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metexplore
met4j
Commits
adea908b
Commit
adea908b
authored
Apr 22, 2022
by
Ludovic Cottret
Browse files
Merge branch 'singularity' into 'develop'
Singularity See merge request
!12
parents
3263d3ba
4928ebdc
Changes
3
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Inline
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.gitlab-ci.yml
View file @
adea908b
image
:
maven:3.6-adoptopenjdk-14
stages
:
-
build
-
test
-
deploy
-
singularity
variables
:
MAVEN_CLI_OPTS
:
"
-s
.m2/settings.xml
--batch-mode"
...
...
@@ -9,17 +15,20 @@ cache:
-
.m2/repository/
build
:
image
:
maven:3.6-adoptopenjdk-14
stage
:
build
script
:
-
mvn compile
test
:
image
:
maven:3.6-adoptopenjdk-14
stage
:
test
script
:
-
mvn clean test
-
cat coverage/target/site/jacoco-aggregate/index.html | grep -o '<tfoot>.*</tfoot>'
deploySnapshot
:
image
:
maven:3.6-adoptopenjdk-14
stage
:
deploy
script
:
-
mvn $MAVEN_CLI_OPTS deploy -Dmaven.test.skip=true
...
...
@@ -27,6 +36,7 @@ deploySnapshot:
-
develop
deployCentral
:
image
:
maven:3.6-adoptopenjdk-14
stage
:
deploy
before_script
:
-
'
which
ssh-agent
||
(
apt-get
update
-qy
&&
apt-get
install
openssh-client
-qqy
)'
...
...
@@ -47,3 +57,14 @@ deployCentral:
-
mvn $MAVEN_CLI_OPTS release:perform -Darguments=-Dgpg.passphrase=${GPG_PASSPHRASE} -DlocalCheckout=true
only
:
-
master
buildSingularity
:
stage
:
singularity
image
:
name
:
quay.io/singularity/singularity:v3.4.0
entrypoint
:
[
"
"
]
script
:
-
singularity build met4j-toolbox.sif met4j.singularity
-
singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" met4j-toolbox.sif oras://"$CI_REGISTRY_IMAGE"/met4j-singularity:"$CI_COMMIT_TAG"
when
:
manual
README.md
View file @
adea908b
...
...
@@ -62,7 +62,7 @@ mv ./target/*-jar-with-dependencies.jar ../../../
## Usage
Documentation for the library modules can be found in each module's own README.
Detailed code examples can be found at
[
https://forgemia.inra.fr/metexplore/tutorialmet4j
](
https://cecill.info/licences/Licence_CeCILL_V2.1-en.html
)
.
Detailed code examples can be found at
[
here
](
https://forgemia.inra.fr/metexplore/tutorialmet4j
)
.
The toolbox can be launched using
```
...
...
@@ -74,6 +74,14 @@ which will list all the contained applications that can be called using
java -cp met4j-toolbox-0.8.0-jar-with-dependencies.jar <App full name> -h
```
### With singularity
You need at least
[
singularity
](
https://sylabs.io/guides/3.5/user-guide/quick_start.html
)
v3.5.
```
console
singularity pull met4j-toolbox.sif oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:latest
```
## Contributing
Pull requests are welcome
**on the gitlab repo**
(
[
https://forgemia.inra.fr/metexplore/met4j
](
https://forgemia.inra.fr/metexplore/met4j
)
). For major changes, please open an issue first to discuss what you would like to change.
...
...
met4j.singularity
0 → 100644
View file @
adea908b
Bootstrap: docker
From: debian:stable-slim
%runscript
if [ $# -lt 1 ]
then
echo "display Help"
exec java -jar /opt/bin/met4j.jar
else
echo "Lauch met4j-toolbox"
exec java -Dlog4j.configuration= -cp /opt/bin/met4j.jar fr.inrae.toulouse.metexplore.met4j_toolbox."$@"
fi
%help
Usage: met4j.sif
This is singularity container for met4j
%labels
Maintainer Ludovic.Cottret@inrae.fr
%post
export DEBIAN_FRONTEND=noninteractive
apt-get update && \
apt-get upgrade -y && \
apt-get install -y \
openjdk-11-jre \
git \
maven
apt-get clean && \
apt-get purge
mkdir -p /opt
cd /opt
git clone https://forgemia.inra.fr/metexplore/met4j.git
cd met4j/
mvn install
cd met4j-toolbox
mvn package
mkdir -p /opt/bin
cp target/met4j*.jar /opt/bin/met4j.jar
cd /opt
rm -rf met4j ~/.m2
apt-get remove -y maven git
apt-get autoremove -y
%environment
export LC_ALL=C
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