m, which can be installed;
- [32mpysam 0.22.1[0m would require
- [32mpython_abi 3.9.* *_cp39[0m, which can be installed;
- [31mpython >=3.11,<3.12.0a0 [0m is not installable because there are no viable options
- [31mpython [3.11.0|3.11.1|...|3.11.9][0m would require
- [31mpython_abi 3.11.* *_cp311[0m, which conflicts with any installable versions previously reported;
- [31mpython 3.11.0[0m would require
- [32mopenssl >=1.1.1q,<1.1.2a [0m, which can be installed;
- [31mpython_abi 3.11.* *_cp311[0m, which conflicts with any installable versions previously reported;
- [31mpython 3.11.0[0m would require
- [32mopenssl >=1.1.1s,<1.1.2a [0m, which can be installed;
- [31mpython_abi 3.11.* *_cp311[0m, which conflicts with any installable versions previously reported;
- [31mpython_abi 3.11.* *_cp311[0m is not installable because it conflicts with any installable versions previously reported.
-# Last 100 lines of the build log.
diff --git a/recipes/cgat-apps/build_failure.osx-64.yaml b/recipes/cgat-apps/build_failure.osx-64.yaml
deleted file mode 100644
index 63feff1b5e2d5..0000000000000
--- a/recipes/cgat-apps/build_failure.osx-64.yaml
+++ /dev/null
@@ -1,105 +0,0 @@
-recipe_sha: cd4db28503c1e8d834aba9be11a1d56ca31801f1fcbbef8169312e7476bc9123 # The hash of the recipe's meta.yaml at which this recipe failed to build.
-skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
-category: dependency issue
-log: |2-
- alignlib-lite 0.3 would require
- python_abi 3.7.* *_cp37m, which can be installed;
- alignlib-lite 0.3 would require
- python >=3.7,<3.8.0a0 , which can be installed;
- alignlib-lite 0.3 would require
- python_abi 3.8.* *_cp38, which can be installed;
- alignlib-lite 0.3 would require
- python_abi 3.9.* *_cp39, which can be installed;
- pysam >=0.22.1,<0.23.0a0 is installable with the potential options
- pysam 0.22.1 would require
- xz >=5.2.6,<6.0a0 , which conflicts with any installable versions previously reported;
- pysam 0.22.1 would require
- python_abi 3.12.* *_cp312, which can be installed;
- python >=3.11,<3.12.0a0 is not installable because it requires
- python_abi 3.11.* *_cp311, which conflicts with any installable versions previously reported;
- python_abi 3.11.* *_cp311 is not installable because it conflicts with any installable versions previously reported.
-
- During handling of the above exception, another exception occurred:
-
- Traceback (most recent call last):
- File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in
- sys.exit(execute())
- File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute
- api.build(
- File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build
- return build_tree(
- File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree
- packages_from_this = build(
- File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2409, in build
- create_build_envs(top_level_pkg, notest)
- File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2247, in create_build_envs
- raise e
- File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2220, in create_build_envs
- environ.get_package_records(
- File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions
- precs = get_package_records(
- File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions
- precs = get_package_records(
- File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 937, in get_install_actions
- precs = get_package_records(
- File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 891, in get_install_actions
- precs = _install_actions(prefix, index, specs)["LINK"]
- File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/environ.py", line 1301, in install_actions
- txn = solver.solve_for_transaction(prune=False, ignore_pinned=False)
- File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 153, in solve_for_transaction
- unlink_precs, link_precs = self.solve_for_diff(
- File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda/core/solve.py", line 222, in solve_for_diff
- final_precs = self.solve_final_state(
- File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 223, in solve_final_state
- out_state = self._solving_loop(in_state, out_state, index)
- File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 303, in _solving_loop
- solved = self._solve_attempt(in_state, out_state, index, attempt=attempt)
- File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 414, in _solve_attempt
- new_conflicts = self._maybe_raise_for_problems(
- File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 712, in _maybe_raise_for_problems
- self._maybe_raise_for_conda_build(
- File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_libmamba_solver/solver.py", line 805, in _maybe_raise_for_conda_build
- raise exc
- conda_libmamba_solver.conda_build_exceptions.ExplainedDependencyNeedsBuildingError: Unsatisfiable dependencies for platform osx-64: {MatchSpec("alignlib-lite==0.2.3=py27_1"), MatchSpec("python=2.7")}
- Encountered problems while solving:
- - package alignlib-lite-0.2.3-py27_1 requires python 2.7*, but none of the providers can be installed
-
- Could not solve for environment specs
- The following packages are incompatible
- alignlib-lite is installable with the potential options
- alignlib-lite [0.2.3|0.3] would require
- python [2.7* |>=2.7,<2.8.0a0 ], which can be installed;
- alignlib-lite [0.2.3|0.3] would require
- python 3.4* , which can be installed;
- alignlib-lite [0.2.3|0.3] would require
- python [3.5* |>=3.5,<3.6.0a0 ] with the potential options
- python [3.5.1|3.5.2] would require
- xz 5.0.* , which can be installed;
- python [3.5.2|3.5.3|3.5.4|3.5.5], which can be installed;
- alignlib-lite 0.3 would require
- python_abi 2.7.* *_cp27m, which can be installed;
- alignlib-lite 0.3 would require
- python_abi 3.10.* *_cp310, which can be installed;
- alignlib-lite 0.3 would require
- python 3.6* , which can be installed;
- alignlib-lite 0.3 would require
- python >=3.6,<3.7.0a0 , which can be installed;
- alignlib-lite 0.3 would require
- python_abi 3.6.* *_cp36m, which can be installed;
- alignlib-lite 0.3 would require
- python_abi 3.7.* *_cp37m, which can be installed;
- alignlib-lite 0.3 would require
- python >=3.7,<3.8.0a0 , which can be installed;
- alignlib-lite 0.3 would require
- python_abi 3.8.* *_cp38, which can be installed;
- alignlib-lite 0.3 would require
- python_abi 3.9.* *_cp39, which can be installed;
- pysam >=0.22.1,<0.23.0a0 is installable with the potential options
- pysam 0.22.1 would require
- xz >=5.2.6,<6.0a0 , which conflicts with any installable versions previously reported;
- pysam 0.22.1 would require
- python_abi 3.12.* *_cp312, which can be installed;
- python >=3.11,<3.12.0a0 is not installable because it requires
- python_abi 3.11.* *_cp311, which conflicts with any installable versions previously reported;
- python_abi 3.11.* *_cp311 is not installable because it conflicts with any installable versions previously reported.
-# Last 100 lines of the build log.
diff --git a/recipes/cgat-apps/meta.yaml b/recipes/cgat-apps/meta.yaml
index 4cf264a7950fe..cc4106af5f493 100644
--- a/recipes/cgat-apps/meta.yaml
+++ b/recipes/cgat-apps/meta.yaml
@@ -1,18 +1,18 @@
{% set name = "cgat-apps" %}
-{% set version = "0.7.2" %}
+{% set version = "0.7.4" %}
package:
name: {{ name|lower }}
version: {{ version }}
source:
- url: https://pypi.io/packages/source/c/cgat/cgat-{{ version }}.tar.gz
- sha256: 746701d1a6677e8200092894c35c942383123fd8e22ab172f3ef6b2222b8eaef
-
+ url: https://github.com/cgat-developers/cgat-apps/archive/refs/tags/v{{ version }}.tar.gz
+ sha256: 3e161597c6e4cf59fc121a8527aeddefd1526f7d13c370d5eaf15b4d3a1894e6
+ patches:
+ - 0001-setup.py.patch
build:
- number: 2
- skip: true # [py == 312]
+ number: 0
run_exports:
- {{ pin_subpackage('cgat-apps', max_pin="x.x") }}
entry_points:
@@ -24,11 +24,11 @@ requirements:
- {{ compiler('cxx') }}
host:
- python
- - cython
+ - pip
+ - cython >=0.29.35
- numpy
- pysam
- htslib
- - setuptools
run:
- python
- cgatcore
@@ -52,7 +52,6 @@ requirements:
- ucsc-wigtobigwig
- coreutils
- grep
- - zlib
test:
imports:
@@ -65,7 +64,10 @@ test:
- cgat bam2bed -h
about:
- home: https://cgat-apps.readthedocs.io/en/latest/
+ home: "https://github.com/cgat-developers/cgat-apps"
license: MIT
+ license_family: MIT
license_file: LICENSE
- summary: "Computational Genomics Analysis Toolkit"
+ summary: "Computational Genomics Analysis Toolkit."
+ dev_url: "https://github.com/cgat-developers/cgat-apps"
+ doc_url: "https://cgat-apps.readthedocs.io/en/latest"
diff --git a/recipes/cnvkit/meta.yaml b/recipes/cnvkit/meta.yaml
index f39326c930829..d4ce6da29663e 100644
--- a/recipes/cnvkit/meta.yaml
+++ b/recipes/cnvkit/meta.yaml
@@ -1,5 +1,5 @@
{% set name = "cnvkit" %}
-{% set version = "0.9.11" %}
+{% set version = "0.9.12" %}
package:
name: {{ name }}
@@ -7,7 +7,7 @@ package:
source:
url: https://github.com/etal/cnvkit/archive/v{{ version }}.tar.gz
- sha256: 1763936427184270108fd51219ebc82f542e28339bdec587579b8745f61179a8
+ sha256: 39d65ba3d9c541dfd80986ace298b2d521067d1b81edef7169196b8dcc5d63d5
build:
noarch: python
@@ -22,6 +22,7 @@ requirements:
host:
- python >=3.8
- pip
+ - setuptools
run:
- python >=3.8
- bioconductor-dnacopy
@@ -49,13 +50,13 @@ test:
- cnvkit.py -h
about:
- home: https://github.com/etal/cnvkit
- license: Apache-2.0
+ home: "https://github.com/etal/cnvkit"
+ license: "Apache-2.0"
license_family: APACHE
license_file: LICENSE
- summary: Copy number variant detection from high-throughput sequencing
- dev_url: https://github.com/etal/cnvkit
- doc_url: https://cnvkit.readthedocs.io/en/stable/
+ summary: "Copy number variant detection from high-throughput sequencing."
+ dev_url: "https://github.com/etal/cnvkit"
+ doc_url: "https://cnvkit.readthedocs.io/en/stable"
extra:
identifiers:
diff --git a/recipes/dupsifter/meta.yaml b/recipes/dupsifter/meta.yaml
index 43bc3d576002f..2e02cdc953848 100644
--- a/recipes/dupsifter/meta.yaml
+++ b/recipes/dupsifter/meta.yaml
@@ -1,17 +1,17 @@
-{% set version = '1.2.1.20240119' %}
+{% set version = '1.3.0.20241113' %}
package:
name: dupsifter
version: {{ version }}
build:
- number: 1
+ number: 0
run_exports:
- {{ pin_subpackage('dupsifter', max_pin='x') }}
source:
url: https://github.com/huishenlab/dupsifter/releases/download/v{{ version }}/release-source.zip
- sha256: ca3db67e36f9a3d054acf9fbaf0dee1037781d468d7f094ea5d3852610448e7a
+ sha256: 270f1c2dfc2152d8ed63b6660aea9eca0398ff34529c606fd0ae30b1858ebb08
patches:
- patch
@@ -25,16 +25,10 @@ requirements:
- xz
- zlib
- libdeflate
- - openssl # [not osx]
+ - openssl # [not osx]
- pthread-stubs
run:
- - libcurl
- - bzip2
- - xz
- - zlib
- - libdeflate
- - openssl # [not osx]
- - pthread-stubs
+ - openssl # [not osx]
test:
commands:
@@ -43,4 +37,11 @@ test:
about:
home: https://github.com/huishenlab/dupsifter
license: MIT
- summary: A tool for PCR duplicate marking of WGBS (and WGS) data
+ license_family: MIT
+ summary: A tool for PCR duplicate marking of WGBS (and WGS) data.
