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Merge pull request #293 from kjsanger/chore/dockerfile-tidy
Update Dockerfiles to current conventions
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,8 @@ | ||
| baton-chmod | ||
| baton-do | ||
| baton-get | ||
| baton-list | ||
| baton-metamod | ||
| baton-metaquery | ||
| baton-put | ||
| baton-specificquery |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,22 +1,10 @@ | ||
| #!/bin/bash | ||
| # | ||
| # Running this script will start an instance of the container, if one is not | ||
| # already running, and then execute the command in the instance. | ||
| # | ||
| # Cleaning up unwanted instances afterwards is outside the scope of this script. | ||
|
|
||
| set -euo pipefail | ||
|
|
||
| DOCKER_REGISTRY=${DOCKER_REGISTRY:?required, but not set} | ||
| DOCKER_USER=${DOCKER_USER:?required, but not set} | ||
| DOCKER_IMAGE=${DOCKER_IMAGE:?required, but was not set} | ||
| DOCKER_TAG=${DOCKER_TAG:?required, but not set} | ||
|
|
||
| # Colons and slashes are not allowed in Singularity instance names | ||
| instance="$DOCKER_REGISTRY--$DOCKER_USER--$DOCKER_IMAGE--$DOCKER_TAG" | ||
|
|
||
| if ! singularity instance list | grep "$instance" 2>&1 >/dev/null ; then | ||
| singularity instance start \ | ||
| "docker://$DOCKER_REGISTRY/$DOCKER_USER/$DOCKER_IMAGE:$DOCKER_TAG" "$instance" 2>&1 >/dev/null | ||
| fi | ||
|
|
||
| singularity exec "instance://$instance" "$@" | ||
| singularity run "docker://$DOCKER_REGISTRY/$DOCKER_USER/$DOCKER_IMAGE:$DOCKER_TAG" "$@" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| #!/bin/bash | ||
| #!/bin/sh | ||
| # | ||
| # Copyright (C) 2023 Genome Research Ltd. All rights reserved. | ||
| # | ||
|
|
@@ -17,17 +17,27 @@ | |
| # | ||
| # Author: Keith James <[email protected]> | ||
|
|
||
| set -euo pipefail | ||
|
|
||
| usage() { | ||
| cat 1>&2 << EOF | ||
| Install singularity proxy wrappers for the executables listed in a | ||
| container's manifest to a nominated directory. | ||
| Usage: $0 [-h] [-i <Docker image name>] | ||
| [-m <JSON manifest path>] | ||
| Two different types of wrapper are available which differ in how | ||
| they run singularity. The default type uses "singularity run", | ||
| while the alternative type uses "singularity exec". | ||
| If the "exec" type is used, the wrapper can additionally be made | ||
| to create a long-running service instance on first use and | ||
| subsequently "exec" within that instance. | ||
| Usage: $0 | ||
| [-e] | ||
| [-h] | ||
| [-i <Docker image name>] | ||
| [-m <manifest path>] | ||
| [-p <wrapper install prefix>] | ||
| [-r <Docker registry name>] | ||
| [-s] | ||
| [-t <Docker image tag>] | ||
| [-u <Docker user name>] [-v] <operation> | ||
|
|
@@ -40,6 +50,8 @@ Operation may be one of: | |
| Options: | ||
| -h Print usage and exit. | ||
| -e Use "singularity exec", rather than "singularity run" in the | ||
| generated wrappers. | ||
| -i Docker image name. Required, defaults to the value of the | ||
| environment variable "\$DOCKER_IMAGE" ("$DOCKER_IMAGE"). | ||
| -m Manifest file path. Optional, defaults to the value of the | ||
|
|
@@ -48,6 +60,7 @@ Options: | |
| environment variable \$PREFIX ("$PREFIX"). | ||
| -r Docker registry name. Optional, defaults to the value of the | ||
| environment variable \$DOCKER_REGISTRY ("$DOCKER_REGISTRY"). | ||
| -s Start a long-running service instance (implies use of exec). | ||
| -t Docker image tag. Optional, defaults to the value of the | ||
