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https://github.com/galaxyproject/galaxy.git
synced 2026-10-16 15:45:04 +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 `$_GALAXY_JOB_TMP_DIR:rw`
33 lines
1.0 KiB
XML
33 lines
1.0 KiB
XML
<tool id="job_environment_default_legacy" name="job_environment_default_legacy" version="0.1.0">
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<requirements>
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<container type="docker">busybox:ubuntu-14.04</container>
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</requirements>
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<command detect_errors="exit_code"><![CDATA[
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mktemp -d &&
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echo \$(id -u) > '$user_id' &&
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echo \$(id -g) > '$group_id' &&
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echo \$(pwd) > '$pwd' &&
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echo "\$HOME" > '$home' &&
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echo "\$TMP" > '$tmp' &&
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echo "\$SOME_ENV_VAR" > '$some_env_var' &&
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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="user_id" format="txt" label="user_id" />
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<data name="group_id" format="txt" label="group_id" />
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<data name="pwd" format="txt" label="pwd" />
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<data name="home" format="txt" label="home" />
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<data name="tmp" format="txt" label="tmp" />
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<data name="some_env_var" format="txt" label="env_var" />
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</outputs>
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<tests>
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</tests>
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<help>
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</help>
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</tool>
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