Merge branch 'master' into cloudspades

bioconda · Oct 16, 2024 · 817a88b · 817a88b
2 parents a373b6b + c191092
commit 817a88b
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diff --git a/recipes/afpdb/meta.yaml b/recipes/afpdb/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "afpdb" %}
-{% set version = "0.2.2" %}
+{% set version = "0.2.3" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: fbdc60785aba0177a3766f952df8bc848aa03adcc0693506cc9f1f3601449e98
+  sha256: aad8f90092630dce86254227bc94e4f42a28598a6ccf69f07d0e619bc88c0ae8
 
 build:
   number: 0

diff --git a/recipes/devider/build.sh b/recipes/devider/build.sh
@@ -1,10 +1,21 @@
-#!/bin/bash -euo
+#!/bin/bash
+
+set -xeuo
 
-# Add workaround for SSH-based Git connections from Rust/cargo.  See https://github.com/rust-lang/cargo/issues/2078 for details.
 # We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct.
-export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo"
+export CARGO_HOME="$(pwd)/.cargo"
 
 # build statically linked binary with Rust
 cargo-bundle-licenses --format yaml --output THIRDPARTY.yml
-RUST_BACKTRACE=1 cargo install --verbose --locked --no-track --root $PREFIX --path .
+
+case $(uname -m) in
+    aarch64 | arm64)
+        FEATURES="--features neon --no-default-features"
+        ;;
+    *)
+        FEATURES=""
+        ;;
+esac
+
+RUST_BACKTRACE=1 cargo install --verbose --locked --no-track --root $PREFIX --path . ${FEATURES}
 cp scripts/* $PREFIX/bin
diff --git a/recipes/devider/devider-aarch64.patch b/recipes/devider/devider-aarch64.patch
@@ -0,0 +1,14 @@
+--- Cargo.toml.orig	2024-10-14 10:59:48.140000000 +0000
++++ Cargo.toml	2024-10-14 11:03:33.120000000 +0000
+@@ -13,9 +13,9 @@
+ rayon="1.7"
+ rand="0.8"
+ rand_core="0.6"
+-rust-htslib= { version = "0.44", default-features = false }
++rust-htslib= { version = "0.47", default-features = false }
+ clap = { version = "=4.2.0", features = ["derive"] }
+-block-aligner = { version = "0.4", default-features = false }
++block-aligner = { version = "0.5", default-features = false }
+ debruijn = "0.3"
+ simple_logger="4"
+ log="0.4"
diff --git a/recipes/devider/meta.yaml b/recipes/devider/meta.yaml
@@ -7,9 +7,11 @@ package:
 source:
   url: https://github.com/bluenote-1577/devider/archive/v{{ version }}.tar.gz
   sha256: e2c5e4a2faa51dbfd0ad4cb867d0dc25ea4012e83ec8fea27c1624592fce7dce
+  patches:
+    - devider-aarch64.patch # [aarch64]
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('devider', max_pin="x.x") }}
 
@@ -20,6 +22,8 @@ requirements:
     - cargo-bundle-licenses
     - make
     - cmake >=3.12
+  host:
+    - clangdev >=16,<17 # [linux and aarch64]
   run:
     - python 
     - samtools
@@ -43,5 +47,7 @@ about:
   summary: Haplotyping small sequences from heterogeneous long-read sequencing samples with a SNP-encoded positional de Bruijn graphs.
 