+ dev_url: https://github.com/huishenlab/dupsifter
+
+extra:
+ additional-platforms:
+ - linux-aarch64
+ - osx-arm64
diff --git a/recipes/ebi-eva-common-pyutils/meta.yaml b/recipes/ebi-eva-common-pyutils/meta.yaml
index f06b115b8bb5c..2753d1c68df3b 100644
--- a/recipes/ebi-eva-common-pyutils/meta.yaml
+++ b/recipes/ebi-eva-common-pyutils/meta.yaml
@@ -1,5 +1,5 @@
{% set name = "ebi-eva-common-pyutils" %}
-{% set version = "0.6.10" %}
+{% set version = "0.6.11" %}
package:
name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
source:
url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/ebi_eva_common_pyutils-{{ version }}.tar.gz
- sha256: f143c703e31f40c94ebe366ba5f8a8247b6c825590ac157a7f5495f36aa7accb
+ sha256: 503f15c55b8438295727661486d610e87b7e9c9ca159ff8e373d0533094eb93b
build:
script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
diff --git a/recipes/fairy/meta.yaml b/recipes/fairy/meta.yaml
index 5eb8910ec915f..02f9abd665509 100644
--- a/recipes/fairy/meta.yaml
+++ b/recipes/fairy/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.5.5" %}
+{% set version = "0.5.7" %}
package:
name: fairy
@@ -11,7 +11,7 @@ build:
source:
url: https://github.com/bluenote-1577/fairy/archive/v{{ version }}.tar.gz
- sha256: 2d36fb115f3c069d4788c46f03ed054dc9b8f73228ed1b04d6b1d6bfd8c4124c
+ sha256: 4a4583f0efa3b818d6c3cef43e1f732b307554465ba76f3916f51e4ae02baefc
requirements:
build:
diff --git a/recipes/fibertools-rs/meta.yaml b/recipes/fibertools-rs/meta.yaml
index 2a13e6f52bfd5..bd4ad503eaa77 100644
--- a/recipes/fibertools-rs/meta.yaml
+++ b/recipes/fibertools-rs/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.5.4" %}
+{% set version = "0.6.0" %}
{% set name = "fibertools-rs" %}
{% set build_number = "0" %}
@@ -8,7 +8,7 @@ package:
source:
url: https://github.com/fiberseq/fibertools-rs/archive/v{{ version }}.tar.gz
- sha256: d0dc8523b9c0f2c2b368fb450d6cf6f45e13fb53bdbbd1847f1bb748fb5af42b
+ sha256: 4f33fb470766ed325f83767cf766e7795afcfc1af8dae4e807876b1560efc193
build:
run_exports:
diff --git a/recipes/get_homologues/meta.yaml b/recipes/get_homologues/meta.yaml
index 0528198c7538b..e6dd0fb579d0f 100644
--- a/recipes/get_homologues/meta.yaml
+++ b/recipes/get_homologues/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "3.7.1" %}
-{% set sha256 = "eeb9361695cafc35a1b92b29b647874713f85641218b1de5cddca551d334fe9d" %}
+{% set version = "3.7.2" %}
+{% set sha256 = "01333d82d29047e2dee0f2e4ccc43303ab23831852e9000aee42ffdf3d33b85c" %}
package:
name: get_homologues
diff --git a/recipes/gfainject/meta.yaml b/recipes/gfainject/meta.yaml
index f3d9aa1891954..22b1d7c8084b7 100644
--- a/recipes/gfainject/meta.yaml
+++ b/recipes/gfainject/meta.yaml
@@ -1,5 +1,5 @@
{% set name = "gfainject" %}
-{% set version = "0.1.0" %}
+{% set version = "0.1.1" %}
package:
name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
source:
url: https://github.com/AndreaGuarracino/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
- sha256: a4388e524d5942f53d2fa94a93b2e82c926506c27cfdf04c04fbe8669a7ecebf
+ sha256: a11f41ee94614d8c089454fdb3d0fb96e2f305db46895e2f64d974fa1707e739
build:
number: 0
@@ -17,6 +17,11 @@ build:
requirements:
build:
- {{ compiler('rust') }}
+ - cmake
+ - make
+ - pkg-config
+ - {{ compiler('c') }} # For zlib-ng compilation
+ - {{ compiler('cxx') }} # For C++ dependencies if any
test:
commands:
diff --git a/recipes/gseapy/meta.yaml b/recipes/gseapy/meta.yaml
index 57e181ec0d301..666784f6c44ed 100644
--- a/recipes/gseapy/meta.yaml
+++ b/recipes/gseapy/meta.yaml
@@ -1,10 +1,10 @@
package:
name: gseapy
- version: "1.1.3"
+ version: "1.1.4"
source:
- url: https://files.pythonhosted.org/packages/28/c2/7c03f74682de640b71ba9a9958c5c8a90867b0f4f9ffef2c15702113d47a/gseapy-1.1.3.tar.gz
- sha256: 7f9218bb4014a862680d4d3e806e59bec8f81601e876a04495922da81da1b395
+ url: https://files.pythonhosted.org/packages/12/92/0a4e24f4a0ac772e8ec652f299a89292eb66d67e329579e1ea48cc006250/gseapy-1.1.4.tar.gz
+ sha256: 7e858752d7684b1abed124c585f3ca2f156ff22985575234232a54c57b88ba66
build:
entry_points:
@@ -12,7 +12,7 @@ build:
run_exports:
- {{ pin_subpackage("gseapy", max_pin="x") }}
skip: True # [py2k or py == 36 ]
- number: 1
+ number: 0
requirements:
build:
diff --git a/recipes/gtotree/meta.yaml b/recipes/gtotree/meta.yaml
index 1a94e22d51527..1a4a923150f61 100644
--- a/recipes/gtotree/meta.yaml
+++ b/recipes/gtotree/meta.yaml
@@ -10,7 +10,7 @@ source:
sha256: 81e5856fa188a5096725605a31a1bf6bf4f8baa1dc2acc83eda29a0ff7a742b5
build:
- number: 0
+ number: 1
run_exports:
- {{ pin_compatible(name, max_pin='x') }}
@@ -21,7 +21,7 @@ requirements:
- python
- biopython
- hmmer
- - muscle =5
+ - muscle =5.1
- trimal
- fasttree
- iqtree >=2.2.2
@@ -38,6 +38,7 @@ requirements:
- file
- coreutils =9.1
- curl
+ - pyarrow
test:
commands:
diff --git a/recipes/gubbins/meta.yaml b/recipes/gubbins/meta.yaml
index 2166a683609f3..a2454b35b7e55 100644
--- a/recipes/gubbins/meta.yaml
+++ b/recipes/gubbins/meta.yaml
@@ -1,6 +1,6 @@
{% set name = "gubbins" %}
-{% set version = "3.3.5" %}
-{% set sha256 = "4ee363f82708bdda0c00d1c6c334cf20127bd852ee488619f61140771a279774" %}
+{% set version = "3.4" %}
+{% set sha256 = "ff134b7c1d06eee548e94f417394fb67229caf1b0d35b097a71309017ac7a91d" %}
package:
name: {{ name|lower }}
@@ -29,6 +29,7 @@ requirements:
- perl
- zlib
- python >=3.8,<3.10
+ - pip
- scipy
- setuptools
- dendropy
diff --git a/recipes/hmftools-chord/build.sh b/recipes/hmftools-chord/build.sh
index a1a96f8a03b8b..4138fe335551c 100644
--- a/recipes/hmftools-chord/build.sh
+++ b/recipes/hmftools-chord/build.sh
@@ -5,9 +5,8 @@ TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM"
[ -d "${PREFIX}/bin" ] || mkdir -p "${PREFIX}/bin"
cd "${SRC_DIR}"
-mv jar/chord*.jar $TGT/chord.jar
-${R} CMD INSTALL --build src/chord/src/main/R/mutSigExtractor
-${R} CMD INSTALL --build src/chord/src/main/R/CHORD
+mv chord*.jar $TGT/chord.jar
cp $RECIPE_DIR/chord.sh $TGT/chord
ln -s $TGT/chord ${PREFIX}/bin/
+chmod 0755 "${PREFIX}/bin/chord"
\ No newline at end of file
diff --git a/recipes/hmftools-chord/meta.yaml b/recipes/hmftools-chord/meta.yaml
index cb5e88a813be6..3634b0ab4f329 100644
--- a/recipes/hmftools-chord/meta.yaml
+++ b/recipes/hmftools-chord/meta.yaml
@@ -1,51 +1,33 @@
{% set version = "2.1.0_beta" %}
-{% set sha256_jar = "26d0a40e20635c4b797d28e0c7819b1653c9f8fa28180b9a556215d22387968c" %}
-{% set sha256_src = "ed039e7b405130a1e52df71c3535c6a5ed8aab0f80724bc83df88ae14aeaa257" %}
+{% set beta_suffix = ".1" %}
+{% set sha256 = "25a4dfd8a0ab436e0f23d94e77cebb59a0830a052a90c823844b798bd409bfc3" %}
package:
name: hmftools-chord
version: '{{ version }}'
source:
- - folder: jar
- url: https://github.com/hartwigmedical/hmftools/releases/download/chord-v{{ version }}/chord-{{ version }}.jar
- sha256: '{{ sha256_jar }}'
- - folder: src
- url: https://github.com/hartwigmedical/hmftools/archive/refs/tags/chord-v{{ version }}.tar.gz
- sha256: '{{ sha256_src }}'
+ url: https://github.com/hartwigmedical/hmftools/releases/download/chord-v{{ version }}/chord_v{{ version }}{{ beta_suffix }}.jar
+ sha256: '{{ sha256 }}'
build:
noarch: generic
- number: 0
+ number: 2
run_exports:
- {{ pin_subpackage("hmftools-chord", max_pin="x.x") }}
requirements:
- host:
- - r-base
- - r-randomforest
- - r-stringr
- - bioconductor-bsgenome
- - bioconductor-bsgenome.hsapiens.ucsc.hg19
- - bioconductor-bsgenome.hsapiens.ucsc.hg38
run:
- openjdk >=8
- r-base
- r-randomforest
- - r-stringr
- - bioconductor-bsgenome
- - bioconductor-bsgenome.hsapiens.ucsc.hg19
- - bioconductor-bsgenome.hsapiens.ucsc.hg38
test:
commands:
- - $R -e "library('CHORD')"
- - $R -e "library('mutSigExtractor')"
- - 'chord com.hartwig.hmftools.chord.ChordRunner -version | grep CHORD'
+ - 'chord -version | grep CHORD'
about:
home: https://github.com/hartwigmedical/hmftools/blob/master/chord/
license: GPL-3.0-only
license_family: GPL3
- license_file: LICENSE
summary: Predict HRD using somatic mutations contexts
diff --git a/recipes/hmftools-esvee/meta.yaml b/recipes/hmftools-esvee/meta.yaml
index 18f76aad8eedf..2707038fefc1e 100644
--- a/recipes/hmftools-esvee/meta.yaml
+++ b/recipes/hmftools-esvee/meta.yaml
@@ -1,6 +1,6 @@
{% set version = "1.0_beta" %}
-{% set beta_suffix = ".3" %}
-{% set sha256 = "da026c1bec9c8314652f7c3870daa2d8eaddd3dc71ef924d86339c87d084d65a" %}
+{% set beta_suffix = ".4" %}
+{% set sha256 = "9a833992f4b8c5c01d845ed60c96fc93c43c5955171658255c545413cedb23d5" %}
package:
name: hmftools-esvee
@@ -12,7 +12,7 @@ source:
build:
noarch: generic
- number: 4
+ number: 5
run_exports:
- {{ pin_subpackage("hmftools-esvee", max_pin="x.x") }}
diff --git a/recipes/hmftools-orange/meta.yaml b/recipes/hmftools-orange/meta.yaml
index df7a40c1b0e4d..e78d3011cc1ce 100644
--- a/recipes/hmftools-orange/meta.yaml
+++ b/recipes/hmftools-orange/meta.yaml
@@ -1,6 +1,6 @@
{% set version = "3.7.1_beta" %}
-{% set beta_suffix = ".2" %}
-{% set sha256 = "c1ba13d266e5197b5cdc20f2691578714784d7669b95f0182f69d174c663e70e" %}
+{% set beta_suffix = ".3" %}
+{% set sha256 = "b729b440aa0361f52e31b446234b98234cde768ec75e97044dca952909e120c1" %}
package:
name: hmftools-orange
@@ -12,7 +12,7 @@ source:
build:
noarch: generic
- number: 1
+ number: 2
run_exports:
- {{ pin_subpackage('hmftools-orange', max_pin="x") }}
diff --git a/recipes/hmftools-pave/meta.yaml b/recipes/hmftools-pave/meta.yaml
index 8d3d58bc78dd7..f75fa9630ac7b 100644
--- a/recipes/hmftools-pave/meta.yaml
+++ b/recipes/hmftools-pave/meta.yaml
@@ -1,17 +1,18 @@
{% set version = "1.7_beta" %}
-{% set sha256 = "b6e67aa0bb96db3b50429afe4a6c6fad168660bf220f61b638e06b0c643969ab" %}
+{% set beta_suffix = ".1" %}
+{% set sha256 = "adfc0bbbf3a8b35faa7a5ce2d1fb0a5c016ae71fcd80cfa2dd28caa4e1b5826a" %}
package:
name: hmftools-pave
version: '{{ version }}'
source:
- url: https://github.com/hartwigmedical/hmftools/releases/download/pave-v{{ version }}/pave_v{{ version }}.jar
+ url: https://github.com/hartwigmedical/hmftools/releases/download/pave-v{{ version }}/pave_v{{ version }}{{ beta_suffix }}.jar
sha256: '{{ sha256 }}'
build:
noarch: generic
- number: 0
+ number: 1
run_exports:
- {{ pin_subpackage('hmftools-pave', max_pin="x.x") }}
diff --git a/recipes/hmftools-redux/meta.yaml b/recipes/hmftools-redux/meta.yaml
index 30f2c8148650d..8d940a51d025b 100644
--- a/recipes/hmftools-redux/meta.yaml
+++ b/recipes/hmftools-redux/meta.yaml
@@ -1,6 +1,6 @@
{% set version = "1.0_beta" %}
-{% set beta_suffix = ".3" %}
-{% set sha256 = "6c7710471c055d228fb569728eccd16d7c0bbea4a59026d4575e9e539ece983a" %}
+{% set beta_suffix = ".4" %}
+{% set sha256 = "e3398c8fba7f9e572ac06def6d957ceed1598f0c6b9b06563814ccfec5c3158f" %}
package:
name: hmftools-redux
@@ -12,13 +12,13 @@ source:
build:
noarch: generic
- number: 4
+ number: 6
run_exports:
- {{ pin_subpackage('hmftools-redux', max_pin="x.x") }}
requirements:
run:
- - openjdk >=8
+ - openjdk >=8,<=21
- sambamba >=1.0.1
test:
diff --git a/recipes/hybracter/meta.yaml b/recipes/hybracter/meta.yaml
index 2084feff2576c..748dac08e3c7b 100644
--- a/recipes/hybracter/meta.yaml
+++ b/recipes/hybracter/meta.yaml
@@ -1,5 +1,5 @@
{% set name = "hybracter" %}
-{% set version = "0.10.0" %}
+{% set version = "0.10.1" %}
package:
name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
source:
url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/hybracter-{{ version }}.tar.gz
- sha256: 6640aacea33671c2bf1714693ecdd48c87a708d8bbf0ad1f964ddd6fc34e0224
+ sha256: 4e8e3454d18a33727156dfea274e83fbb9f2e3b9cc6cd5d5a7a8e53a5c5223ce
build:
number: 0
diff --git a/recipes/isoquant/meta.yaml b/recipes/isoquant/meta.yaml
index ee3930be3b942..b6b2fd3056ed7 100644
--- a/recipes/isoquant/meta.yaml
+++ b/recipes/isoquant/meta.yaml
@@ -1,6 +1,6 @@
{% set name = "IsoQuant" %}
-{% set version = "3.6.1" %}
-{% set sha256 = "6d16e47e9ca45f9a0d029940d5b84e03038d9ba3d640945e3a5087acfd7ed56d" %}
+{% set version = "3.6.2" %}
+{% set sha256 = "b742fe460b44d0d9feb967938176e707cfe4f281c53bf4fe04af2440c31e7862" %}
package:
name: {{ name | lower }}
diff --git a/recipes/itsxpress/meta.yaml b/recipes/itsxpress/meta.yaml
index cbef171ed668d..0f3c1b5b93e26 100644
--- a/recipes/itsxpress/meta.yaml
+++ b/recipes/itsxpress/meta.yaml
@@ -1,8 +1,8 @@
{% set name = "itsxpress" %}
-{% set version = "2.1.2" %}
+{% set version = "2.1.3" %}
{% set file_ext = "tar.gz" %}
{% set hash_type = "sha256" %}
-{% set hash_value = "5a19ef9333ac4acacfa1da9c27ff3f713d7521661fbfe7541c58221c2ce2d08f" %}
+{% set hash_value = "a911701cbcf86ca6fc59b606d20fbee7015577477cfd4aa41d97420f23ad87c0" %}
package:
name: '{{ name|lower }}'
@@ -17,7 +17,7 @@ build:
number: 0
entry_points:
- itsxpress=itsxpress.main:main
- script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation . -vvv
+ script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv
run_exports:
- {{ pin_subpackage('itsxpress', max_pin="x") }}
@@ -25,8 +25,8 @@ requirements:
host:
- pip
- python >=3.8
+ - setuptools
run:
- - pip
- python >=3.8
- biopython >=1.79
- hmmer =3.1b2
@@ -44,7 +44,7 @@ about:
license: CC0-1.0
license_family: 'PUBLIC-DOMAIN'
summary: 'ITSxpress: Software to rapidly trim the Internally Transcribed Spacer (ITS) region from FASTQ files'
-
+ dev_url: http://github.com/usda-ars-gbru/itsxpress
extra:
recipe-maintainers:
diff --git a/recipes/jaeger-bio/meta.yaml b/recipes/jaeger-bio/meta.yaml
index 388ff7957b63e..0e7aa7a4d9a46 100644
--- a/recipes/jaeger-bio/meta.yaml
+++ b/recipes/jaeger-bio/meta.yaml
@@ -1,50 +1,48 @@
{% set name = "jaeger-bio" %}
-{% set version = "1.1.26" %}
+{% set version = "1.1.30" %}
package:
name: "{{ name|lower }}"
version: "{{ version }}"
source:
- url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
- sha256: 7f7d8794cd04185f7787d92a6ccc89fa59bb58acbe0fe929c6bffbee39a90fe4
+ url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/jaeger_bio-{{ version }}.tar.gz"
+ sha256: ffc54d7257201310ff137dd61dcb1d8afe6c7f95bf2fdf578fec79a16145aeae
build:
number: 0
- script: "{{ PYTHON }} -m pip install . --no-cache-dir -vvv"
- noarch: python
+ script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
run_exports:
- - {{ pin_subpackage('jaeger-bio', max_pin="x.x.x") }}
+ - {{ pin_subpackage('jaeger-bio', max_pin="x") }}
+ noarch: python
requirements:
host:
- - python =3
+ - python >=3.9,<3.12
- pip
run:
- - python =3
- - pip
- h5py >=3.8
- - biopython >=1.78
- kneed >=0.8.5
- matplotlib-base >=3.7
- numpy >=1.24
- pandas >=1.5
+ - progressbar2 >=4.4.2
- psutil >=5
+ - pycirclize
+ - pyfastx >=2
+ - python >=3.9,<3.12
- ruptures >=1.1.9
- scikit-learn ==1.3.2
- - seaborn >=0.12.2
- - tqdm >=4.64.0
- - tensorflow >=2.15,<2.16
- parasail-python >=1.3.4
+ - tensorflow >=2.15,<2.16
test:
imports:
- jaegeraa
- jaegeraa.data
- jaegeraa.nnlib
-
commands:
- - Jaeger --help
+ - jaeger --help
about:
home: "https://github.com/Yasas1994/Jaeger"
@@ -56,7 +54,5 @@ about:
doc_url: https://readthedocs.org/projects/jaeger-docs/
extra:
- identifiers:
- - biotools:jaeger
recipe-maintainers:
- Yasas1994
diff --git a/recipes/kestrel/build.sh b/recipes/kestrel/build.sh
new file mode 100644
index 0000000000000..6069aed727d79
--- /dev/null
+++ b/recipes/kestrel/build.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+set -euo pipefail
+
+kestrel="${PREFIX}/opt/${PKG_NAME}-${PKG_VERSION}"
+
+mkdir -p "${kestrel}"
+cp -r ./* "${kestrel}"
+chmod +x "${kestrel}/kestrel"
+mkdir -p "${PREFIX}/bin"
+
+if [[ -L "${PREFIX}/bin/kestrel" ]]; then
+ echo "Error: File ${PREFIX}/bin/kestrel already exists"
+ exit 1
+fi
+
+if [[ ! -f "${kestrel}/kestrel" ]]; then
+ echo "Error: Target file ${kestrel}/kestrel does not exist"
+ exit 1
+fi
+ln -s "${kestrel}/kestrel" "${PREFIX}/bin/kestrel" || exit 1
diff --git a/recipes/kestrel/meta.yaml b/recipes/kestrel/meta.yaml
new file mode 100644
index 0000000000000..0bf3d2202ceb8
--- /dev/null
+++ b/recipes/kestrel/meta.yaml
@@ -0,0 +1,38 @@
+{% set name = "kestrel" %}
+{% set version = "1.0.3" %}
+
+package:
+ name: {{ name }}
+ version: {{ version }}
+
+source:
+ url: https://github.com/paudano/{{ name }}/releases/download/{{ version }}/{{ name }}-{{ version }}-linux.tar.gz
+ sha256: 992c579fc52dce7b9d80e6232914da02663a2480d28b672277d80fdfcdda33e3
+
+build:
+ noarch: generic
+ detect_binary_files_with_prefix: true
+ number: 0
+ run_exports:
+ - {{ pin_subpackage('kestrel', max_pin="x") }}
+
+requirements:
+ run:
+ # Enforce a version requirement on openjdk to ensure
+ # it comes from the conda-forge channel and not default.
+ # Many yaks were shaved to bring us this information.
+ # Version number reference: https://github.com/conda/conda/issues/6948#issuecomment-369360906
+ - openjdk >=8.0.144
+
+test:
+ commands:
+ - kestrel
+ - kestrel -h
+
+about:
+ home: 'https://github.com/paudano/kestrel'
+ license: GPL-3.0-or-later
+ license_family: GPL3
+ license_file: COPYING
+ summary: 'Mapping-free variant caller for short-read Illumina data'
+
diff --git a/recipes/krakentools/meta.yaml b/recipes/krakentools/meta.yaml
index 55c5462baa269..0993897f425fe 100644
--- a/recipes/krakentools/meta.yaml
+++ b/recipes/krakentools/meta.yaml
@@ -12,8 +12,9 @@ source:
build:
noarch: python
- number: 0
-
+ number: 1
+ run_exports:
+ - {{ pin_subpackage("krakentools", max_pin="x.x") }}
requirements:
host:
- python
@@ -21,6 +22,7 @@ requirements:
- python
- biopython
- numpy
+ - scipy
test:
commands:
@@ -40,9 +42,8 @@ about:
home: https://github.com/jenniferlu717/KrakenTools
license: GPL-3.0
license_family: GPL
- summary: {{ name }} is a suite of scripts to be used for post-analysis of
- Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using
- {{ name }} with any of the listed programs.
