Merge branch 'master' into bump/regenie

recipes/delly/meta.yaml

@@ -1,5 +1,5 @@
-{% set version = "1.2.9" %}
-{% set sha256 = "084aec699f266e21b457db2cb86c75d73e29b071bdd837cb987561942aa01510" %}
+{% set version = "1.3.1" %}
+{% set sha256 = "914a29c301556746031586c5880e70ad7f31bd7899cc4e47b23ee4d5426761ae" %}
 
 package:
   name: delly

recipes/earlgrey/meta.yaml

@@ -11,7 +11,8 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 1
+  number: 2
+  skip: True # [osx]
   run_exports:
     - {{ pin_subpackage('earlgrey', max_pin='x') }}
 
@@ -49,10 +50,13 @@ requirements:
     - r-viridis
     - r-cowplot
     - r-ggtext
+    - r-data.table
+    - r-magrittr
     - bedtools
     - emboss
     - pybedtools
     - samtools
+    - heliano
 
 test:
   commands:

recipes/hmftools-chord/build.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM"
+[ -d "$TGT" ] || mkdir -p $TGT
+[ -d "${PREFIX}/bin" ] || mkdir -p "${PREFIX}/bin"
+
+cd "${SRC_DIR}"
+mv jar/chord*.jar $TGT/chord.jar
+${R} CMD INSTALL --build src/chord/src/main/R/mutSigExtractor
+${R} CMD INSTALL --build src/chord/src/main/R/CHORD
+
+cp $RECIPE_DIR/chord.sh $TGT/chord
+ln -s $TGT/chord ${PREFIX}/bin/

recipes/hmftools-chord/chord.sh

@@ -0,0 +1,69 @@
+#!/bin/bash
+# hmftools CHORD executable shell script
+# https://github.com/hartwigmedical/hmftools/tree/master/chord
+set -eu -o pipefail
+
+export LC_ALL=en_US.UTF-8
+
+# Find original directory of bash script, resolving symlinks
+# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in/246128#246128
+SOURCE="${BASH_SOURCE[0]}"
+while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink
+    DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+    SOURCE="$(readlink "$SOURCE")"
+    [[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located
+done
+DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )"
+
+JAR_DIR=$DIR
+ENV_PREFIX="$(dirname $(dirname $DIR))"
+# Use Java installed with Anaconda to ensure correct version
+java="$ENV_PREFIX/bin/java"
+
+# if JAVA_HOME is set (non-empty), use it. Otherwise keep "java"
+if [ -n "${JAVA_HOME:=}" ]; then
+  if [ -e "$JAVA_HOME/bin/java" ]; then
+      java="$JAVA_HOME/bin/java"
+  fi
+fi
+
+# extract memory and system property Java arguments from the list of provided arguments
+# http://java.dzone.com/articles/better-java-shell-script
+default_jvm_mem_opts="-Xms512m -Xmx1g"
+jvm_mem_opts=""
+jvm_prop_opts=""
+pass_args=""
+for arg in "$@"; do
+    case $arg in
+        '-D'*)
+            jvm_prop_opts="$jvm_prop_opts $arg"
+            ;;
+        '-XX'*)
+            jvm_prop_opts="$jvm_prop_opts $arg"
+            ;;
+         '-Xm'*)
+            jvm_mem_opts="$jvm_mem_opts $arg"
+            ;;
+         *)
+	    if [[ ${pass_args} == '' ]] #needed to avoid preceeding space on first arg e.g. ' MarkDuplicates'
+            then
+                pass_args="$arg"
+	    else
+                pass_args="$pass_args \"$arg\"" #quotes later arguments to avoid problem with ()s in MarkDuplicates regex arg
+            fi
+            ;;
+    esac
+done
+
+if [ "$jvm_mem_opts" == "" ]; then
+    jvm_mem_opts="$default_jvm_mem_opts"
+fi
+
+pass_arr=($pass_args)
+if [[ ${pass_arr[0]:=} == com.hartwig.* ]]
+then
+    eval "$java" $jvm_mem_opts $jvm_prop_opts -cp "$JAR_DIR/chord.jar" $pass_args
+else
+    eval "$java" $jvm_mem_opts $jvm_prop_opts -jar "$JAR_DIR/chord.jar" $pass_args
+fi
+exit

