Merge branch 'master' into patch-1

bioconda · Oct 26, 2024 · 637c7e8 · 637c7e8
2 parents 1cf1c64 + fe8fc74
commit 637c7e8
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Showing 13 changed files with 44 additions and 93 deletions.
diff --git a/recipes/crabs/meta.yaml b/recipes/crabs/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "crabs" %}
-{% set version = "1.0.4" %}
-{% set sha256 = "be9308225049cc34fde745587ceddd4b88f334be2f2385d5878136cb34e9d2cf" %}
+{% set version = "1.0.5" %}
+{% set sha256 = "f948244c3b148e7c23b89f7aab68e28149504c60075f1e731e07a05fbd66d8f5" %}
 
 package:
   name: {{ name|lower }}

diff --git a/recipes/genoflu/meta.yaml b/recipes/genoflu/meta.yaml
@@ -1,8 +1,8 @@
 {% set user = "USDA-VS" %}
 {% set name = "GenoFLU" %}
 
-{% set version = "1.03" %}
-{% set sha256 = "fe814ff8e256b57e32a3398d4c16d449eb6222cbb02869bd876534484c5b070e" %}
+{% set version = "1.04" %}
+{% set sha256 = "f8dabd01e5f0fe00443b8991bf31dca38aa4d0064a564fb237dc4e9f0f1eec31" %}
 
 package:
   name: {{ name|lower }}

diff --git a/recipes/haystac/meta.yaml b/recipes/haystac/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "haystac" %}
-{% set version = "0.4.11" %}
+{% set version = "0.4.12" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 77727ce69b8df4211c43b424a292cd703987946e889a370337ce4afc7b6f0edd
+  sha256: 65f87603cb278f69003b8eea1f78d255d37b3c8dcb0f0c9ac71f8a85038c50e2
 
 build:
   number: 0
@@ -17,7 +17,7 @@ build:
   script: "{{ PYTHON }} -m pip install . -vv --ignore-installed --no-deps"
   run_exports:
     - {{ pin_subpackage("haystac", max_pin="x.x") }}
-
+    
 requirements:
   host:
     - numpy

diff --git a/recipes/lofreq/meta.yaml b/recipes/lofreq/meta.yaml
@@ -11,7 +11,7 @@ source:
     - 0001-patches
 
 build:
-  number: 13
+  number: 14
   run_exports:
     - {{ pin_subpackage('lofreq', max_pin='x') }}
 
@@ -32,12 +32,14 @@ requirements:
   run:
     - python
     - samtools
+    - bcftools
     - gsl
 
 test:
   commands:
     - lofreq version
     - samtools --help
+    - bcftools --help
 
 about:
   home: "https://csb5.github.io/lofreq"

diff --git a/recipes/pcst-fast/meta.yaml b/recipes/pcst-fast/meta.yaml
diff --git a/recipes/pretextgraph/build.sh b/recipes/pretextgraph/build.sh
@@ -5,7 +5,7 @@ set -eo pipefail
 if [ `uname` == Darwin ]; then
     meson setup --buildtype=release --prefix=$PREFIX --unity on builddir
 else
-    env CC=clang CXX=clang meson setup --buildtype=release --prefix=$PREFIX --unity on builddir
+    env CC=clang CXX=clang++ meson setup --buildtype=release --prefix=$PREFIX --unity on builddir
 fi
 
 cd builddir

diff --git a/recipes/pretextgraph/meta.yaml b/recipes/pretextgraph/meta.yaml
@@ -1,23 +1,26 @@
 {% set name = "PretextGraph" %}
-{% set version = "0.0.6" %}
-{% set sha256 = "94e69e9c99f62d6112a8e48db4cf9ff92102c2704dacff01924cce5799a6807f" %}
+{% set version = "0.0.7" %}
+{% set sha256 = "4c99c46105cf4de3f22ab3065b0e5445cdf3caed8f66aafaf08249c365455d37" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
-  url: https://github.com/wtsi-hpag/{{ name }}/releases/download/{{ version }}/{{ name }}-{{ version }}.tar.xz
+  url: https://github.com/sanger-tol/PretextGraph/releases/download/{{ version }}/{{ name|lower }}-{{ version }}.tar.gz
   sha256: {{ sha256 }}
 
 build:
-  number: 3
+  number: 0 # the build number should be incremented if the same version of the package is built with different build settings
+  run_exports:
+    - {{ pin_subpackage('pretextgraph', max_pin="x.x") }}
 
 requirements:
   build:
     - {{ compiler('cxx') }}
-    - clang>=9.0.1 # [linux] 
-    - meson>=0.57.1
+    - clang >=11.0.1 # [linux] 
+    - clangxx >=11.0.1 # [linux]
+    - meson >=0.57.1
 
 test:
   commands:

diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "pybiolib" %}
-{% set version = "1.2.211" %}
+{% set version = "1.2.216" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz
-  sha256: 4fa78adc22fa1f04b45c48b4804f7efdef5c0741979f9dc3ed06540667e422c6
+  sha256: 8600ff68710980d26cc0166416383f3020502d62f4a67f54ef863c36f4a8edb2
 
 build:
   number: 0

diff --git 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 = "327FCE45E7B50BF0C52064DA883CC4A21BCE183EBACF4C4A827FE2C5BE934CB3" %}
+{% set hash = "B83DC6502A3AB136D1E5F43E4E66CD41A7B884C99B190B781691C56A6D71998F" %}
 