+ license_file: LICENSE
+ summary: {{ name }} scripts for analysis of Kraken/KrakenUniq/Kraken2/Bracken results
extra:
identifiers:
diff --git a/recipes/libmaus2/build.sh b/recipes/libmaus2/build.sh
index cdd58fb79e892..7d73807646dd1 100644
--- a/recipes/libmaus2/build.sh
+++ b/recipes/libmaus2/build.sh
@@ -1,10 +1,14 @@
#!/bin/bash
set -eu
-export LIBS="-lstdc++fs -lcurl"
+export LIBS="-lstdc++fs -lcurl -lz -ldeflate"
-./configure --prefix $PREFIX --with-snappy --with-io_lib
+autoreconf -if
+./configure --prefix="${PREFIX}" CXX="${CXX}" CC="${CC}" \
+ LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" \
+ CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" \
+ --with-snappy --with-io_lib --with-libdeflate \
+ --with-libsecrecy --with-nettle \
+ --with-lzma --with-gmp
-cat config.log
-
-make -j${CPU_COUNT}
+make -j"${CPU_COUNT}"
make install
diff --git a/recipes/libmaus2/meta.yaml b/recipes/libmaus2/meta.yaml
index 3d8c6738d991c..7a7a7f2f344b6 100644
--- a/recipes/libmaus2/meta.yaml
+++ b/recipes/libmaus2/meta.yaml
@@ -1,7 +1,7 @@
{% set name = "libmaus2" %}
-{% set version = "2.0.810" %}
-{% set datestamp = "20220216151520" %}
-{% set sha256hash = "6639289aba6bbece3057ab7d1782a1b94b80a9ae22fc3d136a78ba8f7b9edaee" %}
+{% set version = "2.0.813" %}
+{% set datestamp = "20221210220409" %}
+{% set sha256 = "4125f8daefd6900185675026498369457088e25e81029597659249be49cd5261" %}
package:
name: {{ name }}
@@ -10,47 +10,61 @@ package:
build:
# There's some issue with clang
skip: True # [osx]
- number: 6
+ number: 0
run_exports:
- - {{ pin_subpackage('libmaus2', max_pin='x.x') }}
+ - {{ pin_subpackage('libmaus2', max_pin='x') }}
source:
url: https://gitlab.com/german.tischler/libmaus2/-/archive/{{ version }}-release-{{ datestamp }}/libmaus2-{{ version }}-release-{{ datestamp }}.tar.gz
- sha256: {{ sha256hash }}
- patches:
+ sha256: {{ sha256 }}
+ #patches:
# Until gcc >=8 is being used
- - patch
+ #- patch
requirements:
build:
- make
- {{ compiler('c') }}
- {{ compiler('cxx') }}
+ - autoconf
+ - automake
+ - libtool
+ - pkg-config
host:
- boost-cpp
+ - libgomp # [linux]
+ - llvm-openmp # [osx]
- libcurl
# snappy 1.1.9 introduced a binary incompatible build change (https://github.com/mhx/dwarfs/issues/56#issuecomment-896857211)
# enabling -fno-rtti. libmaus needs typeid, which is only available with activated rtti.
# Hence, we stick with snappy 1.1.8
- - snappy =1.1.8
+ - snappy =1.1.8
- staden_io_lib >=1.14.14
+ - libdeflate
+ - gmp
+ - nettle
+ - zlib
run:
- boost-cpp
- - libcurl
+ - libgomp # [linux]
+ - llvm-openmp # [osx]
- snappy =1.1.8
- staden_io_lib >=1.14.14
- ignore_run_exports:
- - snappy
-
-about:
- home: https://gitlab.com/german.tischler/libmaus2
- license: GPL3
- summary: collection of data structures and algorithms for NGS data
test:
commands:
- echo
+about:
+ home: https://gitlab.com/german.tischler/libmaus2
+ license: GPL-3.0-or-later
+ license_family: GPL3
+ license_file: GPLv3
+ summary: "Collection of data structures and algorithms for NGS data."
+ dev_url: https://gitlab.com/german.tischler/libmaus2
+
extra:
additional-platforms:
- linux-aarch64
+ identifiers:
+ - biotools:libmaus
diff --git a/recipes/libmaus2/patch b/recipes/libmaus2/patch
index f66efbfe6c761..1d8376b29a4a1 100644
--- a/recipes/libmaus2/patch
+++ b/recipes/libmaus2/patch
@@ -127,36 +127,6 @@ index 134ff0f4..b8fcfe88 100644
setHWTReq (p_hwt_req.string());
setHWT (p_hwt.string());
-diff --git a/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp b/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
-index 1e8e53b9..a91d1916 100644
---- a/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
-+++ b/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
-@@ -111,11 +111,11 @@ namespace libmaus2
- // base tmp directory name
- std::string tmpdirname;
- // tmpdirname as path object
-- std::filesystem::path tmppath;
-- std::filesystem::path base_tmp_path;
-- std::filesystem::path ds_tmp_path_base_ds_tmp;
-- std::filesystem::path merge_tmp_path;
-- std::filesystem::path ds_tmp_path_merge_ds_tmp;
-+ std::experimental::filesystem::path tmppath;
-+ std::experimental::filesystem::path base_tmp_path;
-+ std::experimental::filesystem::path ds_tmp_path_base_ds_tmp;
-+ std::experimental::filesystem::path merge_tmp_path;
-+ std::experimental::filesystem::path ds_tmp_path_merge_ds_tmp;
-
- std::unique_ptr DSbase;
- std::unique_ptr DSmerge;
-@@ -333,7 +333,7 @@ namespace libmaus2
- return C;
- }
-
-- static std::filesystem::path ensureDirectory(std::filesystem::path path)
-+ static std::experimental::filesystem::path ensureDirectory(std::experimental::filesystem::path path)
- {
- libmaus2::aio::OutputStreamFactoryContainer::mkdirp(path.string(),0700);
- return path;
diff --git a/src/libmaus2/util/ArgInfo.cpp b/src/libmaus2/util/ArgInfo.cpp
index 3802cbb7..8ecd441c 100644
--- a/src/libmaus2/util/ArgInfo.cpp
@@ -267,6 +237,42 @@ index 2ff71e4a..0714e612 100644
dictpath /= digest;
std::cerr << "[V] writing " << dictpath << " for " << pat.sid << " in " << ref << std::endl;
---
-2.33.0
-
+diff --git a/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp b/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
+index 180f466..0b69f74 100644
+--- a/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
++++ b/src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
+@@ -111,11 +111,11 @@ namespace libmaus2
+ // base tmp directory name
+ std::string tmpdirname;
+ // tmpdirname as path object
+- std::filesystem::path tmppath;
+- std::filesystem::path base_tmp_path;
+- std::filesystem::path ds_tmp_path_base_ds_tmp;
+- std::filesystem::path merge_tmp_path;
+- std::filesystem::path ds_tmp_path_merge_ds_tmp;
++ std::experimental::filesystem::path tmppath;
++ std::experimental::filesystem::path base_tmp_path;
++ std::experimental::filesystem::path ds_tmp_path_base_ds_tmp;
++ std::experimental::filesystem::path merge_tmp_path;
++ std::experimental::filesystem::path ds_tmp_path_merge_ds_tmp;
+
+ std::unique_ptr DSbase;
+ std::unique_ptr DSmerge;
+@@ -333,7 +333,7 @@ namespace libmaus2
+ return C;
+ }
+
+- static std::filesystem::path ensureDirectory(std::filesystem::path path)
++ static std::experimental::filesystem::path ensureDirectory(std::experimental::filesystem::path path)
+ {
+ libmaus2::aio::OutputStreamFactoryContainer::mkdirp(path.string(),0700);
+ return path;
+@@ -358,7 +358,7 @@ namespace libmaus2
+ preisasamplingrate(std::min(options.maxpreisasamplingrate,blocksizeprevtwo)),
+ V_boundedlcpblockvalues(new libmaus2::util::AtomicArray(numblocks,0)),
+ // tmp directory name
+- tmpdirname(ensureDirectory(std::filesystem::path(options.tmpfilenamebase + "_tmpdir")).string()),
++ tmpdirname(ensureDirectory(std::experimental::filesystem::path(options.tmpfilenamebase + "_tmpdir")).string()),
+ // path object for tmp directory name
+ tmppath(tmpdirname),
+ base_tmp_path(ensureDirectory(tmppath / "base_tmp")),
diff --git a/recipes/merqury/meta.yaml b/recipes/merqury/meta.yaml
index 583ae7429b8e1..d903c7837069f 100644
--- a/recipes/merqury/meta.yaml
+++ b/recipes/merqury/meta.yaml
@@ -11,7 +11,7 @@ source:
sha256: {{ sha256 }}
build:
- number: 2
+ number: 3
noarch: generic
run_exports:
- {{ pin_subpackage("merqury", max_pin='x.x') }}
@@ -22,7 +22,7 @@ requirements:
- openjdk >=11.0.1
- r-base >=4
- r-argparse >=2.0.1
- - r-ggplot2 >=3.3.2
+ - r-ggplot2 >=3.3.2,<=3.3.6
- r-scales >=1.1.1
- bedtools >=2.29.2
- samtools >=1.10
diff --git a/recipes/metabolights-utils/meta.yaml b/recipes/metabolights-utils/meta.yaml
index 62b9ce34f8b48..7984177eb2af4 100644
--- a/recipes/metabolights-utils/meta.yaml
+++ b/recipes/metabolights-utils/meta.yaml
@@ -1,5 +1,5 @@
{% set name = "metabolights-utils" %}
-{% set version = "1.2.2" %}
+{% set version = "1.3.1" %}
package:
name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
source:
url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/metabolights_utils-{{ version }}.tar.gz
- sha256: 6698a1b4bdeda9aa0aea0329900f0fbbc8cae8e60f40fc316e5e5a03eec6ff20
+ sha256: 84cf47a421ef77fa3b14e90290396eec96cd6440128b239de211543b29b59818
build:
entry_points:
diff --git a/recipes/muse/0001-Makefile.patch b/recipes/muse/0001-Makefile.patch
new file mode 100644
index 0000000000000..f74a0587e8375
--- /dev/null
+++ b/recipes/muse/0001-Makefile.patch
@@ -0,0 +1,51 @@
+diff --git a/Makefile b/Makefile
+index 5edd6e1..78d946c 100755
+--- a/Makefile
++++ b/Makefile
+@@ -1,6 +1,6 @@
+-CPP := g++
+-CC := gcc
+-LINK := g++
++CPP := ${CXX}
++CC := ${CC}
++LINK := ${CXX}
+ mkfile_dir := $(dir $(abspath $(lastword $(MAKEFILE_LIST))))
+
+ CSOURCES= $(wildcard src/*.c)
+@@ -11,12 +11,12 @@ COMMONOBJS= lib/libhts.a lib/libboost_iostreams.a lib/libtcmalloc_minimal.a
+ Warnings=-Wreturn-type -Warray-bounds -Wmaybe-uninitialized -Waddress
+ WarningsAsErrors=$(Warnings) -Werror=return-type -Werror=array-bounds -Werror=address
+ CFLAGS= $(WarningsAsErrors) -Wno-unused-function
+-CPPFLAGS= $(WarningsAsErrors) -Wno-unused-function -std=c++11
++CPPFLAGS= $(WarningsAsErrors) -Wno-unused-function -std=c++14
+
+ RELEASE_FLAGS= -O3 -g
+
+ # Includes
+-INCLUDES = -Iinc/
++INCLUDES += -Iinc/ -Iinc/htslib -I$(PREFIX)/include
+ #
+ # Common flags
+ COMMONFLAGS += $(INCLUDES)
+@@ -24,7 +24,7 @@ COMMONFLAGS += $(INCLUDES)
+ CXXFLAGS += $(COMMONFLAGS)
+ CFLAGS += $(COMMONFLAGS)
+ CPPFLAGS += $(COMMONFLAGS)
+-COMMONLIBS= -Llib/ -lz -lm -lpthread -lbz2 -lcurl -lcrypto -llzma -fopenmp
++COMMONLIBS += -Llib/ -lz -lm -lpthread -lbz2 -lcurl -lcrypto -llzma -lhts -ldl -fopenmp -L${PREFIX}/lib
+
+ #LIBS += $(COMMONLIBS) -ltcmalloc
+ LIBS += $(COMMONLIBS)
+@@ -38,10 +38,10 @@ all: $(TARGET)
+ .SUFFIXES: .c .cpp .o
+
+ %.c.o: %.c
+- $(CC) $(CFLAGS) $(RELEASE_FLAGS) -c $< -o $@
++ $(CC) $(CFLAGS) $(RELEASE_FLAGS) $(INCLUDES) $(LIBS) -c $< -o $@
+
+ %.cpp.o: %.cpp
+- $(CPP) $(CPPFLAGS) $(RELEASE_FLAGS) $(OPENMP) -c $< -o $@
++ $(CPP) $(CPPFLAGS) $(RELEASE_FLAGS) $(OPENMP) $(INCLUDES) $(LIBS) -c $< -o $@
+
+ $(TARGET): $(OBJS) Makefile
+ $(LINKLINE)
diff --git a/recipes/muse/0001-add-LDFLAGS.patch b/recipes/muse/0001-add-LDFLAGS.patch
deleted file mode 100644
index f28ec42a45648..0000000000000
--- a/recipes/muse/0001-add-LDFLAGS.patch
+++ /dev/null
@@ -1,7 +0,0 @@
---- Makefile
-+++ Makefile
-@@ -9,3 +9,3 @@
- $(BIN): $(C_OBJ) $(CPP_OBJ)
-- $(CPP) $(C_OBJ) $(CPP_OBJ) -o $(BIN) -lm -lz
-+ $(CPP) $(C_OBJ) $(CPP_OBJ) -o $(BIN) $(LDFLAGS) -lm -lz
-
diff --git a/recipes/muse/build.sh b/recipes/muse/build.sh
index f29124b5ed79f..dc0bf210dc652 100644
--- a/recipes/muse/build.sh
+++ b/recipes/muse/build.sh
@@ -1,6 +1,29 @@
-#!/usr/bin/env bash
+#!/bin/bash
+set -euo pipefail
-make CPP="${CXX}" CPPFLAGS="${CXXFLAGS}"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CFLAGS="${CFLAGS} -O3"
-mkdir -p "${PREFIX}/bin"
-cp MuSE "${PREFIX}/bin/"
+rm -rf boost_1_70_0/
+
+if [[ `uname` == "Darwin" ]]; then
+ ln -sf ${CC} ${PREFIX}/bin/clang
+ ln -sf ${CXX} ${PREFIX}/bin/clang++
+else
+ ln -sf ${CC} ${PREFIX}/bin/gcc
+ ln -sf ${CXX} ${PREFIX}/bin/g++
+fi
+
+./install_muse.sh
+
+if [[ `uname` == "Darwin" ]]; then
+ rm -rf ${PREFIX}/bin/clang
+ rm -rf ${PREFIX}/bin/clang++
+else
+ rm -rf ${PREFIX}/bin/gcc
+ rm -rf ${PREFIX}/bin/g++
+fi
+
+install -d "${PREFIX}/bin"
+install -v -m 0755 MuSE "${PREFIX}/bin"
diff --git a/recipes/muse/fix-install_muse.sh.patch b/recipes/muse/fix-install_muse.sh.patch
new file mode 100644
index 0000000000000..22d3f5f457f2f
--- /dev/null
+++ b/recipes/muse/fix-install_muse.sh.patch
@@ -0,0 +1,99 @@
+diff --git a/install_muse.sh b/install_muse.sh
+index 7bc2153..8a57cf7 100755
+--- a/install_muse.sh
++++ b/install_muse.sh
+@@ -4,13 +4,20 @@ make clean
+
+ mkdir -p lib
+
++if [[ `uname` == "Darwin" ]]; then
++ export TOOL=clang
++else
++ export TOOL=gcc
++fi
++
+ # compile boost library
+-cd boost_1_70_0/
+-./bootstrap.sh
+-./b2 --clean
+-./b2
++cd boost-1.87.0.beta1/
++./bootstrap.sh --with-toolset="${TOOL}" --prefix="$(pwd)"
++./b2 toolset="${TOOL}" --layout=system link=static \
++ threading=multi strip=on \
++ variant=release address-model=64 install
+
+-cp stage/lib/libboost_iostreams.a ../lib/
++cp -f lib/libboost_iostreams.a ../lib/
+ cd ..
