Unverified Commit 9980ebeb authored by Nicola Soranzo's avatar Nicola Soranzo Committed by GitHub
Browse files

Merge pull request #15039 from mvdbeek/fix_tmpdir_mounting 

[22.05] Mount ``$TMPDIR``, ``$TMP`` and ``$TEMP`` into container
parents 77f79169 b3c0428c

lib/galaxy/tool_util/deps/container_classes.py

+1 −1
Original line number Diff line number Diff line
@@ -235,7 +235,7 @@ class HasDockerLikeVolumes: 
                # and Galaxy.

                defaults += ",$tmp_directory:/tmp:rw"

            else:

                defaults += ",$_GALAXY_JOB_TMP_DIR:rw"

                defaults += ",$_GALAXY_JOB_TMP_DIR:rw,$TMPDIR:rw,$TMP:rw,$TEMP:rw"

            if self.job_info.home_directory is not None:

                defaults += ",$home_directory:rw"

            if self.app_info.outputs_to_working_directory:

test/functional/tools/job_environment_default.xml

+1 −0
Original line number Diff line number Diff line
@@ -3,6 +3,7 @@ 
        <container type="docker">busybox:ubuntu-14.04</container>

    </requirements>

    <command detect_errors="exit_code"><![CDATA[

mktemp -d &&

echo 'Writing environment properties to output files.' &&

(>&2 echo 'Example tool stderr output.') &&

echo \$(id -u) > '$user_id' &&

test/functional/tools/job_environment_default_legacy.xml

+1 −0
Original line number Diff line number Diff line
@@ -3,6 +3,7 @@ 
        <container type="docker">busybox:ubuntu-14.04</container>

    </requirements>

    <command detect_errors="exit_code"><![CDATA[

mktemp -d &&

echo \$(id -u) > '$user_id' &&

echo \$(id -g) > '$group_id' &&

echo \$(pwd) > '$pwd' &&

test/functional/tools/job_environment_explicit_isolated_home.xml

+1 −0
Original line number Diff line number Diff line
@@ -3,6 +3,7 @@ 
        <container type="docker">busybox:ubuntu-14.04</container>

    </requirements>

    <command use_shared_home="false"><![CDATA[

mktemp -d &&

echo \$(id -u) > '$user_id' &&

echo \$(id -g) > '$group_id' &&

echo \$(pwd) > '$pwd' &&

test/functional/tools/job_environment_explicit_shared_home.xml

+1 −0
Original line number Diff line number Diff line
@@ -3,6 +3,7 @@ 
        <container type="docker">busybox:ubuntu-14.04</container>

    </requirements>

    <command use_shared_home="true"><![CDATA[

mktemp -d &&

echo \$(id -u) > '$user_id' &&

echo \$(id -g) > '$group_id' &&

echo \$(pwd) > '$pwd' &&