Merge branch 'master' into ega-crypto

.circleci/config.yml

@@ -9,7 +9,7 @@ executors:
   linux-aarch64:
     machine:
       image: ubuntu-2204:current
-    resource_class: arm.large
+    resource_class: arm.medium
 
 jobs: # a basic unit of work in a run
   build_and_test:

build-fail-blacklist

@@ -179,7 +179,6 @@ recipes/gemma
 recipes/roary
 recipes/deltabs
 recipes/gottcha
-recipes/pepnovo
 recipes/ea-utils
 recipes/nextgenmap
 recipes/igor_vdj

recipes/bactopia-py/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "bactopia-py" %}
-{% set version = "1.1.1" %}
+{% set version = "1.2.1" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/bactopia/bactopia-{{ version }}.tar.gz
-  sha256: a7e450658ca609d8fd93bc1beb343aa3fea76ac0cee06842f407cdc4d85299fa
+  sha256: bd375fcea02e5ea20c55f822a7173e70c89d30098585f4b3205bb85a94f821c1
 
 build:
   noarch: python
@@ -29,6 +29,7 @@ requirements:
     - pyyaml
     - requests
     - rich-click >=1.6.0
+    - tqdm
 
 test:
   imports:
@@ -42,6 +43,8 @@ test:
     - bactopia-prepare --help
     - bactopia-search --help
     - bactopia-summary --help
+    - bactopia-atb-formatter --help
+    - bactopia-atb-downloader --help
   requires:
     - pip
 

recipes/bbmap/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "BBMap" %}
-{% set version = "39.09" %}
-{% set sha256 = "df7871a18eff981d405472ff4bba3db8f99cac106acf3bb84d7435f260b33e54" %}
+{% set version = "39.10" %}
+{% set sha256 = "996aff05765ba5e64547f8a34c56da396ce7b18db96ffe7f1076f2d2f49c6148" %}
 
 package:
   name: {{ name|lower }}

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\

recipes/breseq/build.sh

@@ -1,5 +1,16 @@
 #!/bin/bash
+
 set -eux
-./configure --prefix=$PREFIX
-make -j ${CPU_COUNT}
+
+export INCLUDES="-I${PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export M4="${BUILD_PREFIX}/bin/m4"
+
+autoreconf -if
+./configure --prefix="${PREFIX}" \
+	CXX="${CXX}" \
+	CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" \
+	LDFLAGS="${LDFLAGS}"
+make -j "${CPU_COUNT}"
 make install

recipes/breseq/meta.yaml

@@ -9,19 +9,20 @@ source:
   sha256: "39b35e246ecd2b497c82a99765ca4d78a0400bc4a7518b7506b140229ccc0247"
 
 build:
-  number: 1
+  number: 2
   run_exports:
     - {{ pin_subpackage('breseq', max_pin="x.x") }}
 
 requirements:
   build:
     - make
-    - {{ compiler("c") }}
     - {{ compiler("cxx") }}
+    - autoconf
+    - automake
+    - libtool
   host:
     - zlib
   run:
-    - zlib
     - r-base
     - r-cairo
     - bowtie2 >=2.0.0,!=2.0.3,!=2.0.4,!=2.3.1
@@ -36,11 +37,17 @@ about:
   license: GPL-2.0-or-later
   license_family: GPL
   license_file: COPYING
-  summary: A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing
-    data.
+  summary: "A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing
+    data."
   doc_url: "https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/"
+  dev_url: https://github.com/barricklab/breseq
 
 extra:
   additional-platforms:
     - linux-aarch64
     - osx-arm64
+  identifiers:
+    - biotools:breseq
+    - biotools:breseq_bam2aln
+    - biotools:breseq_bam2cov
+    - usegalaxy-eu:breseq

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
 

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

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

recipes/civicpy/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "civicpy" %}
-{% set version = "3.1.0" %}
+{% set version = "3.1.2" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 1e9d5a36dff490c5a806cfc152c5f998ba13a54e409cb72eff392dc2ada14537
+  sha256: c702723367fec4c7cefbac86def0ef64749f12bda120300e43e6540387ce1a7b
 
 build:
   number: 0

recipes/clusty/meta.yaml

@@ -1,11 +1,11 @@
-{% set version = "1.0.0" %}
+{% set version = "1.1.1" %}
 
 package:
   name: clusty
   version: {{ version }}
 
 build:
-  number: 1
+  number: 0
   run_exports:
   - {{ pin_subpackage('clusty', max_pin='x.x.x') }}
 

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}