recipes/hmftools-chord/meta.yaml

@@ -0,0 +1,51 @@
+{% set version = "2.1.0_beta" %}
+{% set sha256_jar = "26d0a40e20635c4b797d28e0c7819b1653c9f8fa28180b9a556215d22387968c" %}
+{% set sha256_src = "ed039e7b405130a1e52df71c3535c6a5ed8aab0f80724bc83df88ae14aeaa257" %}
+
+package:
+  name: hmftools-chord
+  version: '{{ version }}'
+
+source:
+  - folder: jar
+    url: https://github.com/hartwigmedical/hmftools/releases/download/chord-v{{ version }}/chord-{{ version }}.jar
+    sha256: '{{ sha256_jar }}'
+  - folder: src
+    url: https://github.com/hartwigmedical/hmftools/archive/refs/tags/chord-v{{ version }}.tar.gz
+    sha256: '{{ sha256_src }}'
+
+build:
+  noarch: generic
+  number: 0
+  run_exports:
+    - {{ pin_subpackage("hmftools-chord", max_pin="x.x") }}
+
+requirements:
+  host:
+    - r-base
+    - r-randomforest
+    - r-stringr
+    - bioconductor-bsgenome
+    - bioconductor-bsgenome.hsapiens.ucsc.hg19
+    - bioconductor-bsgenome.hsapiens.ucsc.hg38
+  run:
+    - openjdk >=8
+    - r-base
+    - r-randomforest
+    - r-stringr
+    - bioconductor-bsgenome
+    - bioconductor-bsgenome.hsapiens.ucsc.hg19
+    - bioconductor-bsgenome.hsapiens.ucsc.hg38
+
+test:
+  commands:
+    - $R -e "library('CHORD')"
+    - $R -e "library('mutSigExtractor')"
+    - 'chord com.hartwig.hmftools.chord.ChordRunner -version | grep CHORD'
+
+about:
+  home: https://github.com/hartwigmedical/hmftools/blob/master/chord/
+  license: GPL-3.0-only
+  license_family: GPL3
+  license_file: LICENSE
+  summary: Predict HRD using somatic mutations contexts

recipes/hmftools-sage/meta.yaml

@@ -1,17 +1,18 @@
 {% set version = "4.0_beta" %}
-{% set sha256 = "85854164b2d5558e0701d83f13d59072abad3109d70a92fc5f574ef29c29e917" %}
+{% set beta_suffix = ".1" %}
+{% set sha256 = "22a3495f4ebe425114af4b9ba472860b3e2fe16395e3223827d0b6eccba27eb3" %}
 
 package:
   name: hmftools-sage
   version: '{{ version }}'
 
 source:
-  url: https://github.com/hartwigmedical/hmftools/releases/download/sage-v{{ version }}/sage_v{{ version }}.jar
+  url: https://github.com/hartwigmedical/hmftools/releases/download/sage-v{{ version }}/sage_v{{ version }}{{ beta_suffix }}.jar
   sha256: '{{ sha256 }}'
 
 build:
   noarch: generic
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('hmftools-sage', max_pin="x") }}
 

recipes/kmer-db/meta.yaml

@@ -1,28 +1,33 @@
-{% set version = "1.11.1" %}
-{% set sha256 = "63886057a752a890f492bf4ca7ec97435eceebb4ac5ecb5664c69ae2736eaa80" %}
+{% set version = "2.2.2" %}
+
+{% set system = "x64_linux" %}       # [linux and x86_64]
+{% set system = "x64_mac" %}         # [osx and x86_64]
+{% set system = "arm64_linux" %}     # [linux and aarch64]
+{% set system = "arm64_mac" %}       # [osx and arm64]
+
+{% set sha256 = "e4bccee6380b7c0bfb4746285d36af52a9874b1cf66d62a8862e8579097b5e77" %}  # [linux and x86_64]
+{% set sha256 = "bfb22576eef88293af4695d297b0b6d3cddc726a882e09ef29bd4684a705977f" %}  # [osx and x86_64]
+{% set sha256 = "62055ecaf81fac76cfc05a8cd64eba958d2c45350312556777dc4db7355a802a" %}  # [linux and aarch64]
+{% set sha256 = "6ba58753b1141a005e8a97bf581c1eada5cec6713a1f516518167f1da71b820b" %}  # [osx and arm64]
 