+
+ # compile libtcmalloc
+@@ -22,12 +29,21 @@ fi
+
+ git clone https://github.com/gperftools/gperftools.git
+ cd gperftools
+-git checkout gperftools-2.9.1
++git checkout gperftools-2.10
+ ./autogen.sh
+-./configure --libdir="$PWD"
+-make -j4
+-make install
+-cp libtcmalloc_minimal.a ../lib/
++if [[ $(uname) == 'Darwin' ]]; then
++ export CFLAGS="$CFLAGS -D_XOPEN_SOURCE"
++ ./configure --prefix="${PREFIX}" --libdir="${PWD}" \
++ --disable-debugalloc --disable-libunwind
++ make -j"${CPU_COUNT}"
++ make install
++else
++ ./configure --prefix="${PREFIX}" --libdir="${PWD}" \
++ --enable-libunwind --enable-frame-pointers
++ make -j"${CPU_COUNT}"
++ make install
++fi
++cp -f libtcmalloc_minimal.a ../lib/
+ cd ..
+
+ # combine htslib
+@@ -41,28 +57,20 @@ git clone https://github.com/samtools/htslib.git
+ cd htslib
+ git checkout 1.9
+ #git submodule update --init --recursive
+-autoreconf -i
+-./configure
+-make -j4
+-cp libhts.a ../lib/
++autoreconf -if
++./configure --enable-libcurl --enable-plugins \
++ LDFLAGS="-L${PREFIX}/lib -Wl,-R${PREFIX}/lib" \
++ CPPFLAGS="-I${PREFIX}/include"
++make -j${CPU_COUNT}
++cp -f libhts.a ../lib/
+
+ cd ..
+
+-make
+-
+-#clean htslib and gperftools and boost libraries
+-rm -r boost_1_70_0/stage
+-
+-chmod -R 755 gperftools
+-rm -r gperftools
+-
+-chmod -R 755 htslib
+-rm -r htslib
+-
+-
+-
+-
+-
+-
+-
++CFLAGS="${CFLAGS} -O3 ${LDFLAGS}" \
++ CC="${CC}" CXX="${CXX}" CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" \
++ LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" \
++ make -j"${CPU_COUNT}"
+
++rm -rf htslib
++rm -rf gperftools
++rm -rf boost-1.87.0.beta1
diff --git a/recipes/muse/meta.yaml b/recipes/muse/meta.yaml
index 690bc876e5203..2ebcef1e3f1a7 100644
--- a/recipes/muse/meta.yaml
+++ b/recipes/muse/meta.yaml
@@ -1,31 +1,63 @@
+{% set name = "MuSE" %}
+{% set version = "2.1.2" %}
+{% set sha256 = "48df7ec3f64244400243163b48eb658105854b7b0d6287af98242dd89f396f59" %}
+
package:
- name: muse
- version: 1.0.rc
+ name: {{ name|lower }}
+ version: {{ version }}
source:
- md5: c63fdb48c041f6f9545879f1a7e4da58
- url: https://github.com/danielfan/MuSE/archive/v1.0-rc.tar.gz
+- url: https://github.com/wwylab/MuSE/archive/refs/tags/v{{ version }}.tar.gz
+ sha256: {{ sha256 }}
patches:
- - 0001-add-LDFLAGS.patch
+ - 0001-Makefile.patch
+ - fix-install_muse.sh.patch
+ - version.patch
+- url: https://github.com/boostorg/boost/releases/download/boost-1.87.0.beta1/boost-1.87.0.beta1-b2-nodocs.tar.gz
+ sha256: f12e906fde4c9d04d88c3aa821f00501817a37503441cbca8ce7852a2194aeb0
+ folder: boost-1.87.0.beta1
build:
- number: 8
+ number: 2
+ skip: True # [osx]
+ run_exports:
+ - {{ pin_subpackage('muse', max_pin="x") }}
requirements:
build:
- - make
- {{ compiler('cxx') }}
- - {{ compiler('c') }}
+ - make
+ - autoconf
+ - automake
+ - libtool
host:
+ - llvm-openmp # [osx]
+ - libgomp # [linux]
+ - libcurl
+ - icu
+ - bzip2
+ - xz
- zlib
run:
- - zlib
+ - llvm-openmp # [osx]
+ - libgomp # [linux]
test:
commands:
- - MuSE 2>&1 | grep Version > /dev/null
+ - 'MuSE 2>&1 | grep "Version"'
about:
- home: "http://bioinformatics.mdanderson.org/main/MuSE"
- license: "https://github.com/danielfan/MuSE/blob/master/LICENSE"
- summary: Somatic point mutation caller
+ home: "https://bioinformatics.mdanderson.org/public-software/muse"
+ license: "GPL-2.0-or-later"
+ license_family: GPL
+ license_file: "LICENSE"
+ summary: "An accurate and ultra-fast somatic point mutation calling tool for whole-genome sequencing (WGS) and whole-exome sequencing (WES) data from heterogeneous tumor samples."
+ doc_url: "https://github.com/wwylab/MuSE/blob/v{{ version }}/README.md"
+ dev_url: "https://github.com/wwylab/MuSE"
+
+extra:
+ identifiers:
+ - doi:10.1101/gr.278456.123
+ - doi:10.1186/s13059-016-1029-6
+ additional-platforms:
+ - linux-aarch64
diff --git a/recipes/muse/version.patch b/recipes/muse/version.patch
new file mode 100644
index 0000000000000..0b826335c5820
--- /dev/null
+++ b/recipes/muse/version.patch
@@ -0,0 +1,32 @@
+diff --git a/src/main_muse.cpp b/src/main_muse.cpp
+old mode 100755
+new mode 100644
+index c2b7ef6..d8ac21d
+--- a/src/main_muse.cpp
++++ b/src/main_muse.cpp
+@@ -362,15 +362,19 @@ int main(int argc, char* argv[]){
+ if(argc < 2)
+ return usage();
+
+- if(strcmp(argv[1], "call") == 0){
++ if(strcmp(argv[1], "call") == 0){
+ get_MuseCallOpts(argc, argv);
+- }
+- else if(strcmp(argv[1], "sump") == 0) {
+- get_MuseSumpOpts(argc-1, argv+1);
+- }
++ }
++ else if(strcmp(argv[1], "sump") == 0) {
++ get_MuseSumpOpts(argc-1, argv+1);
++ }
++ else if (strcmp(argv[1], "--version") == 0 || strcmp(argv[1], "--v") == 0) {
++ fprintf(stdout, "MuSE %s\n", Version.c_str());
++ return 0; // Successfully printed version
++ }
+ else {
+ fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
+ return 1;
+ }
+- return 0;
++ return 0;
+ }
diff --git a/recipes/mvip/meta.yaml b/recipes/mvip/meta.yaml
index 613e0bbbd9bb8..4dfddf3a53a2e 100644
--- a/recipes/mvip/meta.yaml
+++ b/recipes/mvip/meta.yaml
@@ -1,5 +1,5 @@
{% set name = "mvip" %}
-{% set version = "1.1.4" %}
+{% set version = "1.1.5" %}
package:
name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
source:
url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
- sha256: ca056513e45714c5988aba02572aa179055b17100a0c4192a274324a02e8cc46
+ sha256: 61f1c5de4bd74b8453eaad5bdd8c95ad46c6b7e10a13977e3734696696785b42
build:
number: 0
diff --git a/recipes/nextflow/meta.yaml b/recipes/nextflow/meta.yaml
index 5a044738b8906..e6c8bb30f6e99 100644
--- a/recipes/nextflow/meta.yaml
+++ b/recipes/nextflow/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "24.10.0" %}
-{% set sha256 = "e848918fb9b85762822c078435d9ff71979a88cccff81ce5babd75d5eee52fe6" %}
+{% set version = "24.10.1" %}
+{% set sha256 = "fd034b2d854010c7dfb7ae1b54d29209f45a2735504fa9c34becac44201f9e75" %}
package:
name: nextflow
diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml
index c7fe2167f1b4e..aea97c79af554 100644
--- a/recipes/oakvar/meta.yaml
+++ b/recipes/oakvar/meta.yaml
@@ -1,6 +1,6 @@
{% set name = "OakVar" %}
-{% set version = "2.12.2" %}
-{% set sha256 = "1f5f961a2c8d04857bc3a63ae165254501e806ff84dfff39780ea0415505a4c4" %}
+{% set version = "2.12.3" %}
+{% set sha256 = "223ccb54ff43abc144b82d586b537bb111cdaa8a43e2efd05c182e774a911829" %}
package:
name: {{ name|lower }}
diff --git a/recipes/oarfish/build.sh b/recipes/oarfish/build.sh
index 580d388d2cf18..fc13873f768bd 100644
--- a/recipes/oarfish/build.sh
+++ b/recipes/oarfish/build.sh
@@ -2,5 +2,9 @@
set -xe
+curl https://sh.rustup.rs -sSf | sh -s -- --default-toolchain stable --profile=minimal -y
+export PATH="$HOME/.cargo/bin:$PATH"
+
+
# build statically linked binary with Rust
-RUST_BACKTRACE=1 cargo install --verbose --root $PREFIX --path .