 extra:
+  additional-platforms:
+    - linux-aarch64
   recipe-maintainers:
     - bluenote-1577
diff --git a/recipes/easypqp/meta.yaml b/recipes/easypqp/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "easypqp" %}
-{% set version = "0.1.49" %}
-{% set sha256 = "96fffd59e617de0007f1fbe88ab223d605a7d4a4e94a7b4f4d4a94b4016e327c" %}
+{% set version = "0.1.50" %}
+{% set sha256 = "d3ebc1c7cbe61f081c5ab71e76e7130aa7fae955895ffe8f719363b29870a000" %}
 
 package:
   name: {{ name|lower }}
@@ -23,6 +23,7 @@ requirements:
   host:
     - python >=3.6
     - pip
+    - setuptools
   run:
     - python >=3.6
     - numba

diff --git a/recipes/gencove/meta.yaml b/recipes/gencove/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "gencove" %}
-{% set version = "2.21.0" %}
-{% set sha256 = "805be8b0c0f3e8d189bca16a805649e9594d455c0fa183ecd856ee3208287258" %}
+{% set version = "2.23.0" %}
+{% set sha256 = "edb1a4855f88d87c41902745d6f823142747005a29932700afcabc0c216f16e9" %}
 
 package:
   name: {{ name }}

diff --git a/recipes/metabolights-utils/meta.yaml b/recipes/metabolights-utils/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "metabolights-utils" %}
-{% set version = "1.2.0" %}
+{% set version = "1.2.1" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/metabolights_utils-{{ version }}.tar.gz
-  sha256: 4e8c7eb7fd06243389dfe13545ee517a76606ceaaa46d3e55a961dc333572fcf
+  sha256: 2db0e90df0540f87820955de31f8ec7bf9cbc6a0f669632c252c1f5908b31c9d
 
 build:
   entry_points:

diff --git a/recipes/rmats/meta.yaml b/recipes/rmats/meta.yaml
@@ -10,7 +10,7 @@ source:
   url: https://github.com/Xinglab/rmats-turbo/releases/download/v{{ version }}/rmats_turbo_v{{ version|replace(".","_") }}.tar.gz
 
 build:
-  number: 2
+  number: 3
   run_exports:
     - {{ pin_subpackage(name, max_pin="x") }}
 
@@ -26,14 +26,14 @@ requirements:
     - python
     - cython
     - numpy
-    - gsl
+    - gsl 2.5
     - zlib
     - libblas
     - liblapack
   run:
     - python
     - numpy
-    - gsl
+    - gsl 2.5
     - zlib
     - star >=2.5
 
@@ -50,4 +50,4 @@ about:
 
 extra:
   additional-platforms:
-    - linux-aarch64
+    - linux-aarch64
diff --git a/recipes/rseqc/meta.yaml b/recipes/rseqc/meta.yaml
@@ -1,55 +1,53 @@
-{% set name = "RSeQC" %}
-{% set version = "5.0.3" %}
+{% set name = "rseqc" %}
+{% set version = "5.0.4" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
-  url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 869f542e08f50c8874280d58e4f5565857b0aebac66a8eceef3f23016175061e
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/rseqc-{{ version }}.tar.gz
+  sha256: b7f3996f3de0b0b0a09eec949281a8f3e665a20827fcb3cbbd7546b94574a088
 
 build:
-  number: 3
-  skip: True  # [py2k]
-  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv"
+  number: 0
+  noarch: python
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   run_exports:
     - {{ pin_subpackage(name|lower, max_pin="x") }}
 
 requirements:
-  build:
-    - {{ compiler('c') }}
   host:
     - pip
-    - python
-    - cython >=0.12
-    - nose
+    - python >=3.5
+    - setuptools
   run:
     - bx-python
     - numpy
     - pybigwig
     - pysam
-    - python
-    - r-base
-    - pandas
+    - python >=3.5
+    - logomaker
 
 test:
   imports:
     - qcmodule
     - qcmodule.SAM
+    - psyco_full
   commands:
     - read_distribution.py 2>&1 | grep Usage > /dev/null
     - geneBody_coverage.py 2>&1 | grep Usage > /dev/null
 
