Add version attribute to tool requirements

instead of relying on `lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml` . Follow-up on #5544 . See https://github.com/galaxyproject/galaxy/pull/5544/files#r183909746 for an explanation why that's preferrable for future-proof reproducibility. Also, small fixes to `tools/evolution/codingSnps.xml` .
galaxyproject · Apr 25, 2018 · 2515267 · 2515267
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diff --git a/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
@@ -1,8 +1,8 @@
 <tool id="CONVERTER_bam_to_bigwig_0" name="Convert BAM to BigWig" version="1.0.1" hidden="true">
     <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package">ucsc-bedgraphtobigwig</requirement>
-        <requirement type="package">bedtools</requirement>
+        <requirement type="package" version="357">ucsc-bedgraphtobigwig</requirement>
+        <requirement type="package" version="2.27.1">bedtools</requirement>
     </requirements>
     <command><![CDATA[
         bedtools genomecov -bg -split -ibam '$input' -g '$chromInfo'

diff --git a/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
@@ -1,8 +1,8 @@
 <tool id="CONVERTER_bed_gff_or_vcf_to_bigwig_0" name="Convert BED, GFF, or VCF to BigWig" version="1.0.1" hidden="true">
     <!--  <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package">ucsc-bedgraphtobigwig</requirement>
-        <requirement type="package">bedtools</requirement>
+        <requirement type="package" version="357">ucsc-bedgraphtobigwig</requirement>
+        <requirement type="package" version="2.27.1">bedtools</requirement>
     </requirements>
     <command>
 <![CDATA[

diff --git a/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_bedgraph_to_bigwig" name="Convert BedGraph to BigWig" version="1.0.1" hidden="true">
     <!-- Used internally to generate track indexes -->
     <requirements>
-        <requirement type="package">ucsc-wigtobigwig</requirement>
+        <requirement type="package" version="357">ucsc-wigtobigwig</requirement>
     </requirements>
     <command>grep -v "^track" '$input' | wigToBigWig -clip stdin '$chromInfo' '$output'</command>
     <inputs>

diff --git a/lib/galaxy/datatypes/converters/fasta_to_2bit.xml b/lib/galaxy/datatypes/converters/fasta_to_2bit.xml
@@ -2,7 +2,7 @@
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <!-- Used on the metadata edit page. -->
     <requirements>
-        <requirement type="package">ucsc-fatotwobit</requirement>
+        <requirement type="package" version="357">ucsc-fatotwobit</requirement>
     </requirements>
     <command>faToTwoBit '$input' '$output'</command>
     <inputs>

diff --git a/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
@@ -1,8 +1,8 @@
 <tool id="CONVERTER_interval_to_bigwig_0" name="Convert Genomic Intervals To Coverage" version="1.0.1">
     <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
     <requirements>
-        <requirement type="package">ucsc-bedgraphtobigwig</requirement>
-        <requirement type="package">bedtools</requirement>
+        <requirement type="package" version="357">ucsc-bedgraphtobigwig</requirement>
+        <requirement type="package" version="2.27.1">bedtools</requirement>
     </requirements>
     <command>
 <![CDATA[

diff --git a/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
@@ -1,8 +1,8 @@
 <tool id="CONVERTER_sam_to_bigwig_0" name="Convert SAM to BigWig" version="1.0.1" hidden="true">
     <requirements>
-        <requirement type="package">ucsc-bedgraphtobigwig</requirement>
-        <requirement type="package">samtools</requirement>
-        <requirement type="package">bedtools</requirement>
+        <requirement type="package" version="357">ucsc-bedgraphtobigwig</requirement>
+        <requirement type="package" version="1.6">samtools</requirement>
+        <requirement type="package" version="2.27.1">bedtools</requirement>
     </requirements>
     <command>
 <![CDATA[

diff --git a/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml b/lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
@@ -1,7 +1,7 @@
 <tool id="CONVERTER_wig_to_bigwig" name="Convert Wiggle to BigWig" version="1.0.1" hidden="true">
     <!-- Used internally to generate track indexes -->
     <requirements>
-        <requirement type="package">ucsc-wigtobigwig</requirement>
+        <requirement type="package" version="357">ucsc-wigtobigwig</requirement>
     </requirements>
     <command>
 <![CDATA[

diff --git a/lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml b/lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml
@@ -44,46 +44,3 @@
   to:
     name: bowtie
     version: 1.2.0
-- from:
-    name: ucsc-bedgraphtobigwig
-    unversioned: true
-  to:
-    name: ucsc-bedgraphtobigwig
-    version: 357
-- from:
-    name: ucsc-bedtobigbed
-    unversioned: true
-  to:
-    name: ucsc-bedtobigbed
-    version: 357
-- from:
-    name: ucsc-fatotwobit
-    unversioned: true
-  to:
-    name: ucsc-fatotwobit
-    version: 357
-- from:
-    name: ucsc-liftover
-    unversioned: true
-  to:
-    name: ucsc-liftover
-    version: 357
-- from:
-    name: ucsc-nibfrag
-    unversioned: true
-  to:
-    name: ucsc-nibfrag
-    version: 357
-- from:
-    name: ucsc-twobittofa
-    unversioned: true
-  to:
-    name: ucsc-twobittofa
-    version: 357
-- from:
-    name: ucsc-wigtobigwig
-    unversioned: true
-  to:
-    name: ucsc-wigtobigwig
-    version: 357
-
diff --git a/tools/evolution/codingSnps.xml b/tools/evolution/codingSnps.xml
@@ -1,9 +1,17 @@
 <tool id="hgv_codingSnps" name="aaChanges" version="1.0.1">
   <description>amino-acid changes caused by a set of SNPs</description>
 
-  <command interpreter="perl">
-    codingSnps.pl $input1 $input2 Galaxy build=${input1.metadata.dbkey} loc=${GALAXY_DATA_INDEX_DIR}/codingSnps.loc chr=${input1.metadata.chromCol} start=${input1.metadata.startCol} end=${input1.metadata.endCol} snp=$col1 keepColumns=$keep strand=${strand_source.strand_col} unique=$uniqpos > $out_file1
-  </command>
+  <requirements>
+    <requirement type="package" version="8.25">coreutils</requirement>
+    <requirement type="package" version="357">ucsc-twobittofa</requirement>
+    <requirement type="package" version="357">ucsc-nibfrag</requirement>
+  </requirements>
+
+  <code file="codingSnps_filter.py"></code>
+
+  <command><![CDATA[
+perl '$__tool_directory__/codingSnps.pl' '$input1' '$input2' Galaxy build=${input1.metadata.dbkey} loc=${GALAXY_DATA_INDEX_DIR}/codingSnps.loc chr=${input1.metadata.chromCol} start=${input1.metadata.startCol} end=${input1.metadata.endCol} snp=$col1 keepColumns=$keep strand=${strand_source.strand_col} unique=$uniqpos > '$out_file1'
+  ]]></command>
 
   <inputs>
     <param format="interval" name="input1" type="data" label="SNP dataset">
@@ -43,14 +51,6 @@
     <data format="interval" name="out_file1" />
   </outputs>
 
-  <code file="codingSnps_filter.py"></code>
-
-  <requirements>
-    <requirement type="package">gnu_coreutils</requirement>
-    <requirement type="package">ucsc-twobittofa</requirement>
-    <requirement type="package">ucsc-nibfrag</requirement>
-  </requirements>
-
   <tests>
     <test>
       <param name="input1" ftype="interval" value="codingSnps_input1.interval" dbkey="hg18" />
@@ -59,7 +59,7 @@
       <param name="strand_choice" value="all_pos" />
       <param name="strand_col" value="+" />
       <param name="uniqpos" value="0" />
-      <output name="output" file="codingSnps_output1.interval" />
+      <output name="out_file1" file="codingSnps_output1.interval" />
     </test>
     <test>
       <param name="input1" ftype="interval" value="codingSnps_input2.interval" dbkey="hg18" />
@@ -68,15 +68,15 @@
       <param name="strand_choice" value="all_pos" />
       <param name="strand_col" value="+" />
       <param name="uniqpos" value="0" />
-      <output name="output" file="codingSnps_output2.interval" />
+      <output name="out_file1" file="codingSnps_output2.interval" />
     </test>
     <test>
       <param name="input1" ftype="interval" value="codingSnps_input2.interval" dbkey="hg18" />
       <param name="input2" ftype="interval" value="codingSnps_inputGenes2.bed" dbkey="hg18" />
       <param name="col1" value="4" />
       <param name="strand_choice" value="all_neg" />
       <param name="strand_col" value="-" />
-      <output name="output" file="codingSnps_output3.interval" />
+      <output name="out_file1" file="codingSnps_output3.interval" />
     </test>
   </tests>
 
@@ -173,6 +173,5 @@ or is synonymous then it is not included in the output file.
     chr22  15848885  15848886  C/T  uc010gqs.1  Ser:Trp/Stop  200  C  TCG:TGG/TAG
     chr22  15849048  15849049  A/C  uc002zlw.1  Gly:Stop/Gly  163  G  GGA:TGA/GGA
     etc.
-
   </help>
 </tool>
diff --git a/tools/extract/extract_genomic_dna.xml b/tools/extract/extract_genomic_dna.xml
@@ -1,7 +1,7 @@
 <tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.2.4">
   <description>using coordinates from assembled/unassembled genomes</description>
   <requirements>
-      <requirement type="package">ucsc-fatotwobit</requirement>
+      <requirement type="package" version="357">ucsc-fatotwobit</requirement>
   </requirements>
   <command>
       python '$__tool_directory__/extract_genomic_dna.py' '${input}' '${out_file1}' -o ${out_format} -d '${dbkey}'

diff --git a/tools/extract/liftOver_wrapper.xml b/tools/extract/liftOver_wrapper.xml
@@ -1,7 +1,7 @@
 <tool id="liftOver1" name="Convert genome coordinates" version="1.0.6">
   <description> between assemblies and genomes</description>
   <requirements>
-    <requirement type="package">ucsc-liftover</requirement>
+    <requirement type="package" version="357">ucsc-liftover</requirement>
   </requirements>
   <command>
   python $__tool_directory__/liftOver_wrapper.py

diff --git a/tools/filters/bed_to_bigbed.xml b/tools/filters/bed_to_bigbed.xml
@@ -3,15 +3,15 @@
   <edam_operations>
     <edam_operation>operation_3434</edam_operation>
   </edam_operations>
+  <requirements>
+    <requirement type="package" version="357">ucsc-bedtobigbed</requirement>
+  </requirements>
   <command>bedToBigBed $input1 $chromInfo $out_file1
     #if $settings.settingsType == "full":
       -blockSize=${settings.blockSize} -itemsPerSlot=${settings.itemsPerSlot} ${settings.unc}
     #end if
     2&gt;&amp;1 || echo "Error running bedToBigBed." >&amp;2
   </command>
-  <requirements>
-    <requirement type="package">ucsc-bedtobigbed</requirement>
-  </requirements>
   <inputs>
     <param format="bed" name="input1" type="data" label="Convert">
       <validator type="unspecified_build" />

diff --git a/tools/filters/wig_to_bigwig.xml b/tools/filters/wig_to_bigwig.xml
@@ -1,7 +1,7 @@
 <tool id="wig_to_bigWig" name="Wig/BedGraph-to-bigWig" version="1.1.1">
   <description>converter</description>
   <requirements>
-    <requirement type="package">ucsc-wigtobigwig</requirement>
+    <requirement type="package" version="357">ucsc-wigtobigwig</requirement>
   </requirements>
   <stdio>
       <!-- Anything other than zero is an error -->