Unverified Commit 4588b8fb authored by Nicola Soranzo's avatar Nicola Soranzo Committed by mvdbeek
Browse files

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

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Also, replace outdated `tabix` requirement with the latest `htslib`.
parent 468d5e0c

lib/galaxy/datatypes/converters/uncompressed_to_gz.xml

+6 −6
Original line number Diff line number Diff line 
<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": {