Update hmftools-{chord,esvee,pave,redux} (#52078)

* Update Chord to 2.1.0_beta.1 * Update Esvee to 1.0_beta.4 * Update Pave to 1.7_beta.1 * Update Redux to 1.0_beta.4 * Fix typo in Chord jar URL * Fix typo in Chord jar URL again * Remove install commands for mutSigExtractor and CHORD R packages
bioconda · Nov 13, 2024 · 638d885 · 638d885
1 parent e9318b2
commit 638d885
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diff --git a/recipes/hmftools-chord/build.sh b/recipes/hmftools-chord/build.sh
@@ -5,9 +5,8 @@ TGT="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM"
 [ -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
+mv chord*.jar $TGT/chord.jar
 
 cp $RECIPE_DIR/chord.sh $TGT/chord
 ln -s $TGT/chord ${PREFIX}/bin/
+chmod 0755 "${PREFIX}/bin/chord"
diff --git a/recipes/hmftools-chord/meta.yaml b/recipes/hmftools-chord/meta.yaml
@@ -1,51 +1,33 @@
 {% set version = "2.1.0_beta" %}
-{% set sha256_jar = "26d0a40e20635c4b797d28e0c7819b1653c9f8fa28180b9a556215d22387968c" %}
-{% set sha256_src = "ed039e7b405130a1e52df71c3535c6a5ed8aab0f80724bc83df88ae14aeaa257" %}
+{% set beta_suffix = ".1" %}
+{% set sha256 = "25a4dfd8a0ab436e0f23d94e77cebb59a0830a052a90c823844b798bd409bfc3" %}
 
 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 }}'
+  url: https://github.com/hartwigmedical/hmftools/releases/download/chord-v{{ version }}/chord_v{{ version }}{{ beta_suffix }}.jar
+  sha256: '{{ sha256 }}'
 
 build:
   noarch: generic
-  number: 0
+  number: 2
   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'
+    - 'chord -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
diff --git a/recipes/hmftools-esvee/meta.yaml b/recipes/hmftools-esvee/meta.yaml
@@ -1,6 +1,6 @@
 {% set version = "1.0_beta" %}
-{% set beta_suffix = ".3" %}
-{% set sha256 = "da026c1bec9c8314652f7c3870daa2d8eaddd3dc71ef924d86339c87d084d65a" %}
+{% set beta_suffix = ".4" %}
+{% set sha256 = "9a833992f4b8c5c01d845ed60c96fc93c43c5955171658255c545413cedb23d5" %}
 
 package:
   name: hmftools-esvee
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: generic
-  number: 4
+  number: 5
   run_exports:
     - {{ pin_subpackage("hmftools-esvee", max_pin="x.x") }}
 

diff --git a/recipes/hmftools-pave/meta.yaml b/recipes/hmftools-pave/meta.yaml
@@ -1,17 +1,18 @@
 {% set version = "1.7_beta" %}
-{% set sha256 = "b6e67aa0bb96db3b50429afe4a6c6fad168660bf220f61b638e06b0c643969ab" %}
+{% set beta_suffix = ".1" %}
+{% set sha256 = "adfc0bbbf3a8b35faa7a5ce2d1fb0a5c016ae71fcd80cfa2dd28caa4e1b5826a" %}
 
 package:
   name: hmftools-pave
   version: '{{ version }}'
 
 source:
-  url: https://github.com/hartwigmedical/hmftools/releases/download/pave-v{{ version }}/pave_v{{ version }}.jar
+  url: https://github.com/hartwigmedical/hmftools/releases/download/pave-v{{ version }}/pave_v{{ version }}{{ beta_suffix }}.jar
   sha256: '{{ sha256 }}'
 
 build:
   noarch: generic
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('hmftools-pave', max_pin="x.x") }}
 

diff --git a/recipes/hmftools-redux/meta.yaml b/recipes/hmftools-redux/meta.yaml
@@ -1,6 +1,6 @@
 {% set version = "1.0_beta" %}
-{% set beta_suffix = ".3" %}
-{% set sha256 = "6c7710471c055d228fb569728eccd16d7c0bbea4a59026d4575e9e539ece983a" %}
+{% set beta_suffix = ".4" %}
+{% set sha256 = "e3398c8fba7f9e572ac06def6d957ceed1598f0c6b9b06563814ccfec5c3158f" %}
 
 package:
   name: hmftools-redux
@@ -12,7 +12,7 @@ source:
 
 build:
   noarch: generic
-  number: 4
+  number: 5
   run_exports:
     - {{ pin_subpackage('hmftools-redux', max_pin="x.x") }}