Merge branch 'master' into osx-arm-builds

bioconda · Apr 2, 2024 · 1b177cc · 1b177cc
2 parents 965fde4 + 5a5fbcd
commit 1b177cc
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diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -802,7 +802,6 @@ recipes/ucsc-axtsort
 recipes/ucsc-axtswap
 recipes/ucsc-axttomaf
 recipes/ucsc-bamtopsl
-recipes/ucsc-bedclip
 recipes/ucsc-bedcommonregions
 recipes/ucsc-bedcoverage
 recipes/ucsc-bedextendranges
@@ -1062,3 +1061,6 @@ recipes/mudskipper
 
 # md5 mismatch when downloading source
 recipes/komb
+
+# duplicate recipe
+recipes/treeqmc
diff --git a/recipes/3seq/meta.yaml b/recipes/3seq/meta.yaml
@@ -7,7 +7,9 @@ package:
   version: {{ version }}
 
 build:
-  number: 3
+  number: 4
+  run_exports:
+    - {{ pin_subpackage("3seq", max_pin="x") }}  
 
 source:
   url: https://gitlab.com/lamhm/{{ name|lower }}/-/archive/v{{ version }}/3seq-v{{ version }}.tar.gz
@@ -28,6 +30,10 @@ test:
 
 about:
   home: https://mol.ax/software/3seq/
-  license: CC BY-NC-SA 4.0
+  license: CC-BY-NC-SA-4.0
   license_file: LICENSE.md
   summary: '3SEQ tests all sequence triplets in an alignment for a mosaic recombination signal.'
+
+extra:
+  additional-platforms:
+    - linux-aarch64
diff --git a/recipes/abawaca/meta.yaml b/recipes/abawaca/meta.yaml
@@ -11,7 +11,9 @@ source:
     - 0001-Use-CXX-and-flags.patch
 
 build:
-  number: 6
+  number: 7
+  run_exports:
+    - {{ pin_subpackage("abawaca", max_pin="x") }}
 
 requirements:
   build:
@@ -34,3 +36,5 @@ extra:
     - keuv-grvl
   identifiers:
     - doi:10.1038/nature14486
+  additional-platforms:
+    - linux-aarch64
diff --git a/recipes/abritamr/meta.yaml b/recipes/abritamr/meta.yaml
@@ -11,7 +11,7 @@ source:
   sha256: "{{ sha256 }}"
 
 build:
-  number: 0
+  number: 1
   noarch: python
   entry_points:
     - abritamr=abritamr.abritamr:main
@@ -29,7 +29,10 @@ requirements:
     - python >=3.9
     - pandas
     - xlsxwriter
-    - ncbi-amrfinderplus =3.10.42
+    # Please review ncbi-amrfinderplus pinning every release
+    # The version should be pinned to the database version used by abritamr
+    # Please see the "changes.txt" file in https://github.com/MDU-PHL/abritamr/blob/master/abritamr/db/amrfinderplus/data/<DATABASE_VERSION>/changes.txt
+    - ncbi-amrfinderplus =3.12.8
     - blast
     - hmmer
 

diff --git a/recipes/abromics_galaxy_json_extractor/meta.yaml b/recipes/abromics_galaxy_json_extractor/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.8.3.4" %}
+{% set version = "0.8.3.6" %}
 
 context: {}
 
@@ -8,7 +8,7 @@ package:
 
 source:
   url: https://gitlab.com/ifb-elixirfr/abromics/abromics-galaxy-json-extractor/-/archive/{{ version }}/abromics-galaxy-json-extractor-{{ version }}.tar.gz
-  sha256:  '4106ed76eb759f3bd3fcb866d18fdafce64f4ef6d364967f7ccee29b6af06d19'
+  sha256:  '364997088a29c30cdc45d2c66af40a3d6b8e3398efe1d7eb242d31b0e68abd77'
 
 build:
   noarch: python

diff --git a/recipes/abundancebin/meta.yaml b/recipes/abundancebin/meta.yaml
@@ -14,7 +14,9 @@ source:
     - 0001-Use-CXX-and-flags.patch
 