 
 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_2.tar.gz
+  url: https://github.com/saccharis/SACCHARIS_2/releases/download/v2.0.1.dev21/saccharis-2.0.1.dev21_3.tar.gz
   sha256: {{ hash|lower }}
 
 build:
   noarch: python
-  number: 2
+  number: 3
   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
   entry_points:
@@ -54,7 +54,6 @@ requirements:
     - psutil
     - python >=3.8
     - python-dotenv >=0.20.0
-    - python-wget >=3.2
     - raxml >=8.2.12 # [not win]
     - raxml-ng >=1.2 # [not win]
     - requests >=2.28.0

diff --git a/recipes/snipe/meta.yaml b/recipes/snipe/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "snipe" %}
-{% set version = "0.1.4" %}
+{% set version = "0.1.5" %}
 
 package:
   name: {{ name|lower }}
   version: "{{ version }}"
 
 source:
   url: https://github.com/snipe-bio/snipe/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 18f49da162e426dede11a8836b77a347e94bb618a1f0ae9eb8ae967960c81b16
+  sha256: 70fbf5dddc7e843cf5a2225e66423e4842c21757b7d8646542913aa2cddbf1b6
 
 build:
   number: 0

diff --git a/recipes/strainy/meta.yaml b/recipes/strainy/meta.yaml
@@ -1,33 +1,33 @@
 {% set version = "1.2" %}
 {% set name = "strainy" %}
 
-
 package:
    name: strainy
    version: {{ version }}
 
-
 source:
    url: https://github.com/katerinakazantseva/strainy/archive/refs/tags/{{ version }}.tar.gz
    sha256: 6ea476eb4a3dcbe1f1af10d2e73982b1aa57aedeedd2b688043a480052655d24
 
-
 build:
-  number: 0
+  number: 1
   noarch: python
-  script: {{ PYTHON }} -m pip install -vv .
+  script: {{ PYTHON }} -m pip install -vvv . --no-deps --no-build-isolation --no-cache-dir
+  entry_points:
+    - strainy = strainy.main:main
   run_exports:
     - {{ pin_subpackage("strainy", max_pin="x") }}  
 
-
 requirements:
   host:
-  - python
+  - python >=3.8
+  - pip
+  - setuptools
   run:
   - python >=3.8
   - samtools >=1.14
   - bcftools >=1.14
-  - minimap2
+  - minimap2 >=2.28
   - pygraphviz
   - matplotlib-base
   - biopython
@@ -41,7 +41,6 @@ requirements:
   - scipy >=1.8,<1.13
   - flye
 
-
 test:
    commands:
    - strainy -h
@@ -51,4 +50,4 @@ about:
    license: GPL-3.0-or-later
    license_family: GPL3
    license_file: LICENSE
-   summary: Assembly-based metagenomic strain phasing using long reads
+   summary: "Assembly-based metagenomic strain phasing using long reads."
diff --git a/recipes/zol/build.sh b/recipes/zol/build.sh
@@ -4,20 +4,10 @@ $PYTHON -m pip install . --ignore-installed --no-deps -vv
 
 mkdir -p ${PREFIX}/bin
 
-# (re)-compile RBH/InParanoid-esque programs written in C++
-${CXX} -std=c++11 -o zol/orthologs/runRBH zol/orthologs/runRBH.cpp
-${CXX} -std=c++11 -o zol/orthologs/splitDiamondResults zol/orthologs/splitDiamondResults.cpp
-${CXX} -std=c++11 -o zol/splitDiamondResultsForFai zol/splitDiamondResultsForFai.cpp
-
-cp zol/orthologs/runRBH ${PREFIX}/bin/
-cp zol/orthologs/splitDiamondResults ${PREFIX}/bin/
-cp zol/splitDiamondResultsForFai ${PREFIX}/bin/
-cp zol/clusterHeatmap.R ${PREFIX}/bin/
-cp zol/plotTinyAAI.R ${PREFIX}/bin/
-cp zol/plotSegments.R ${PREFIX}/bin/
-cp zol/njTree.R ${PREFIX}/bin/
-cp zol/phyloHeatmap.R ${PREFIX}/bin/
-cp zol/salt_gc_vs_ribo_aai.R ${PREFIX}/bin/
+export LDFLAGS=
+${CXX} -std=c++11 -Wl,-headerpad_max_install_names -o ${PREFIX}/bin/runRBH src/zol/orthologs/runRBH.cpp
+${CXX} -std=c++11 -Wl,-headerpad_max_install_names -o ${PREFIX}/bin/splitDiamondResults src/zol/orthologs/splitDiamondResults.cpp
+${CXX} -std=c++11 -Wl,-headerpad_max_install_names -o ${PREFIX}/bin/splitDiamondResultsForFai src/zol/splitDiamondResultsForFai.cpp
 
 chmod +x ${PREFIX}/bin/runRBH
 chmod +x ${PREFIX}/bin/splitDiamondResults

diff --git a/recipes/zol/meta.yaml b/recipes/zol/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "zol" %}
-{% set version = "1.4.12" %}
+{% set version = "1.5.0" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://github.com/Kalan-Lab/zol/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: cb02a98c7257a9d7ef089bc585637aa9ee5671c6b3a65dbaed6c0dd2331b651b
+  sha256: e1d0d090a08a26d2ecbb958d398dc47df94ffbaa034265086c7084d1e88cfb2d
 
 build:
   number: 0
@@ -56,6 +56,8 @@ requirements:
     - bioconductor-ggtree
     - ete3
     - codoff
+    - gravis
+    - colour
 
 test:
   commands: