upgrade conda package, version (macro) and .shed.yml

ARTbio · Feb 10, 2024 · b9ce1f9 · b9ce1f9
1 parent 5eb8570
commit b9ce1f9
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Showing 2 changed files with 15 additions and 11 deletions.
diff --git a/tools/mutational_patterns/.shed.yml b/tools/mutational_patterns/.shed.yml
@@ -9,6 +9,6 @@ long_description: |
 categories:
   - Variant Analysis
 homepage_url: http://artbio.fr
-remote_repository_url: https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns
+remote_repository_url: https://github.com/ARTbio/tools-artbio/tree/main/tools/mutational_patterns
 toolshed:
   - toolshed
diff --git a/tools/mutational_patterns/mutational_patterns.xml b/tools/mutational_patterns/mutational_patterns.xml
@@ -1,15 +1,19 @@
-<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.4.0+galaxy2">
+<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>from genomic variations in vcf files</description>
+    <macros>
+        <token name="@TOOL_VERSION@">3.12.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">23.0</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="3.4.0=r41hdfd78af_0">bioconductor-mutationalpatterns</requirement>
-        <!--requirement type="package" version="1.1.1l=h7f98852_0">openssl</requirement> -->
-        <requirement type="package" version="3.3.6=r41hc72bb7e_0">r-ggplot2</requirement>
-        <requirement type="package" version="1.7.1=r41hc72bb7e_0">r-optparse</requirement>
-        <requirement type="package" version="0.2.21=r41h7525677_1">r-rjson</requirement>
-        <requirement type="package" version="0.21.0=r41h03ef668_1004">r-nmf</requirement>
-        <requirement type="package" version="2.3=r41hc72bb7e_1003">r-gridextra</requirement>
-        <requirement type="package" version="1.4.3=r41hdfd78af_4">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement>
-        <requirement type="package" version="1.4.4=r41hdfd78af_0">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">bioconductor-mutationalpatterns</requirement>
+        <requirement type="package" version="3.4.4">r-ggplot2</requirement>
+        <requirement type="package" version="1.7.4">r-optparse</requirement>
+        <requirement type="package" version="0.2.21">r-rjson</requirement>
+        <requirement type="package" version="0.21.0">r-nmf</requirement>
+        <requirement type="package" version="2.3">r-gridextra</requirement>
+        <requirement type="package" version="1.4.3">bioconductor-bsgenome.hsapiens.ucsc.hg19</requirement>
+        <requirement type="package" version="1.4.5">bioconductor-bsgenome.hsapiens.ucsc.hg38</requirement>
 <!--
 install more bioconda genomes
 bioconductor-bsgenome.mmusculus.ucsc.mm9