+RUST_BACKTRACE=1 RUSTFLAGS="-C linker=$CC" cargo install --verbose --root $PREFIX --path .
diff --git a/recipes/oarfish/meta.yaml b/recipes/oarfish/meta.yaml
index 41e7e84dcf8ce..4dd80c87da7fb 100644
--- a/recipes/oarfish/meta.yaml
+++ b/recipes/oarfish/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.6.2" %}
+{% set version = "0.6.3" %}
package:
name: oarfish
@@ -11,13 +11,15 @@ build:
source:
url: https://github.com/COMBINE-lab/oarfish/archive/v{{ version }}.tar.gz
- sha256: 78b523fc459fec5ae3680395925862b4d367bd56d051120f28c689dd387e1758
+ sha256: 98cc4b939e81cd0018c38d47f4596dc3079680a7b076a7dfca2e80b67094c783
requirements:
build:
- make
- - {{ compiler('rust') }}
+ #- rust >=1.82.0
+ #- {{ compiler('rust') }} >=1.82.0
- {{ compiler('c') }}
+ - {{ compiler('cxx') }}
host:
- zlib
run:
diff --git a/recipes/omamer/meta.yaml b/recipes/omamer/meta.yaml
index 2efe270cd63c8..d3fa8987df269 100644
--- a/recipes/omamer/meta.yaml
+++ b/recipes/omamer/meta.yaml
@@ -1,5 +1,5 @@
{% set name = "omamer" %}
-{% set version = "2.0.4" %}
+{% set version = "2.0.5" %}
package:
name: {{ name|lower }}
@@ -7,28 +7,29 @@ package:
source:
url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/omamer-{{ version }}.tar.gz
- sha256: 292a9bc0534452f0480144620a57135a498b5e54cb252f1ee6f93a816037e3e0
+ sha256: eb1e62703c6b68a345880294ddac73721d753364dbde4f3a75f17d8a13a2d0da
build:
entry_points:
- omamer = omamer.main:main
noarch: python
- script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+ script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation --no-cache-dir
number: 0
run_exports:
- - {{ pin_subpackage(name, max_pin="x.x") }}
+ - {{ pin_subpackage(name, max_pin="x") }}
requirements:
host:
- python >=3.8
- pip
+ - setuptools
run:
- python >=3.8
- alive-progress
- biopython
- ete3
- numba
- - numpy
+ - numpy <2
- pandas >2.0.0
- property-manager
- rmath4
diff --git a/recipes/pacu_snp/meta.yaml b/recipes/pacu_snp/meta.yaml
index 6798465c0519a..8c18219362599 100644
--- a/recipes/pacu_snp/meta.yaml
+++ b/recipes/pacu_snp/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.0.5" %}
+{% set version = "0.0.6" %}
package:
name: pacu_snp
@@ -6,7 +6,7 @@ package:
source:
url: https://pypi.io/packages/source/p/pacu_snp/pacu_snp-{{ version }}.tar.gz
- sha256: 68979d53d8a591351a3de4edcde38bb508a8fcf8a4b1878999c9e63c932ffeb6
+ sha256: 5ba982f196852e380a130897108bedf401a1a256fc1bd262a2ec3dac42cfd8d1
build:
noarch: python
diff --git a/recipes/pathogen-profiler/meta.yaml b/recipes/pathogen-profiler/meta.yaml
index 886f0db348512..12cf7af7e81d4 100644
--- a/recipes/pathogen-profiler/meta.yaml
+++ b/recipes/pathogen-profiler/meta.yaml
@@ -1,6 +1,6 @@
{% set name = "pathogen-profiler" %}
-{% set version = "4.5.0" %}
-{% set sha256 = "55b23983ebd1a4de0e9fd9805a0a3a839fdfc89e61f5605bb58a5966b737349c" %}
+{% set version = "4.5.1" %}
+{% set sha256 = "e48994cb52005f1c2eb5a963bcf9c60d596352d80bf2bcb1e6475653caaf91fb" %}
package:
name: {{name}}
@@ -13,7 +13,7 @@ source:
build:
script: python -m pip install --no-deps --ignore-installed .
noarch: python
- number: 1
+ number: 0
run_exports:
- { pin_subpackage('pathogen-profiler', max_pin="x") }
diff --git a/recipes/perl-class-methodmaker/meta.yaml b/recipes/perl-class-methodmaker/meta.yaml
index c7b7743f1fcf9..008ce2d081dce 100644
--- a/recipes/perl-class-methodmaker/meta.yaml
+++ b/recipes/perl-class-methodmaker/meta.yaml
@@ -1,20 +1,20 @@
{% set name = "perl-class-methodmaker" %}
-{% set version = "2.24" %}
-{% set sha256 = "5eef58ccb27ebd01bcde5b14bcc553b5347a0699e5c3e921c7780c3526890328" %}
+{% set version = "2.25" %}
+{% set sha256 = "70bd3a6595cc40e54a9521eae3247e7d69166e6783ea5faebd59b84537e1b588" %}
package:
name: {{ name }}
version: {{ version }}
source:
- url: http://search.cpan.org/CPAN/authors/id/S/SC/SCHWIGON/class-methodmaker/Class-MethodMaker-2.24.tar.gz
+ url: https://cpan.metacpan.org/authors/id/S/SC/SCHWIGON/class-methodmaker/Class-MethodMaker-2.25.tar.gz
sha256: {{ sha256 }}
build:
run_exports:
- {{ pin_subpackage(name, max_pin="x") }}
- number: 5
+ number: 0
requirements:
build:
diff --git a/recipes/polap/meta.yaml b/recipes/polap/meta.yaml
index 17890cfb02e16..2ca4d29359c56 100644
--- a/recipes/polap/meta.yaml
+++ b/recipes/polap/meta.yaml
@@ -1,6 +1,6 @@
{% set name = "polap" %}
-{% set version = "0.3.7.1" %}
-{% set sha256 = "c2a119c986035519b8252f4d85c91cfa060371ee0decc8c5d400b87428a81cfe" %}
+{% set version = "0.3.7.2" %}
+{% set sha256 = "7ac79618aa16cacd8bb5dd6fa7a1284b75bbbeeb526a418c9297d7324e9359c7" %}
package:
name: "{{ name }}"
diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml
index bb70bf88a32f9..b22fd18cf58ee 100644
--- a/recipes/pybiolib/meta.yaml
+++ b/recipes/pybiolib/meta.yaml
@@ -1,5 +1,5 @@
{% set name = "pybiolib" %}
-{% set version = "1.2.221" %}
+{% set version = "1.2.223" %}
package:
name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
source:
url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz
- sha256: cba8e863eec447c4290e0a103657d9d8d83fccb79a7088e0f5b15176574da263
+ sha256: 40873a8acc8b30656f3bdb4aa267efef6052b53b83738e6b806615eefe8adbd9
build:
number: 0
diff --git a/recipes/r-facets/meta.yaml b/recipes/r-facets/meta.yaml
index 4bbd9aa678bdd..f0ea43f0f9c9d 100644
--- a/recipes/r-facets/meta.yaml
+++ b/recipes/r-facets/meta.yaml
@@ -7,7 +7,7 @@ source:
sha256: aa671d4fc66e10ce2fe4c8b2cbac4946da8a1564627240ea916db6cd8ec2a6c5
build:
- number: 5
+ number: 6
run_exports:
- {{ pin_subpackage("r-facets", max_pin="x") }}
rpaths:
@@ -39,5 +39,6 @@ about:
extra:
additional-platforms:
- linux-aarch64
+ - osx-arm64
identifiers:
- biotools:facets
diff --git a/recipes/r-locuszoomr/build.sh b/recipes/r-locuszoomr/build.sh
new file mode 100755
index 0000000000000..03cb951f643eb
--- /dev/null
+++ b/recipes/r-locuszoomr/build.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+export DISABLE_AUTOBREW=1
+if [ ! -f DESCRIPTION ]; then
+ echo "Error: DESCRIPTION file not found"
+ exit 1
+fi
+mv DESCRIPTION DESCRIPTION.old || exit 1
+grep -va '^Priority: ' DESCRIPTION.old > DESCRIPTION || exit 1
+${R} CMD INSTALL --build . ${R_ARGS}
diff --git a/recipes/r-locuszoomr/meta.yaml b/recipes/r-locuszoomr/meta.yaml
new file mode 100644
index 0000000000000..10a955fc63a37
--- /dev/null
+++ b/recipes/r-locuszoomr/meta.yaml
@@ -0,0 +1,83 @@
+{% set version = '0.3.5' %}
+
+package:
+ name: r-locuszoomr
+ version: {{ version|replace("-", "_") }}
+
+source:
+ url:
+ - {{ cran_mirror }}/src/contrib/locuszoomr_{{ version }}.tar.gz
+ - {{ cran_mirror }}/src/contrib/Archive/locuszoomr/locuszoomr_{{ version }}.tar.gz
+ sha256: 92c8bb3a84ceed82e3cf142129eb83c21a1eb780cd6c0fb4b084e099917c2c3d
+
+build:
+ run_exports:
+ - {{ pin_subpackage("r-locuszoomr", max_pin="x.x") }}
+ noarch: generic
+ merge_build_host: True # [win]
+ number: 0
+
+ rpaths:
+ - lib/R/lib/
+ - lib/
+
+requirements:
+ host:
+ - r-base
+ - bioconductor-annotationfilter
+ - bioconductor-biocgenerics
+ - bioconductor-genomeinfodb
+ - bioconductor-genomicranges
+ - bioconductor-iranges
+ - r-ldlinkr
+ - r-cowplot
+ - r-dplyr
+ - bioconductor-ensembldb
+ - r-gggrid
+ - r-ggplot2
+ - r-ggrepel
+ - r-memoise
+ - r-plotly
+ - r-rlang
+ - bioconductor-rtracklayer
+ - r-zoo
+
+ run:
+ - r-base
+ - bioconductor-annotationfilter
+ - bioconductor-biocgenerics
+ - bioconductor-genomeinfodb
+ - bioconductor-genomicranges
+ - bioconductor-iranges
+ - r-ldlinkr
+ - r-cowplot
+ - r-dplyr
+ - bioconductor-ensembldb
+ - r-gggrid
+ - r-ggplot2
+ - r-ggrepel
+ - r-memoise
+ - r-plotly
+ - r-rlang
+ - bioconductor-rtracklayer
+ - r-zoo
+
+test:
+ commands:
+ - $R -e "library('locuszoomr')"
+ - $R -e "packageVersion('locuszoomr')"
+ - $R -e "help(package = 'locuszoomr')"
+
+about:
+ home: https://github.com/myles-lewis/locuszoomr
+ license: GPL-3
+ summary: Publication-ready regional gene locus plots similar to those produced by the web interface
+ 'LocusZoom' , but running locally in R. Genetic or genomic
+ data with gene annotation tracks are plotted via R base graphics, 'ggplot2' or 'plotly',
+ allowing flexibility and easy customisation including laying out multiple locus
+ plots on the same page. It uses the 'LDlink' API
+ to query linkage disequilibrium data from the 1000 Genomes Project and can overlay
+ this on plots.
