Merge branch 'bioconda:master' into zamp

bioconda · Oct 16, 2024 · 1f8b1a4 · 1f8b1a4
2 parents 33881d6 + c5610fa
commit 1f8b1a4
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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/biobb_common/meta.yaml b/recipes/biobb_common/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "biobb_common" %}
-{% set version = "4.2.0" %}
+{% set version = "5.0.0" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: f261b4b306670506b2cc45372322000996830541b7c1bcc9e13daa9a903da14b
+  sha256: d1ad551e8e3f029d6396d3ac5e7ec7dc58d30b1f81fd4a339067325ee7ffc515
 
 build:
   number: 0
@@ -18,16 +18,18 @@ build:
 
 requirements:
   host:
-    - python >=3.8.0
+    - python >=3.9.0
     - setuptools
     - pyyaml
     - requests
     - biopython
+    - jsonschema
   run:
-    - python >=3.8.0
+    - python >=3.9.0
     - pyyaml
     - requests
     - biopython
+    - jsonschema
 
 test:
   imports:
@@ -47,7 +49,7 @@ about:
     \n# biobb_common\n\n### Introduction\nBiobb_common is the base package required to use the biobb\npackages.\nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate new layer\
     \ of compatibility and interoperability over popular\nbioinformatics tools.\nThe latest documentation of this package can be found in our readthedocs site:\n[latest API documentation](http://biobb_common.readthedocs.io/en/latest/).\n\
     \n\n### Copyright & Licensing\n### Copyright & Licensing\nThis software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\
-    \n\n* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\
+    \n\n* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\
     Licensed under the\n\
     [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.\n\
     \n\

diff --git a/recipes/busco/build.sh b/recipes/busco/build.sh
@@ -2,9 +2,9 @@
 
 set -euxo pipefail
 
-"${PYTHON}" -m pip install . --no-deps -vv
+"${PYTHON}" -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
 
 mkdir -p $PREFIX/bin/
-cp bin/busco $PREFIX/bin/busco #python script
+cp bin/busco $PREFIX/bin/busco  #python script
 cp scripts/generate_plot.py $PREFIX/bin/generate_plot.py
 
diff --git a/recipes/busco/meta.yaml b/recipes/busco/meta.yaml
@@ -1,16 +1,16 @@
 {% set name = "busco" %}
-{% set version = "5.7.1" %}
-{% set sha256 = "d57066b68d533f0b86518653430ba47b748ef14db56d2a992601d3e26096cad6" %}
+{% set version = "5.8.0" %}
+{% set sha256 = "201218349224d35b4ad2de345505710e7778904e0f1158874b2a4d0cb2dce1ed" %}
 
 package:
   name: busco
   version: {{ version }}
 
 build:
-  number: 1
+  number: 0
   noarch: python
   run_exports:
-    - {{ pin_subpackage(name, max_pin="x.x") }}
+    - {{ pin_subpackage(name, max_pin="x") }}
 
 source:
   url: https://gitlab.com/ezlab/busco/-/archive/{{ version }}/busco-{{ version }}.tar.gz
@@ -24,29 +24,29 @@ requirements:
     - python >=3.3
     - pip
     - wget
-    - blast >=2.10.1 # There is a multithreading problem for all BLAST versions between 2.4 and 2.10.0
-    - hmmer >=3.1b2 # sepp needs this version
+    - blast >=2.10.1  # There is a multithreading problem for all BLAST versions between 2.4 and 2.10.0
+    - hmmer >=3.1b2  # sepp needs this version
     - augustus >=3.3
     - biopython >=1.79
     - prodigal
     - sepp >=4.3.10
-    - metaeuk >=6.a5d39d9 # needed for gff bug fix
+    - metaeuk >=6.a5d39d9  # needed for gff bug fix
     - pandas
     - bbmap
     - miniprot
     - requests
   run:
     - python >=3.3
     - wget
-    - blast >=2.10.1 # There is a multithreading problem for all BLAST versions between 2.4 and 2.10.0
-    - hmmer >=3.1b2 # sepp needs this version
+    - blast >=2.10.1  # There is a multithreading problem for all BLAST versions between 2.4 and 2.10.0
+    - hmmer >=3.1b2  # sepp needs this version
     - augustus >=3.3
     - biopython >=1.79
     - r-base
     - r-ggplot2 >=2.2.1
     - prodigal
     - sepp >=4.3.10
-    - metaeuk >=6.a5d39d9 # needed for gff bug fix
+    - metaeuk >=6.a5d39d9  # needed for gff bug fix
     - pandas
     - bbmap
     - miniprot
@@ -62,16 +62,17 @@ test:
     - test_data
 
 about:
-  home: https://busco.ezlab.org/
+  home: "https://busco.ezlab.org"
   license: MIT
   license_family: MIT
   license_file: LICENSE
-  summary: Assessment of assembly completeness using Universal Single Copy Orthologs
+  summary: "Assessment of assembly completeness using Universal Single Copy Orthologs."
   description: BUSCO provides measures for quantitative assessment of genome
            assembly, gene set, and transcriptome completeness based on
            evolutionarily informed expectations of gene content from
            near-universal single-copy orthologs selected from OrthoDB.
-  dev_url: https://gitlab.com/ezlab/busco
+  dev_url: "https://gitlab.com/ezlab/busco"
+  doc_url: "https://busco.ezlab.org/busco_userguide.html"
 