 
 package:
   name: kmer-db
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
+  run_exports:
+  - {{ pin_subpackage('kmer-db', max_pin='x') }}
+  script: |
+    mkdir -p "${PREFIX}/bin"
+    cp -v kmer-db "${PREFIX}/bin/" || { echo "Error: Failed to copy kmer-db binary"; exit 1; }
+
 
 source:
-  url: https://github.com/refresh-bio/kmer-db/archive/v{{ version }}.tar.gz
+  url: https://github.com/refresh-bio/kmer-db/releases/download/v{{ version }}/kmer-db-v{{ version }}-{{ system }}.tar.gz
   sha256: {{ sha256 }}
 
-requirements:
-  build:
-    - make
-    - {{ compiler('cxx') }}
-    - make 
-  host:
-    - zlib
-  run:
-    - zlib
-
 about:
   home: https://github.com/refresh-bio/kmer-db
   summary: "Kmer-db is a fast and memory-efficient tool for estimating evolutionary distances."
@@ -33,3 +38,13 @@ about:
 test:
   commands:
     - kmer-db > /dev/null
+    - kmer-db -help
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+  skip-lints:
+    - should_be_noarch_generic
+    - should_not_be_noarch_source
+

recipes/kmercamel/build.sh

@@ -1,5 +1,7 @@
 #!/bin/bash
 
-make CXX="${CXX} ${CXXFLAGS} ${CPPFLAGS} ${LDFLAGS}"
+set -xe
+
+make -j ${CPU_COUNT} CXX="${CXX} ${CXXFLAGS} ${CPPFLAGS} ${LDFLAGS}"
 install -d "${PREFIX}/bin"
 install kmercamel "${PREFIX}/bin/"

recipes/kmercamel/meta.yaml

@@ -10,7 +10,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('kmercamel', max_pin="x") }}
 
@@ -36,3 +36,7 @@ about:
   license_file: LICENSE.txt
   summary: KmerCamel🐫 - compressing k-mer sets using masked superstrings
 
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64

recipes/orthologer/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "orthologer" %}
-{% set version = "3.4.2" %}
-{% set sha256 = "fb8d11ef54d7232b150e5e46fbd15f9540a083064544d481f8fe9c9aea6b653e" %}
+{% set version = "3.5.0" %}
+{% set sha256 = "76bd68cd73d5989d658a6ba0ecefec84e674f85878b75904c76fa557ce5dd2b5" %}
 
 package:
   name: {{ name }}
@@ -41,6 +41,7 @@ requirements:
     - diamond
     - biopython
     - numpy
+    - busco >=5.7.0
 
 test:
   commands:
@@ -51,7 +52,8 @@ about:
   license: GPL3
   license_family: GPL3
   license_file: LICENSE
-  summary: "Find orthologous genes as well as mapping to OrthoDB."
+  summary: Establish orthology among fasta files.
+  description: Map genes to OrthoDB as well as finding orthology among a set of fasta files.
   dev_url: https://gitlab.com/ezlab/orthologer_container
   doc_url: https://orthologer.ezlab.org/#on-orthodb-data
 

recipes/patchify/meta.yaml

@@ -0,0 +1,45 @@
+{% set name = "patchify" %}
+{% set version = "0.2.3" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/patchify-{{ version }}.tar.gz
+  sha256: 6cc409124f34ceee672f1931d818923f88f5116f323ac7bb9be7e6c5d0845502
+
+build:
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('patchify', max_pin="x.x") }}
+
+requirements:
+  host:
+    - python >=3.7,<4.0
+    - poetry >=0.12
+    - poetry-core
+    - pip
+  run:
+    - python >=3.7.0,<4.0.0
+    - numpy >=1.0.0,<2.0.0
+
+test:
+  imports:
+    - patchify
+  commands:
+    - pip check
+  requires:
+    - pip
+
+about:
+  home: https://github.com/dovahcrow/patchify.py
+  summary: A library that helps you split image into small, overlappable patches, and merge patches back into the original image.
+  license: MIT
+  license_file: LICENSE
+
+extra:
+  recipe-maintainers:
+    - hexylena