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Fix attempt for issue apptainer#1053
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@@ -62,6 +62,11 @@ if [ ! -z "$runscript_command" ]; then | |
| echo "$runscript_command" > "$SINGULARITY_ROOTFS/singularity" | ||
| fi | ||
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| if ! CHROOT=`singularity_which chroot`; then | ||
| message ERROR "chroot command not found\n" | ||
| exit 1 | ||
| fi | ||
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| ### EXPORT ENVARS | ||
| DEBIAN_FRONTEND=noninteractive | ||
| SINGULARITY_ENVIRONMENT="/.singularity.d/env/91-environment.sh" | ||
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@@ -117,16 +122,15 @@ fi | |
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| ### ENVIRONMENT | ||
| SINGULARITY_SOURCE_ENV="/dev/null" | ||
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| if [ -z "${SINGULARITY_BUILDSECTION:-}" -o "${SINGULARITY_BUILDSECTION:-}" == "environment" ]; then | ||
| if singularity_section_exists "environment" "$SINGULARITY_BUILDDEF"; then | ||
| message 1 "Adding environment to container\n" | ||
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| singularity_section_get "environment" "$SINGULARITY_BUILDDEF" >> "$SINGULARITY_ROOTFS/.singularity.d/env/90-environment.sh" | ||
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| SINGULARITY_SOURCE_ENV="$SINGULARITY_ROOTFS/.singularity.d/env/90-environment.sh" | ||
| fi | ||
| else | ||
| message 2 "Skipping environment section\n" | ||
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@@ -139,7 +143,10 @@ if [ -z "${SINGULARITY_BUILDSECTION:-}" -o "${SINGULARITY_BUILDSECTION:-}" == "p | |
| message 1 "Running post scriptlet\n" | ||
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| ARGS=`singularity_section_args "post" "$SINGULARITY_BUILDDEF"` | ||
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| singularity_section_get "post" "$SINGULARITY_BUILDDEF" \ | ||
| | (set +u && . $SINGULARITY_SOURCE_ENV && set -u && $CHROOT "$SINGULARITY_ROOTFS" /bin/sh -e -x $ARGS) \ | ||
| || ABORT 255 | ||
| fi | ||
| else | ||
| message 2 "Skipping post section\n" | ||
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@@ -229,7 +236,7 @@ if [ -z "${SINGULARITY_BUILDSECTION:-}" -o "${SINGULARITY_BUILDSECTION:-}" == "t | |
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| chmod 0755 "$SINGULARITY_ROOTFS/.singularity.d/test" | ||
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| (set +u && . $SINGULARITY_SOURCE_ENV && set -u && $CHROOT "$SINGULARITY_ROOTFS" /bin/sh -e -x $ARGS "/.singularity.d/test" "$@") || ABORT 255 | ||
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cclerget
Author
Owner
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| fi | ||
| fi | ||
| else | ||
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@@ -316,17 +323,18 @@ fi | |
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| ### APPENVIRONMENT | ||
| declare -A SINGULARITY_SOURCE_ENV_APP | ||
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| if [ -z "${SINGULARITY_BUILDSECTION:-}" -o "${SINGULARITY_BUILDSECTION:-}" == "appenv" ]; then | ||
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| if singularity_section_exists "appenv" "$SINGULARITY_BUILDDEF"; then | ||
| APPNAMES=(`singularity_section_args "appenv" "$SINGULARITY_BUILDDEF"`) | ||
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| for APPNAME in "${APPNAMES[@]}"; do | ||
| message 1 "Adding custom environment to ${APPNAME}\n" | ||
| singularity_app_init "${APPNAME}" "${SINGULARITY_ROOTFS}" | ||
| get_section "appenv ${APPNAME}" "$SINGULARITY_BUILDDEF" >> "$SINGULARITY_ROOTFS/scif/apps/${APPNAME}/scif/env/90-environment.sh" | ||
| SINGULARITY_SOURCE_ENV_APP[${APPNAME}]="$SINGULARITY_ROOTFS/scif/apps/${APPNAME}/scif/env/90-environment.sh" | ||
| done | ||
| fi | ||
| fi | ||
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@@ -361,7 +369,14 @@ if [ -z "${SINGULARITY_BUILDSECTION:-}" -o "${SINGULARITY_BUILDSECTION:-}" == "a | |
| export SINGULARITY_APPROOT | ||
| singularity_app_init "${APPNAME}" "${SINGULARITY_ROOTFS}" | ||
| singularity_app_save "${APPNAME}" "$SINGULARITY_BUILDDEF" "${APPBASE}/scif/Singularity" | ||
| if [ "${SINGULARITY_SOURCE_ENV_APP[${APPNAME}]:-}" ]; then | ||
| singularity_app_install_get "${APPNAME}" "$SINGULARITY_BUILDDEF" \ | ||
| | (set +u && . ${SINGULARITY_SOURCE_ENV_APP[${APPNAME}]} && set -u && $CHROOT "$SINGULARITY_ROOTFS" /bin/sh -xe) \ | ||
| || ABORT 255 | ||
| else | ||
| singularity_app_install_get "${APPNAME}" "$SINGULARITY_BUILDDEF" \ | ||
| | $CHROOT "$SINGULARITY_ROOTFS" /bin/sh -xe || ABORT 255 | ||
| fi | ||
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| APPFOLDER_SIZE=$(singularity_calculate_size "${APPBASE}") | ||
| $ADD_LABEL --key "SINGULARITY_APP_SIZE" --value "${APPFOLDER_SIZE}MB" --file "$APPBASE/scif/labels.json" --quiet -f | ||
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I don't think the
set +uandset -uare necessary anymore once we pop into the environment. At least when I tested in my PR it seemed to be OK without. I also think we should probably source every file in/.singularity.d/env/in a loop just to make sure we are picking everything up.