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Don't create a BGZF index when running the compressing converter

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The index file is not used because it is generated again in `set_meta()`
for the `VcfGz` datatype, and ignored for all others.

Additionally, the index file is currently generated alongside the input
dataset, which fails when the input directory is not writeable (such as
when running in a container).

Fix https://github.com/galaxyproject/galaxy/issues/13916 .

Also, replace outdated `tabix` requirement with the latest `htslib`.
This commit is contained in:
Nicola Soranzo
2022-05-26 19:25:09 +01:00
parent 8a6a717418
commit 801fa9415d
1 changed files with 6 additions and 6 deletions
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lib/galaxy/datatypes/converters/uncompressed_to_gz.xml
+6 -6
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@@ -1,19 +1,19 @@
<tool id="CONVERTER_uncompressed_to_gz" name="Convert uncompressed file to compressed" hidden="true" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
<macros>
<token name="@TOOL_VERSION@">1.11</token>
<token name="@TOOL_VERSION@">1.15.1</token>
<token name="@VERSION_SUFFIX@">0</token>
</macros>
<requirements>
<requirement type="package" version="1.11">tabix</requirement>
<requirement type="package" version="@TOOL_VERSION@">htslib</requirement>
</requirements>
<command><![CDATA[
cp '$ext_config' 'galaxy.json' &&
bgzip -@ \${GALAXY_SLOTS:-1} -ci '$input1' > '$output1'
cp '$ext_config' galaxy.json &&
bgzip -@ "\${GALAXY_SLOTS:-1}" -c '$input1' > '$output1'
]]></command>
<configfiles>
<configfile name="ext_config">{"output1": {
"name": "${input1.name+'.gz' if not $input1.name.endswith('.vcf') else $input1.name+'.bgzip'} compressed",
"ext": "${input1.ext+'.gz' if $input1.ext != 'vcf' else 'vcf_bgzip'}"
"name": "${input1.name + '.gz' if not $input1.name.endswith('.vcf') else $input1.name + '.bgzip'} compressed",
"ext": "${input1.ext + '.gz' if $input1.ext != 'vcf' else 'vcf_bgzip'}"
}}</configfile>
</configfiles>
<inputs>