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synced 2026-09-24 16:30:27 +08:00
Matthias Bernt
9e48ceb169
fixes https://github.com/galaxyproject/galaxy/issues/15673 - singularity: add `--no_mount tmp` (analogous to docker's default) - do not bind `$TMPDIR:rw,$TMP:rw,$TEMP:rw` by default - instead (by default )provide a writable `/tmp` via `$_GALAXY_JOB_TMP_DIR/:/tmp:rw` note that this dir is still also available as `$_GALAXY_JOB_TMP_DIR:rw`
29 lines
827 B
XML
29 lines
827 B
XML
<!-- Containers with upper case names should be coerced to lower case as docker/singularity
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do not accept mixed case image names -->
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<tool id="mulled_example_invalid_case" name="mulled_example_invalid_case" version="0.1.0">
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<requirements>
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<requirement type="package" version="0.7.15">bwa</requirement>
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<container type="docker">quay.io/biocontainers/BwA:0.7.15--0</container>
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</requirements>
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<stdio>
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<exit_code range="2:" />
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</stdio>
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<command><![CDATA[
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bwa > '$output_1' 2>&1 &&
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touch "\${TMP:-/tmp}/job_tmp" &&
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touch "\${TEMP:-/tmp}/job_temp" &&
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touch "\${TMPDIR:-/tmp}/job_tmpdir"
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]]></command>
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<inputs>
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</inputs>
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<outputs>
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<data name="output_1" />
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</outputs>
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<tests>
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</tests>
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<help><![CDATA[
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TODO: Fill in help.
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]]></help>
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</tool>
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