 build:
-  number: 6
+  number: 7
+  run_exports:
+    - {{ pin_subpackage("abundancebin", max_pin="x.x.x") }}  
   skip: True  # [osx]
 
 requirements:
@@ -45,3 +47,5 @@ extra:
     - keuv-grvl
   identifiers:
     - doi:10.1007/978-3-642-12683-3_35
+  additional-platforms:
+    - linux-aarch64
diff --git a/recipes/adapterremoval/meta.yaml b/recipes/adapterremoval/meta.yaml
@@ -10,7 +10,9 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 2
+  number: 3
+  run_exports:
+    - {{ pin_subpackage("adapterremoval", max_pin="x") }}  
 
 requirements:
   build:
@@ -34,3 +36,7 @@ about:
   license: GPL3
   license_file: LICENSE
   summary: The AdapterRemoval v2 tool for merging and clipping reads.
+
+extra:
+  additional-platforms:
+    - linux-aarch64
diff --git a/recipes/addrg/meta.yaml b/recipes/addrg/meta.yaml
@@ -6,7 +6,9 @@ package:
   version: {{ version }}
 
 build:
-  number: 11
+  number: 12
+  run_exports:
+    - {{ pin_subpackage("addrg", max_pin="x.x") }}
 
 source:
   url: https://github.com/holtgrewe/addrg/archive/v{{ version }}.tar.gz
@@ -17,6 +19,7 @@ requirements:
     - {{ compiler('c') }}
   host:
     - htslib
+    - zlib
   run:
     - htslib
 
@@ -28,3 +31,7 @@ about:
   home: https://github.com/holtgrewe/addrg
   license: MIT
   summary: Add read group to BAM files
+
+extra:
+  additional-platforms:
+    - linux-aarch64
diff --git a/recipes/agat/meta.yaml b/recipes/agat/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "AGAT" %}
-{% set version = "1.3.1" %}
-{% set sha256 = "0361f5f5708b0010045a410e3656d6b16571d5ebaf72898f6df846c49f282a3c" %}
+{% set version = "1.3.3" %}
+{% set sha256 = "08fa159f7badb418a681a514d471d7233bb1cc09a5e41d875118eaec4c2ec813" %}
 
 package:
   name: "{{ name|lower }}"

diff --git a/recipes/agc/meta.yaml b/recipes/agc/meta.yaml
@@ -1,20 +1,26 @@
-{% set version = "3.0" %}
-{% set system = "linux"%}  # [linux]
-{% set system = "mac"%}  # [osx]
-{% set sha256 = "3ee3245e556221d246f9afe5d9ad86888f4eb5aea6b10f621241c3170ef8835e" %}  # [linux]
-{% set sha256 = "3d68b6b76948b6d9a36c4e848e37969eda6ae0ec1abace4ca61a7cc585dcdabf" %}  # [osx]
+{% set version = "3.1" %}
+
 package:
   name: agc
   version: {{ version }}
+
 build:
   number: 0
   script: "mkdir -p ${PREFIX}/bin; cp agc ${PREFIX}/bin"
+  run_exports:
+    - {{ pin_subpackage('agc', max_pin="x") }}
 source:
-  url: https://github.com/refresh-bio/agc/releases/download/v{{ version }}/agc-{{ version }}_x64-{{ system }}.tar.gz
-  sha256: {{ sha256 }}
+  - url: https://github.com/refresh-bio/agc/releases/download/v{{ version }}/agc-{{ version }}_arm_linux.tar.gz # [aarch64]
+    sha256: 5fee3ccbb2691d82a877987e204c5946dbdbe40b9603af5d2421cb8506577534                                           # [aarch64]
+  - url: https://github.com/refresh-bio/agc/releases/download/v{{ version }}/agc-{{ version }}_x64_linux.tar.gz   # [linux64]
+    sha256: 4868dd45c1ed31a7f36bcbc536174249de27b87ec83858d22b128cbec8deef53                                           # [linux64]
+  - url: https://github.com/refresh-bio/agc/releases/download/v{{ version }}/agc-{{ version }}_x64_mac.tar.gz       # [osx and x86_64]
+    sha256: 0ef911e6bb8df791593ee6e89b5bddbf82b5823684955d249d6a67a39e6d0d4e                                           # [osx and x86_64]
+  - url: https://github.com/refresh-bio/agc/releases/download/v{{ version }}/agc-{{ version }}_m1_mac.tar.gz       # [osx and arm64]
+    sha256: ff8cc5dd4c5825a41e042567a93e9e01ef43fc91624c983640a29fd3c7ac03e4                                           # [osx and arm64]
 requirements:
   build:
-  run:
+  run: 
 about:
   home: https://github.com/refresh-bio/agc
   summary: "Assembled Genomes Compressor (AGC) is a tool designed to compress collections of de-novo assembled genomes. It can be used for various types of datasets: short genomes (viruses) as well as long (humans)."
@@ -23,6 +29,8 @@ test:
   commands:
     - agc
 extra:
+  additional-platforms:
+    - linux-aarch64
   skip-lints:
     - should_be_noarch_generic
     - should_not_be_noarch_source