+ license_family: GPL3
+ license_file:
+ - '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
diff --git a/recipes/rdeval/Makefile.patch b/recipes/rdeval/Makefile.patch
new file mode 100644
index 0000000000000..b9243d5f94b5d
--- /dev/null
+++ b/recipes/rdeval/Makefile.patch
@@ -0,0 +1,25 @@
+--- a/Makefile
++++ b/Makefile
+@@ -12,7 +12,12 @@
+ INCLUDE = include
+ BINDIR := $(BUILD)/.o
+
+-LDFLAGS := -pthread
++ifeq ($(origin LDFLAGS), undefined)
++ LDFLAGS := -pthread
++else
++ LDFLAGS := $(LDFLAGS) -pthread
++endif
++
+ LIBS = -lz
+
+ OBJS := main input reads
+@@ -27,7 +32,7 @@
+ all: head validate regenerate
+
+ $(BINDIR)%: $(SOURCE)/%.cpp $(INCLUDE)/%.h | $(BINDIR)
+- $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@
+
+ .PHONY: gfalibs
+ gfalibs:
diff --git a/recipes/rdeval/build.sh b/recipes/rdeval/build.sh
new file mode 100644
index 0000000000000..3f30b2376ac7a
--- /dev/null
+++ b/recipes/rdeval/build.sh
@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+
+set -o errexit
+set -o nounset
+
+if [ -e "$PREFIX/include" ]; then
+ export CPPFLAGS="${CPPFLAGS:+$CPPFLAGS }-I$PREFIX/include"
+fi
+
+if [ -e "$PREFIX/lib" ]; then
+ export LDFLAGS="${LDFLAGS:+$LDFLAGS }-L$PREFIX/lib"
+fi
+
+echo "CPPFLAGS=\"$CPPFLAGS\""
+echo "LDFLAGS=\"$LDFLAGS\""
+
+cd "$SRC_DIR"
+
+make
+
+install -d "$PREFIX/bin"
+install -v -m 0755 build/bin/rdeval "$PREFIX/bin/"
diff --git a/recipes/rdeval/foo.patch b/recipes/rdeval/foo.patch
new file mode 100644
index 0000000000000..417701560725a
--- /dev/null
+++ b/recipes/rdeval/foo.patch
@@ -0,0 +1,38 @@
+diff --git a/Makefile b/Makefile
+index 5823f28..6f4a60f 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,5 +1,5 @@
+-CXX ?= g++
+-INCLUDE_DIR = -I./include -I./gfalibs/include
++CXX ?= ${CXX}
++INCLUDE_DIR = -I${PREFIX}/include -I./include -I./gfalibs/include
+ WARNINGS = -Wall -Wextra
+
+ CXXFLAGS = -g -std=gnu++14 -O3 $(INCLUDE_DIR) $(WARNINGS)
+@@ -12,8 +12,8 @@ SOURCE = src
+ INCLUDE = include
+ BINDIR := $(BUILD)/.o
+
+-LDFLAGS := -pthread
+-LIBS = -lz
++LDFLAGS := -pthread -L${PREFIX}/lib
++LIBS := -lz -lpthread
+
+ OBJS := main input reads
+ BINS := $(addprefix $(BINDIR)/, $(OBJS))
+@@ -22,12 +22,12 @@ BINS := $(addprefix $(BINDIR)/, $(OBJS))
+ GFALIBS_DIR := $(CURDIR)/gfalibs
+
+ head: $(BINS) gfalibs | $(BUILD)
+- $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $(BUILD)/$(TARGET) $(BINDIR)/* $(GFALIBS_DIR)/*.o $(LIBS)
++ $(CXX) $(CXXFLAGS) $(INCLUDE_DIR) $(LDFLAGS) -o $(BUILD)/$(TARGET) $(BINDIR)/* $(GFALIBS_DIR)/*.o $(LIBS)
+
+ all: head validate regenerate
+
+ $(BINDIR)%: $(SOURCE)/%.cpp $(INCLUDE)/%.h | $(BINDIR)
+- $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@
++ $(CXX) $(CXXFLAGS) $(INCLUDE_DIR) $(LDFLAGS) -c $(SOURCE)/$(notdir $@).cpp -o $@ $(LIBS)
+
+ .PHONY: gfalibs
+ gfalibs:
diff --git a/recipes/rdeval/gfalibs-Makefile.patch b/recipes/rdeval/gfalibs-Makefile.patch
new file mode 100644
index 0000000000000..d43d6346dadaa
--- /dev/null
+++ b/recipes/rdeval/gfalibs-Makefile.patch
@@ -0,0 +1,25 @@
+--- a/gfalibs/Makefile
++++ b/gfalibs/Makefile
+@@ -1,4 +1,4 @@
+-CXX = g++
++CXX ?= g++
+ INCLUDE_DIR = -I./include
+ WARNINGS = -Wall -Wextra
+
+@@ -8,15 +8,13 @@
+ BUILD = build/bin
+ SOURCE = src
+ INCLUDE = include
+-LDFLAGS :=
+
+ SOURCES = $(addsuffix .o, input-filters input-gfa input-agp gfa gfa-lines log stream-obj uid-generator struct output memory)
+
+ all: $(SOURCES)
+- @
+
+ %.o: $(SOURCE)/%.cpp $(INCLUDE)/%.h
+- $(CXX) $(CXXFLAGS) $(LDFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@
++ $(CXX) $(CPPFLAGS) $(CXXFLAGS) -c $(SOURCE)/$(basename $@).cpp -o $@
+
+ clean:
+ $(RM) *.o
diff --git a/recipes/rdeval/meta.yaml b/recipes/rdeval/meta.yaml
new file mode 100644
index 0000000000000..a495d435df647
--- /dev/null
+++ b/recipes/rdeval/meta.yaml
@@ -0,0 +1,43 @@
+{% set name = "rdeval" %}
+{% set version = "0.0.2" %}
+
+package:
+ name: {{ name|lower }}
+ version: {{ version }}
+
+source:
+ url: https://github.com/vgl-hub/{{ name }}/releases/download/v{{ version }}/{{ name }}.v{{ version }}-with_submodules.zip
+ sha256: 56c2f4d7d2c22b27d1b380dc41b81cc77a2d97c792a69b9360bed9e0027bac4d
+ patches:
+ - Makefile.patch
+ - gfalibs-Makefile.patch
+
+build:
+ number: 1
+ run_exports:
+ - {{ pin_subpackage(name|lower, max_pin="x.x") }}
+
+requirements:
+ build:
+ - {{ compiler('cxx') }}
+ - make
+ host:
+ - zlib
+
+test:
+ commands:
+ - rdeval --help
+
+about:
+ home: https://github.com/vgl-hub/{{ name }}
+ summary: A general purpose, multithreaded read analysis and manipulation tool.
+ license: MIT
+ license_family: MIT
+ license_file: LICENSE
+ dev_url: https://github.com/vgl-hub/{{ name }}
+ doc_url: https://github.com/vgl-hub/rdeval/blob/v{{ version }}/README.md
+
+extra:
+ additional-platforms:
+ - linux-aarch64
+ - osx-arm64
diff --git a/recipes/saccharis/meta.yaml b/recipes/saccharis/meta.yaml
index 5dd7db2b51e4d..dc9c7a06898df 100644
--- a/recipes/saccharis/meta.yaml
+++ b/recipes/saccharis/meta.yaml
@@ -1,6 +1,6 @@
{% set name = "SACCHARIS" %}
{% set version = "2.0.1.dev21" %}
-{% set hash = "DEFE4B98CFF4F5ED58A102D7FFE0CC219C4EC44C257AC0469255CDC73F124F57" %}
+{% set hash = "C808429EADDAA31E0E611DF0564BA6CA36CE6CBB69A98DFB79CC59972352FD16" %}
package:
@@ -9,12 +9,12 @@ package:
source:
# url: https://github.com/saccharis/SACCHARIS_2/releases/download/v{{ version }}/saccharis-{{ version }}.tar.gz
- url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_7.tar.gz
+ url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_8.tar.gz
sha256: {{ hash|lower }}
build:
noarch: python
- number: 7
+ number: 8
script: {{ PYTHON }} setup.py install --single-version-externally-managed --record=record.txt
preserve_egg_dir: True # added because the entry points below seem to be causing a build error
diff --git a/recipes/sfold/build.sh b/recipes/sfold/build.sh
index 0584640650b30..b86e125258d17 100755
--- a/recipes/sfold/build.sh
+++ b/recipes/sfold/build.sh
@@ -13,4 +13,12 @@ cp -r STarMir ${SFOLD_DIR}
# modify the sfoldenv file
cp sfoldenv ${SFOLD_DIR}/sfoldenv
-sed -i "s|SFOLDDIR=.*|SFOLDDIR=${SFOLD_DIR}|g" ${SFOLD_DIR}/sfoldenv
\ No newline at end of file
+sed -i.bak "s|SFOLDDIR=.*|SFOLDDIR=${SFOLD_DIR}|g" ${SFOLD_DIR}/sfoldenv
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${SFOLD_DIR}/STarMir/*.pl
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${SFOLD_DIR}/STarMir/starmir-param/*.pl
+sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' ${SFOLD_DIR}/bin/*.pl
+
+rm -rf ${SFOLD_DIR}/*.bak
+rm -rf ${SFOLD_DIR}/STarMir/*.bak
+rm -rf ${SFOLD_DIR}/STarMir/starmir-param/*.bak
+rm -rf ${SFOLD_DIR}/bin/*.bak
diff --git a/recipes/sfold/meta.yaml b/recipes/sfold/meta.yaml
index 98dce74f72249..b6509c09158c3 100644
--- a/recipes/sfold/meta.yaml
+++ b/recipes/sfold/meta.yaml
@@ -7,7 +7,7 @@ source:
sha256: c25e4d8cf055e13c523ef59f68c8847b66584e36359ce4fb9dc675a97f1a2939
build:
- number: 1
+ number: 3
skip: True # [osx]
run_exports:
- {{ pin_subpackage('sfold', max_pin='x') }}
diff --git a/recipes/snipit/meta.yaml b/recipes/snipit/meta.yaml
index 6145586560291..1f1ae926cc1a6 100644
--- a/recipes/snipit/meta.yaml
+++ b/recipes/snipit/meta.yaml
@@ -1,5 +1,5 @@
{% set name = "snipit" %}
-{% set version = "1.2" %}
+{% set version = "1.6" %}
package:
name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
source:
url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
- sha256: 92e4395a23ef5e55ae753868723daa3e68d5803a10db6ae27fc6722a99bcc708
+ sha256: 4d3080926bebfd3eeb52e98a35e69bbd66a99e3752dbf436c8d5ccb428bfdb10
build:
number: 0
diff --git a/recipes/snk-cli/meta.yaml b/recipes/snk-cli/meta.yaml
index 9e1434504395f..809eeffb36f15 100644
--- a/recipes/snk-cli/meta.yaml
+++ b/recipes/snk-cli/meta.yaml
@@ -1,5 +1,5 @@
{% set name = "snk-cli" %}
-{% set version = "0.5.5" %}
+{% set version = "0.7.0" %}
package:
name: {{ name|lower }}
@@ -7,14 +7,14 @@ package:
source:
url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name | replace("-","_") }}-{{ version }}.tar.gz
- sha256: 5ba6a88aca3473751152cdcd22b0cdc31b0f4034d9eabf859a3dfc6dcc4a487f
+ sha256: eec5fb4411e54a97927586f2cf0018219513a6ef8de1e38ec0741a642521c299
build:
run_exports:
- {{ pin_subpackage('snk-cli', max_pin="x.x") }}
noarch: python
script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
- number: 0
+ number: 1
requirements:
host:
@@ -31,6 +31,7 @@ requirements:
- ascii-art >=5.9,<6.dev0
- makefun >=1.15,<2.dev0
- datrie >=0.8.2
+ - graphviz >=2.38.0
test:
imports:
diff --git a/recipes/strangepg/build.sh b/recipes/strangepg/build.sh
index 3040da4a94b98..b120ae649490a 100644
--- a/recipes/strangepg/build.sh
+++ b/recipes/strangepg/build.sh
@@ -2,6 +2,8 @@
set -xe
-export CFLAGS="$CFLAGS -I${PREFIX}/include"
-export LDFLAGS="$LDFLAGS -ldl -lpthread"
-make -j ${CPU_COUNT} install
+export C_INCLUDE_PATH="${PREFIX}/include"
+export LIBRARY_PATH="${PREFIX}/lib"
+export LDLIBS="-ldl -lpthread"
+
+make CC="${CC}" PREFIX="${PREFIX}" -j ${CPU_COUNT} install
diff --git a/recipes/strangepg/meta.yaml b/recipes/strangepg/meta.yaml
index 9590c0f9fee59..1be6b9d623d57 100644
--- a/recipes/strangepg/meta.yaml
+++ b/recipes/strangepg/meta.yaml
@@ -1,25 +1,20 @@
{% set name = "strangepg" %}
-{% set version = "0.8.13" %}
+{% set version = "0.8.14" %}
+{% set ref = "1e666b80f464f9e898e8fce1e42f96eaf10953be" %}
package:
name: {{ name }}
version: {{ version }}
source:
- url: https://github.com/qwx9/{{ name }}/archive/refs/tags/{{ version }}.tar.gz