 extra:
   container:
@@ -84,6 +85,4 @@ extra:
     - doi:10.1093/bioinformatics/btv351
     - usegalaxy-eu:busco
   recipe-maintainers:
-    - silask
-    - matsepp
     - berkelem
diff --git a/recipes/cenote-taker3/meta.yaml b/recipes/cenote-taker3/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "cenote-taker3" %}
-{% set version = "3.3.1" %}
+{% set version = "3.3.2" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
-  url: "https://github.com/mtisza1/{{ name }}/archive/v{{ version }}.tar.gz"
-  sha256: ce595208f3d925f7798e579b2d72b995b192eac802e24bb3d9d0a2ca856b5a99
+  url: "https://github.com/mtisza1/Cenote-Taker3/archive/v{{ version }}.tar.gz"
+  sha256: b3b646825cedaaee15ac4e448408b8cedda2f3e1faa13a4601930bc7ff482d8b
 
 build:
   number: 0
@@ -18,14 +18,15 @@ build:
     - cenotetaker3 = cenote.cenotetaker3:cenotetaker3
     - get_ct3_dbs = cenote.get_ct3_databases:get_ct3_dbs
   script:
-    - {{ PYTHON }} -m pip install . --no-deps -vv
+    - {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
 
 requirements:
   host:
     - pip
-    - python >=3.10
+    - python >=3.6
+    - setuptools
   run:
-    - python >=3.10
+    - python >=3.6
     - seqkit
     - prodigal
     - pyrodigal-gv >=0.3.1
@@ -45,7 +46,7 @@ requirements:
     - samtools
     - pandas
     - pyarrow
-
+    - numpy
 
 test:
   commands:
@@ -55,10 +56,12 @@ test:
 about:
   home: "https://github.com/mtisza1/Cenote-Taker3"
   license: MIT
+  license_family: MIT
   license_file: LICENSE
   summary: "Cenote-Taker 3: Discover and annotate the virome"
   dev_url: "https://github.com/mtisza1/Cenote-Taker3"
+  doc_url: "https://github.com/mtisza1/Cenote-Taker3/blob/v{{ version }}/README.md"
 
 extra:
   recipe-maintainers:
-    - mtisza1
+    - mtisza1
diff --git a/recipes/cmat/build.sh b/recipes/cmat/build.sh
@@ -1,6 +1,6 @@
 #!/bin/bash -euo
 
-$PYTHON -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
+$PYTHON -m pip install . --no-deps --no-build-isolation --no-cache-dir --use-pep517 -vvv
 
 CMAT="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}"
 mkdir -p ${PREFIX}/bin ${CMAT}

diff --git a/recipes/cmat/meta.yaml b/recipes/cmat/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "cmat" %}
-{% set version = "3.2.2" %}
+{% set version = "3.3.0" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://github.com/EBIvariation/CMAT/archive/v{{version}}.tar.gz
-  sha256: 63b052052e6c3809e2d55835bfbe1dbd5ee312d6ef12906b25e5c67816fa6186
+  sha256: d39137937c2827b401fe7ca10ccaaf4f8dbbac049e7ea5b86ded6713bf1efdba
 
 build:
   number: 0
@@ -27,6 +27,7 @@ requirements:
     - pandas ==1.5.3
     - pytest ==7.2.2
     - pytest-cov ==2.10.0
+    - pyyaml ==6.0.1
     - requests ==2.32.3
     - requests-mock ==1.8.0
     - retry ==0.9.2
@@ -41,6 +42,7 @@ requirements:
     - pandas ==1.5.3
     - pytest ==7.2.2
     - pytest-cov ==2.10.0
+    - pyyaml ==6.0.1
     - requests ==2.32.3
     - requests-mock ==1.8.0
     - retry ==0.9.2
@@ -57,7 +59,9 @@ about:
   home: https://github.com/EBIvariation/CMAT
   summary: ClinVar Mapping and Annotation Toolkit
   license: Apache-2.0
+  license_family: APACHE
   license_file: LICENSE
+  dev_url: https://github.com/EBIvariation/CMAT
 
 extra:
   recipe-maintainers:

diff --git a/recipes/cosigt/build.sh b/recipes/cosigt/build.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+mkdir -p $PREFIX/bin
+go mod init cosigt
+go mod tidy
+go get -d ./...
+CGO_ENABLED=0 go build -o $PREFIX/bin/cosigt .
diff --git a/recipes/cosigt/meta.yaml b/recipes/cosigt/meta.yaml
@@ -0,0 +1,38 @@
+{% set name = "cosigt" %}
+{% set version = "0.1.2" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+build:
+  number: 0
+  run_exports:
+      - {{ pin_subpackage(name, max_pin='x.x') }}
+
+source:
+  - url: https://github.com/davidebolo1993/{{ name }}/archive/tags/v{{ version }}.tar.gz
+    sha256: 8cd92c395643720492cc1626d16aa5258bf44a6f448c2ea3407a257bf0ab6416
+
+requirements:
+  build:
+    - {{ compiler('go') }}
+
+test:
+  commands:
+    - cosigt -h
+
+about:
+  home: https://github.com/davidebolo1993/{{ name }}
+  license: 'GNU General Public License v3 (GPLv3)'
+  license_family: GPL3
+  license_file: LICENSE
+  summary: Cosigt (COsine SImilarity-based GenoTyper)
+  dev_url: https://github.com/davidebolo1993/{{ name }}
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+  recipe-maintainers:
+    - AndreaGuarracino
diff --git a/recipes/devider/build.sh b/recipes/devider/build.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+set -xeuo
+
+# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct.
+export CARGO_HOME="$(pwd)/.cargo"
+
+# build statically linked binary with Rust
+cargo-bundle-licenses --format yaml --output THIRDPARTY.yml
+
+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"