diff --git a/recipes/akt/build.sh b/recipes/akt/build.sh
@@ -1,4 +1,8 @@
 #!/bin/bash
+if [ `uname -m` == "aarch64" ]; then
+sed -i 's/\-mpopcnt//g' Makefile
+fi
+
 make \
     CC="${CC} ${CFLAGS} ${CPPFLAGS} ${LDFLAGS}" \
     CXX="${CXX} ${CXXFLAGS} ${CPPFLAGS} ${LDFLAGS}"

diff --git a/recipes/akt/meta.yaml b/recipes/akt/meta.yaml
@@ -10,7 +10,9 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 4
+  number: 5
+  run_exports:
+    - {{ pin_subpackage("akt", max_pin="x.x.x") }}  
 
 requirements:
   build:
@@ -38,3 +40,5 @@ about:
 extra:
   identifiers:
     - doi:10.1093/bioinformatics/btw576
+  additional-platforms:
+    - linux-aarch64
diff --git a/recipes/alignoth/meta.yaml b/recipes/alignoth/meta.yaml
@@ -5,7 +5,7 @@ package:
   version: {{ version }}
 
 build:
-  number: 0
+  number: 1
   # TODO fails to build on osx with
   # Undefined symbols for architecture x86_64: "_SSLCopyALPNProtocols", referenced from: _sectransp_connect_step2 in libcurl_sys-1f07db570920ba9f.rlib(sectransp.o)
   skip: true  #[osx]
@@ -30,6 +30,7 @@ requirements:
     - libcurl
     - openssl
 
+
 test:
   commands:
     - alignoth --help
@@ -43,3 +44,5 @@ extra:
   recipe-maintainers:
     - fxwiegand
     - johanneskoester
+  additional-platforms:  #add aarch64
+    - linux-aarch64
diff --git a/recipes/alignstats/meta.yaml b/recipes/alignstats/meta.yaml
@@ -10,7 +10,9 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 1
+  number: 2
+  run_exports:
+    - {{ pin_subpackage("alignstats", max_pin="x.x.x") }}  
 
 requirements:
   build:
@@ -33,3 +35,7 @@ about:
   home: https://github.com/jfarek/alignstats
   license: BSD-3-Clause
   summary: Comprehensive alignment, whole-genome coverage, and capture coverage statistics.
+
+extra:
+  additional-platforms:
+    - linux-aarch64
diff --git a/recipes/allegro/build.sh b/recipes/allegro/build.sh
@@ -1,4 +1,8 @@
 #!/bin/bash
+rm -rf src/config.guess
+rm -rf src/config.sub
+wget "http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD" -O src/config.guess
+wget "http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD" -O src/config.sub
 ./configure
 make CXXFLAGS="${CXXFLAGS} -std=c++03"
 

diff --git a/recipes/allegro/meta.yaml b/recipes/allegro/meta.yaml
@@ -18,7 +18,9 @@ source:
 
 build:
   skip: True  # [osx]
-  number: 7
+  number: 8
+  run_exports:
+    - {{ pin_subpackage("allegro", max_pin="x.x.x") }}  
 
 requirements:
   build:
@@ -27,6 +29,7 @@ requirements:
   host:
     - zlib
     - patch
+    - wget
   run:
     - zlib
 