| environment variable \$DOCKER_TAG ("$DOCKER_TAG"). | ||
| -u Docker user name. Optional, defaults to the value of the | ||
|
|
@@ -58,7 +71,7 @@ EOF | |
|
|
||
| # Print an application manifest | ||
| print_manifest() { | ||
| jq . "$MANIFEST_PATH" | ||
| cat "$MANIFEST_PATH" | ||
| } | ||
|
|
||
| # Write a bash script wrapping an application in a Docker container | ||
|
|
@@ -86,7 +99,7 @@ export DOCKER_TAG="$DOCKER_TAG" | |
| # time, be permanently set in the installed wrapper. E.g. a candidate | ||
| # is SINGULARITY_CACHEDIR. | ||
| "\$(dirname "\${BASH_SOURCE[0]}")/singularity-run-docker" "$exe" "\$@" | ||
| "\$(dirname "\${BASH_SOURCE[0]}")/$singularity_wrap_impl" "$exe" "\$@" | ||
| EOF | ||
|
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||
| chmod +x "$dir/$exe" | ||
|
|
@@ -96,11 +109,11 @@ chmod +x "$dir/$exe" | |
| install_wrappers() { | ||
| local dir="$PREFIX/bin" | ||
| install -d "$dir" | ||
| cp /usr/local/bin/singularity-run-docker "$PREFIX/bin" | ||
| cp "/usr/local/bin/$singularity_wrap_impl" "$PREFIX/bin" | ||
|
|
||
| for exe in "${wrappers[@]}" ; do | ||
| while IFS= read -r exe; do | ||
| write_wrapper "$dir" "$exe" | ||
| done | ||
| done < "$MANIFEST_PATH" | ||
| } | ||
|
|
||
| DOCKER_REGISTRY=${DOCKER_REGISTRY:-ghcr.io} | ||
|
|
@@ -109,10 +122,15 @@ DOCKER_IMAGE=${DOCKER_IMAGE:-""} | |
| DOCKER_TAG=${DOCKER_TAG:-latest} | ||
|
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||
| PREFIX=${PREFIX:-/opt/wtsi-npg} | ||
| MANIFEST_PATH=${MANIFEST_PATH:-"$PREFIX/etc/manifest.json"} | ||
| MANIFEST_PATH=${MANIFEST_PATH:-"$PREFIX/etc/manifest.txt"} | ||
|
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||
| while getopts "hi:m:p:r:t:u:v" option; do | ||
| singularity_wrap_impl="singularity-run-docker" | ||
|
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||
| while getopts "hei:m:p:r:st:u:v" option; do | ||
| case "$option" in | ||
| e) | ||
| singularity_wrap_impl="singularity-exec-docker" | ||
| ;; | ||
| h) | ||
| usage | ||
| exit 0 | ||
|
|
@@ -129,6 +147,9 @@ while getopts "hi:m:p:r:t:u:v" option; do | |
| r) | ||
| DOCKER_REGISTRY="$OPTARG" | ||
| ;; | ||
| s) | ||
| singularity_wrap_impl="singularity-service-docker" | ||
| ;; | ||
| t) | ||
| DOCKER_TAG="$OPTARG" | ||
| ;; | ||
|
|
@@ -148,22 +169,19 @@ done | |
|
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||
| shift $((OPTIND -1)) | ||
|
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||
| declare -a wrappers | ||
| if [ ! -e "$MANIFEST_PATH" ] ; then | ||
| echo -e "\nERROR:\n The manifest of executables at '$MANIFEST_PATH' does not exist" | ||
| exit 4 | ||
| fi | ||
|
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||
| wrappers=($(jq -j '.executable[] + " "' "$MANIFEST_PATH")) | ||
|
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||
| OPERATION="$@" | ||
| if [ -z "$OPERATION" ] ; then | ||
| operation="$1" | ||
| if [ -z "$operation" ] ; then | ||
| usage | ||
| echo -e "\nERROR:\n An operation argument is required" | ||
| exit 4 | ||
| fi | ||
|
|
||
| case "$OPERATION" in | ||
| case "$operation" in | ||
| list) | ||
| print_manifest | ||
| exit 0 | ||
|
|
@@ -173,7 +191,7 @@ case "$OPERATION" in | |
| ;; | ||
| *) | ||
| usage | ||
| echo -e "\nERROR:\n Invalid wrapper operation '$OPERATION'" | ||
| echo -e "\nERROR:\n Invalid wrapper operation '$operation'" | ||
| exit 4 | ||
| ;; | ||
| esac | ||
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