 about:
-  home: http://rseqc.sourceforge.net/
-  license: GNU General Public License v2 (GPLv2)
-  summary: 'RNA-seq QC Package'
+  home: "https://rseqc.sourceforge.net"
+  license: "GPL-2.0-or-later"
+  summary: 'QC package for RNA-seq data.'
   license_family: GPL2
+  license_file: LICENSE
+  dev_url: "https://rseqc.sourceforge.net"
+  doc_url: "https://rseqc.sourceforge.net/#usage-information"
 
 extra:
-  additional-platforms:
-    - linux-aarch64
   identifiers:
     - biotools:rseqc
     - doi:10.1093/bioinformatics/bts356
diff --git a/recipes/seqfu/meta.yaml b/recipes/seqfu/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "seqfu" %}
-{% set version = "1.22.2" %}
-{% set sha256 = "0b66405ca98a80be614874fd1c1f651ecb410d953ac5070a0e93c77d2dbe1919" %}
+{% set version = "1.22.3" %}
+{% set sha256 = "65c1090cafe0e760e68d15d450bccfd57c0a03d553fdabca26e2191f566fef62" %}
 
 package:
   name: {{ name }}

diff --git a/recipes/seqwish/meta.yaml b/recipes/seqwish/meta.yaml
@@ -1,19 +1,19 @@
 {% set name = "seqwish" %}
-{% set version = "0.7.10" %}
+{% set version = "0.7.11" %}
 
 package:
   name: "{{ name }}"
   version: "{{ version }}"
 
 source:
   url: https://github.com/ekg/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz
-  sha256: 133b32c9c99caf44eba955b74bae338681da78300e4b21269e07475f88c88b29
+  sha256: 9cbf51990787a93c58a1ee04239608785beb7e8a38efeb02929121b3c8c4a103
 
 build:
   skip: True  # [osx]
   run_exports:
     - {{ pin_subpackage(name, max_pin='x.x') }}
-  number: 1
+  number: 0
 
 requirements:
   build:

diff --git a/recipes/smoothxg/meta.yaml b/recipes/smoothxg/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "smoothxg" %}
-{% set version = "0.7.4" %}
+{% set version = "0.8.0" %}
 
 package:
   name: "{{ name }}"
   version: "{{ version }}"
 
 source:
   url: https://github.com/pangenome/{{ name }}/releases/download/v{{ version }}/{{ name }}-v{{ version }}.tar.gz
-  sha256: 6c15c1156ac3e1a29cdb4db20f46e1b22382b22640beaa7ec8e0d76564dc53ca
+  sha256: b2b1402971c2e5cf85b318ab98583bf33f78cee33c4bcd8faa140624a76e84be
   patches:
     - CMakeLists.patch
 

diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml
@@ -12,7 +12,7 @@ source:
   sha256: 5c4348f55256eb62b2af10c64b0422ca08206193aef725b6412372a7804ef54b
 
 build:
-  number: 0
+  number: 1
   noarch: generic
   run_exports:
     - {{ pin_subpackage("snakemake", max_pin="x") }}
@@ -110,7 +110,6 @@ outputs:
         - snakemake-interface-report-plugins >=1.0.0,<2.0.0
         - tabulate
         - throttler
-        - toposort >=1.10,<2.0
         - wrapt
         - yte >=1.5.1,<2.0
         - dpath >=2.1.6,<3.0.0

diff --git a/recipes/squirrel/meta.yaml b/recipes/squirrel/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.0.10" %}
+{% set version = "1.0.11" %}
 {% set name = "squirrel" %}
 
 package:
@@ -7,10 +7,10 @@ package:
 
 source:
   url: https://github.com/aineniamh/squirrel/archive/refs/tags/{{ version }}.tar.gz
-  sha256: f59e433906b995004f4e266235b0cfd58d80a08fd63c776d86c1846c8565254e
+  sha256: 2d3a4e1a3227372f32ffb6d97005efb08839b53e71f1b6e3d844fe8327835fe5
 
 build:
-  number: 1
+  number: 0
   noarch: python
   script: python -m pip install --no-deps --ignore-installed .
   run_exports: