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Update all tools/converters using UCSC binaries to depend only on the

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binary they are using.
This commit is contained in:
Nate Coraor
2018-02-15 10:54:04 -05:00
parent 3de8593e19
commit 4b09027ebb
13 changed files with 57 additions and 16 deletions
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lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
+1 -1
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@@ -1,7 +1,7 @@
<tool id="CONVERTER_bam_to_bigwig_0" name="Convert BAM to BigWig" version="1.0.0" hidden="true">
<!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
<requirements>
<requirement type="package">ucsc_tools</requirement>
<requirement type="package">ucsc-bedgraphtobigwig</requirement>
<requirement type="package">bedtools</requirement>
</requirements>
<command><![CDATA[
lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
+1 -1
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@@ -1,7 +1,7 @@
<tool id="CONVERTER_bed_gff_or_vcf_to_bigwig_0" name="Convert BED, GFF, or VCF to BigWig" version="1.0.0" hidden="true">
<!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
<requirements>
<requirement type="package">ucsc_tools</requirement>
<requirement type="package">ucsc-bedgraphtobigwig</requirement>
<requirement type="package">bedtools</requirement>
</requirements>
<command>
lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
+1 -1
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@@ -1,7 +1,7 @@
<tool id="CONVERTER_bedgraph_to_bigwig" name="Convert BedGraph to BigWig" version="1.0.0" hidden="true">
<!-- Used internally to generate track indexes -->
<requirements>
<requirement type="package">ucsc_tools</requirement>
<requirement type="package">ucsc-wigtobigwig</requirement>
</requirements>
<command>grep -v "^track" '$input' | wigToBigWig -clip stdin '$chromInfo' '$output'</command>
<inputs>
lib/galaxy/datatypes/converters/fasta_to_2bit.xml
+1 -2
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@@ -2,8 +2,7 @@
<!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
<!-- Used on the metadata edit page. -->
<requirements>
<requirement type="package" version="332">ucsc-fatotwobit</requirement>
<requirement type="package">ucsc_tools</requirement>
<requirement type="package">ucsc-fatotwobit</requirement>
</requirements>
<command>faToTwoBit '$input' '$output'</command>
<inputs>
lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
+1 -1
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@@ -1,7 +1,7 @@
<tool id="CONVERTER_interval_to_bigwig_0" name="Convert Genomic Intervals To Coverage" version="1.0.0">
<!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
<requirements>
<requirement type="package">ucsc_tools</requirement>
<requirement type="package">ucsc-bedgraphtobigwig</requirement>
<requirement type="package">bedtools</requirement>
</requirements>
<command>
lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
+1 -1
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@@ -1,6 +1,6 @@
<tool id="CONVERTER_sam_to_bigwig_0" name="Convert SAM to BigWig" version="1.0.0" hidden="true">
<requirements>
<requirement type="package">ucsc_tools</requirement>
<requirement type="package">ucsc-bedgraphtobigwig</requirement>
<requirement type="package">samtools</requirement>
<requirement type="package">bedtools</requirement>
</requirements>
lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
+1 -1
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@@ -1,7 +1,7 @@
<tool id="CONVERTER_wig_to_bigwig" name="Convert Wiggle to BigWig" version="1.0.0" hidden="true">
<!-- Used internally to generate track indexes -->
<requirements>
<requirement type="package">ucsc_tools</requirement>
<requirement type="package">ucsc-wigtobigwig</requirement>
</requirements>
<command>
<![CDATA[
lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml
+44 -2
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@@ -13,7 +13,7 @@
unversioned: true
to:
name: ucsc_tools
version: 332
version: 357
- from:
name: bedtools
unversioned: true
@@ -44,4 +44,46 @@
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
tools/evolution/codingSnps.xml
+2 -1
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@@ -47,7 +47,8 @@
<requirements>
<requirement type="package">gnu_coreutils</requirement>
<requirement type="package">ucsc_tools</requirement>
<requirement type="package">ucsc-twobittofa</requirement>
<requirement type="package">ucsc-nibfrag</requirement>
</requirements>
<tests>
tools/extract/extract_genomic_dna.xml
+1 -2
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@@ -1,8 +1,7 @@
<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.2.3">
<description>using coordinates from assembled/unassembled genomes</description>
<requirements>
<requirement type="package">ucsc_tools</requirement>
<requirement type="binary">faToTwoBit</requirement>
<requirement type="package">ucsc-fatotwobit</requirement>
</requirements>
<command>
python '$__tool_directory__/extract_genomic_dna.py' '${input}' '${out_file1}' -o ${out_format} -d '${dbkey}'
tools/extract/liftOver_wrapper.xml
+1 -1
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@@ -1,7 +1,7 @@
<tool id="liftOver1" name="Convert genome coordinates" version="1.0.5">
<description> between assemblies and genomes</description>
<requirements>
<requirement type="package">ucsc_tools</requirement>
<requirement type="package">ucsc-liftover</requirement>
</requirements>
<command>
python $__tool_directory__/liftOver_wrapper.py
tools/filters/bed_to_bigbed.xml
+1 -1
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@@ -10,7 +10,7 @@
2&gt;&amp;1 || echo "Error running bedToBigBed." >&amp;2
</command>
<requirements>
<requirement type="package">ucsc_tools</requirement>
<requirement type="package">ucsc-bedtobigbed</requirement>
</requirements>
<inputs>
<param format="bed" name="input1" type="data" label="Convert">
tools/filters/wig_to_bigwig.xml
+1 -1
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@@ -1,7 +1,7 @@
<tool id="wig_to_bigWig" name="Wig/BedGraph-to-bigWig" version="1.1.0">
<description>converter</description>
<requirements>
<requirement type="package">ucsc_tools</requirement>
<requirement type="package">ucsc-wigtobigwig</requirement>
</requirements>
<stdio>
<!-- Anything other than zero is an error -->