@@ -43,3 +46,5 @@ about:
 extra:
   skip-lints:
     - should_not_be_noarch_source
+  additional-platforms:
+    - linux-aarch64
diff --git a/recipes/altair-mf/meta.yaml b/recipes/altair-mf/meta.yaml
@@ -10,7 +10,9 @@ package:
 build:
    # Passes some invalid flags for clang
    skip: True  # [osx]
-   number: 2
+   number: 3
+   run_exports:
+    - {{ pin_subpackage("altair-mf", max_pin="x.x.x") }}  
 
 source:
   url: https://github.com/cobilab/altair/archive/v{{ version }}.tar.gz
@@ -37,3 +39,7 @@ about:
   license_file: LICENSE
   license_family: GPL
   summary: Software for alignment-free and spatial-temporal analysis of multi-FASTA data
+
+extra:
+  additional-platforms:
+    - linux-aarch64
diff --git a/recipes/ampcombi/meta.yaml b/recipes/ampcombi/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "AMPcombi" %}
-{% set version = "0.2.1" %}
+{% set version = "0.2.2" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: da699d66190e654b6c9ca333228678fd759f4ce8e84b8022c24417cf5a300c86
+  sha256: da9a179851a8f2041d05ccd10dd45b58099e84059e2e66a9ee405d1913471b58
 
 build:
   noarch: python

diff --git a/recipes/ampliconsuite/meta.yaml b/recipes/ampliconsuite/meta.yaml
@@ -1,7 +1,7 @@
 {% set name="ampliconsuite" %}
-{% set AS_version="1.2.2" %}
-{% set AA_version="1.3.r8" %}
-{% set AC_version="1.1.2" %}
+{% set AS_version="1.3.1" %}
+{% set AA_version="1.4.r1" %}
+{% set AC_version="1.1.3" %}
 
 package:
     name: {{ name }}
@@ -11,12 +11,12 @@ source:
     # the sha256 sum is generated by doing
     # $ wget -O- [URL] | shasum -a 256
     - url: https://github.com/AmpliconSuite/AmpliconSuite-pipeline/archive/v{{ AS_version }}.tar.gz
-      sha256: 40d3b4560fb2c9fd0cbc5166b9d136751ff16217a6228fb38b74e12207ef5b63
+      sha256: b74c8201b9e53493a8f1604f6035fa9e42c0ce7d1a258f9095b037afe2d5f2d8
     - url: https://github.com/AmpliconSuite/AmpliconArchitect/archive/v{{ AA_version }}.tar.gz
-      sha256: 44466fb4a275f5dd1a142269bb72dc53a651b9d9193e5ba799eee14f0f693f89
+      sha256: d62e30999c69b994691c8a61b09255a0b223906fd76709febc0ae8387164f208
       folder: ampliconarchitectlib
     - url: https://github.com/AmpliconSuite/AmpliconClassifier/archive/v{{ AC_version }}.tar.gz
-      sha256: 0f57d0775d7b68a76fab6cc375e45410fe76dd9245697855f257378bd1f21650
+      sha256: 105f3d0dfd99c52bb8cd988f3fd71afb064b01167a36b72d8fe789f5dfe8c9f5
 
 build:
     noarch: python
@@ -41,12 +41,14 @@ requirements:
         - pysam
         - samtools
         - scipy
+        - bedtools
     host:
         - python >=3
 
 test:
     commands:
     - AmpliconSuite-pipeline.py -v
+    - GroupedAnalysisAmpSuite.py -v
     - amplicon_classifier.py -v
     - feature_similarity.py -h
     - make_results_table.py -h