- sha256: b7dc45385297fa46458bf83931acd7dbc0fdbb594f63fe59db12d9a5080a95d8
+ url: https://github.com/qwx9/{{ name }}/archive/{{ ref }}.tar.gz
+ sha256: 23b154d12ea00326e57083c4a4907f80132fdbc0c7310bfc6b5bad5b53d26a63
build:
number: 0
- skip: True # [not linux]
+ skip: True # [not linux]
run_exports:
- - {{ pin_subpackage('strangepg', max_pin=None) }}
- ignore_run_exports:
- - libxcb
- - xorg-libxau
- - xorg-libxdmcp
- - xorg-libxext
- - xorg-libxfixes
+ - {{ pin_subpackage('strangepg', max_pin='x.x') }}
requirements:
build:
@@ -55,10 +50,9 @@ about:
license: MIT
license_family: MIT
license_file: LICENSE
+ dev-url: https://github.com/qwx9/{{ name }}
extra:
- additional-platforms:
- - linux-aarch64
recipe-maintainers:
- qwx9
container:
diff --git a/recipes/strangepg/run_test.sh b/recipes/strangepg/run_test.sh
index 0093b29f85b73..31a5f72a4ef42 100644
--- a/recipes/strangepg/run_test.sh
+++ b/recipes/strangepg/run_test.sh
@@ -3,4 +3,3 @@
strangepg -h 2>/dev/null
strangepg /dev/mordor 2>/dev/null || [[ $? == 1 ]]
-echo | strawk -f cmd/main.awk
diff --git a/recipes/svtopovz/meta.yaml b/recipes/svtopovz/meta.yaml
index d885d82b8a86a..41baadd6ae65c 100644
--- a/recipes/svtopovz/meta.yaml
+++ b/recipes/svtopovz/meta.yaml
@@ -1,6 +1,6 @@
{% set name = "svtopovz" %}
-{% set version = "0.1.1" %}
-{% set shasum = "275acf6d296a04a981bc396e37836324d47eeedef61b04ab8073ac0c95c3b422" %}
+{% set version = "0.2.1" %}
+{% set shasum = "c6161f978bdbacce9bd279971dde712f481cb3659541f183a4014791d4d0f44f" %}
package:
name: {{ name }}
diff --git a/recipes/tb-profiler/meta.yaml b/recipes/tb-profiler/meta.yaml
index a32b773cc9d37..87bc58310c21e 100644
--- a/recipes/tb-profiler/meta.yaml
+++ b/recipes/tb-profiler/meta.yaml
@@ -1,6 +1,6 @@
{% set name = "tb-profiler" %}
-{% set version = "6.4.0" %}
-{% set sha256 = "7868c95b1d2578723622f226f254e6bb7d1f35480a575e235f8e0b9984aca166" %}
+{% set version = "6.4.1" %}
+{% set sha256 = "1f325cfc32f3276b52e3e2b5078cce8492b495361799938e4540e1f0dc5d7938" %}
package:
name: {{name}}
diff --git a/recipes/teloclip/meta.yaml b/recipes/teloclip/meta.yaml
index 08bbe62e72bd4..8ec2478fa2848 100644
--- a/recipes/teloclip/meta.yaml
+++ b/recipes/teloclip/meta.yaml
@@ -1,5 +1,5 @@
{% set name = "teloclip" %}
-{% set version = "0.0.5" %}
+{% set version = "0.1.0" %}
package:
name: '{{ name|lower }}'
@@ -7,7 +7,7 @@ package:
source:
url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
- sha256: eb699124a35ad44ef9f5a71e2f20cfcefd3b473ac3ef47fc28cf2394610b1f6f
+ sha256: da2cc882b0e31db76de2cf485601ce26f28b2b95a3056d754c288d87fb9a83df
build:
run_exports:
diff --git a/recipes/teloscope/meta.yaml b/recipes/teloscope/meta.yaml
index df6fb7ece9654..b8d7346a1e3a0 100644
--- a/recipes/teloscope/meta.yaml
+++ b/recipes/teloscope/meta.yaml
@@ -1,11 +1,11 @@
{% set name = "teloscope" %}
-{% set version = "0.0.2" %}
+{% set version = "0.0.3" %}
package:
name: {{ name }}
version: {{ version }}
source:
url: https://github.com/vgl-hub/teloscope/releases/download/v{{version}}/teloscope.v{{version}}-with_submodules.zip
- sha256: 1c186d3531686fb37fd5236a87b024a4e0d9923f992baa6425962acf22174418
+ sha256: 73267c978e8175f53f2fef034f110d3c98dd15ea5b0e0b2814c65b34207bc499
build:
number: 0
run_exports:
diff --git a/recipes/tttrlib/build.sh b/recipes/tttrlib/build.sh
new file mode 100755
index 0000000000000..b5970e094f4eb
--- /dev/null
+++ b/recipes/tttrlib/build.sh
@@ -0,0 +1,34 @@
+#!/bin/bash
+
+mkdir b2 && cd b2
+
+if [[ "${target_platform}" == osx-* ]]; then
+ # See https://conda-forge.org/docs/maintainer/knowledge_base.html#newer-c-features-with-old-sdk
+ export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
+ export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+ export CONFIG_ARGS=""
+fi
+
+cmake -S .. -B . \
+ -DCMAKE_CXX_COMPILER="${CXX}" \
+ -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+ -DBUILD_PYTHON_INTERFACE=ON \
+ -DCMAKE_BUILD_TYPE=Release \
+ -DBUILD_LIBRARY=ON \
+ -DPYTHON_VERSION=$(python -c 'import platform; print(platform.python_version())') \
+ -DPython_ROOT_DIR="${PREFIX}/bin" \
+ -DBUILD_PYTHON_DOCS=ON \
+ -DBoost_USE_STATIC_LIBS=OFF \
+ -DWITH_AVX=OFF \
+ -G Ninja \
+ "${CONFIG_ARGS}"
+
+# On some platforms (notably aarch64 with Drone) builds can fail due to
+# running out of memory. If this happens, try the build again; if it
+# still fails, restrict to one core.
+ninja install -k 0 || ninja install -k 0 || ninja install -j ${CPU_COUNT}
+
+# Copy programs to bin
+chmod 0755 $SRC_DIR/bin/*
+cp -f $SRC_DIR/bin/* $PREFIX/bin
diff --git a/recipes/tttrlib/meta.yaml b/recipes/tttrlib/meta.yaml
new file mode 100644
index 0000000000000..daf00affe224d
--- /dev/null
+++ b/recipes/tttrlib/meta.yaml
@@ -0,0 +1,72 @@
+{% set name = "tttrlib" %}
+{% set version = "0.25.1" %}
+
+package:
+ name: {{ name }}
+ version: {{ version }}
+
+source:
+ url: https://github.com/Fluorescence-Tools/tttrlib/archive/refs/tags/v{{ version }}.tar.gz
+ sha256: a224214e50d7a202ef1d264c64641ab0b26f29bf756a96659489847953b698a6
+
+build:
+ number: 0
+ run_exports: '{{ pin_subpackage("tttrlib", max_pin="x.x") }}'
+
+requirements:
+ build:
+ - {{ compiler('c') }}
+ - {{ compiler('cxx') }}
+ - pkg-config
+ - cmake
+ - ninja
+ - make
+ host:
+ - swig <4.3.0
+ - doxygen
+ - llvm-openmp # [osx]
+ - libgomp # [linux]
+ - boost-cpp
+ - hdf5
+ - python
+ - pip
+ - numpy
+ run:
+ - python
+ - llvm-openmp # [osx]
+ - libgomp # [linux]
+ - boost-cpp
+ - tqdm
+ - click
+ - click-didyoumean
+ - numpy
+ - scikit-image
+ - matplotlib-base
+ - hdf5
+
+test:
+ imports:
+ - tttrlib
+ commands:
+ - tttrlib --help
+
+about:
+ home: https://github.com/fluorescence-tools/tttrlib
+ summary: 'A file format agnostic library for time-resolved imaging and spectroscopic data.'
+ description: |
+ tttrlib is a simple, fast, libray to read, write and process
+ time-resolved imaging and spectroscopic data. For speed, it
+ is written in C++ and wrapped for Python via SWIG.
+ license: BSD-3-Clause
+ license_family: BSD
+ license_file: LICENSE.txt
+ doc_url: https://tttrlib.readthedocs.io
+ dev_url: https://github.com/fluorescence-tools/tttrlib
+
+extra:
+ recipe-maintainers:
+ - tpeulen
+ - khemmen
+ additional-platforms:
+ - linux-aarch64
+ - osx-arm64
diff --git a/recipes/unikseq/meta.yaml b/recipes/unikseq/meta.yaml
index 6eee8a084f202..097d8f6d62ea2 100644
--- a/recipes/unikseq/meta.yaml
+++ b/recipes/unikseq/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.3.5" %}
+{% set version = "2.0.0" %}
package:
name: unikseq
@@ -6,7 +6,7 @@ package:
source:
url: https://github.com/bcgsc/unikseq/releases/download/v{{ version }}/unikseq-{{ version }}.tar.gz
- sha256: 9b497384ce023a06fd79353c2488455f1517f10e575c86f1f5df1e21463d09e8
+ sha256: 5682d54e15ca41662f958c402c13328f9f19a6dd6a13043e4198679b10a6acb0
patches:
- unikseq-bloom.patch
- unikseq-write-bloom.patch
diff --git a/recipes/virheat/meta.yaml b/recipes/virheat/meta.yaml
index 6b485917f485d..ee07000da75ec 100644
--- a/recipes/virheat/meta.yaml
+++ b/recipes/virheat/meta.yaml
@@ -1,5 +1,5 @@
{% set name = "virheat" %}
-{% set version = "0.7.1" %}
+{% set version = "0.7.3" %}
package:
name: {{ name|lower }}
@@ -7,13 +7,13 @@ package:
source:
url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/virheat-{{ version }}.tar.gz
- sha256: 142b62f05dfe91b9d04a8fe3e7b27d0d20e502dbfa3163d839666262143f67d6
+ sha256: 35ce98dd10af4d2519195c6351321b6f5f26d699ad662c0c5e75f7cec00c3dd1
build:
entry_points:
- virheat = virheat.command:main
noarch: python
- script: {{ PYTHON }} -m pip install . --no-deps -vvv
+ script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
number: 0
run_exports:
- {{ pin_subpackage('virheat', max_pin="x.x") }}
@@ -22,6 +22,7 @@ requirements:
host:
- python >=3.9
- pip
+ - setuptools
run:
- python >=3.9
- matplotlib-base >=3.5.1,<=3.8.0
@@ -32,10 +33,7 @@ test:
imports:
- virheat
commands:
- - pip check
- virheat --help
- requires:
- - pip
about:
home: https://github.com/jonas-fuchs/virHEAT
diff --git a/recipes/zamp/meta.yaml b/recipes/zamp/meta.yaml
index 15dc951847f5f..bb8a79067fb0d 100644
--- a/recipes/zamp/meta.yaml
+++ b/recipes/zamp/meta.yaml
@@ -10,7 +10,7 @@ source:
sha256: 366d1a1bdff60e1a8100298608f20ab2294ef476a1da1bee9c1975641c495f6e
build:
- number: 0
+ number: 1
noarch: python
entry_points:
- zamp=zamp.__main__:main
@@ -25,7 +25,7 @@ requirements:
- setuptools
run:
- python >=3.11
- - snakemake-minimal >=8.0.0
+ - snakemake-minimal >=8.0.0,<=8.24.1
- Click >=8.1.3
- attrmap >=0.0.7
- snaketool-utils >=0.0.5
diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml
index b6bfbab475b0a..d9994831effb8 100644
--- a/recipes/zol/meta.yaml
+++ b/recipes/zol/meta.yaml
@@ -1,5 +1,5 @@
{% set name = "zol" %}
-{% set version = "1.5.2" %}
+{% set version = "1.5.5" %}
package:
name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
source:
url: https://github.com/Kalan-Lab/zol/archive/refs/tags/v{{ version }}.tar.gz
- sha256: 2e42064bacad5a6bd1b3d22fbdd2bb5f150b2e6aa0beb656794579ae7c9f6079
+ sha256: fa8f23071c519daf9cfc2c3ca96121d8119dbc55c2359c3901f8ed2081583ddb
build:
number: 0
@@ -26,7 +26,8 @@ requirements:
- python >=3.10
- r-base
- biopython
- - muscle >=5.0
+ - muscle >=5.0,<=5.1 [osx]
+ - muscle >=5.0 [not osx]
- mcl
- pal2nal >=14.1
- hmmer >=3.0.0
@@ -52,8 +53,8 @@ requirements:
- slclust
- trimal
- gzip
- - miniprot =0.7 # [x86_64]
- - miniprot >=0.7 # [aarch64]
+ - miniprot =0.13 # [x86_64]
+ - miniprot >=0.13 # [aarch64]
- bioconductor-ggtree
- ete3
- codoff