Addressing PO's comments

.github/workflows/docker-publish.yml

@@ -67,6 +67,28 @@ jobs:
           push: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
+      - name: Build and push Apptainer image
+        if: ${{ ! startsWith(github.ref, 'refs/tags/') }}
+        steps:
+          - uses: actions/checkout@v4
+          - uses: eWaterCycle/setup-apptainer@v2
+            with:
+              apptainer-version: 1.3.4
+          - name: Create sif image
+            run: |
+              apptainer build -F container/wrapper_genpipes/images/genpipes-${{ env.TAG_NAME }}.sif docker-daemon://${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ env.TAG_NAME }}
+              cd container/wrapper_genpipes/images/
+              ln -sf genpipes-${{ env.TAG_NAME }}.sif genpipes.sif
+              cd ../../
+              tar -zcvf wrapper_genpipes.tgz wrapper_genpipes
+          - name: Upload sif image
+            uses: svenstaro/upload-release-action@v2
+            with:
+              repo_token: ${{ secrets.GITHUB_TOKEN }}
+              file: container/wrapper_genpipes.tgz
+              asset_name: wrapper_genpipes.tgz
+              tag: ${{ github.ref }}
+              overwrite: true
 
       # This step generates an artifact attestation for the image, which is an unforgeable statement about where and how it was built.
       # It increases supply chain security for people who consume the image.

Dockerfile

@@ -9,25 +9,25 @@ ENV MODULE_VERSION=4.1.2
 
 # All apt-get cmd
 RUN apt-get update -y && \
-    apt-get install -y wget lsb-release
-RUN wget https://ecsft.cern.ch/dist/cvmfs/cvmfs-release/cvmfs-release-${CVMFS_VERSION}_all.deb && \
+    apt-get install -y wget lsb-release && \
+    wget https://ecsft.cern.ch/dist/cvmfs/cvmfs-release/cvmfs-release-${CVMFS_VERSION}_all.deb && \
     dpkg -i cvmfs-release-${CVMFS_VERSION}_all.deb && \
     rm -f cvmfs-release-${CVMFS_VERSION}_all.deb && \
     apt-get update -y && \
-    apt-get install -y cvmfs
-RUN wget https://package.computecanada.ca/yum/cc-cvmfs-public/prod/other/cvmfs-config-computecanada-${CC_STACK}.all.deb && \
+    apt-get install -y cvmfs && \
+    wget https://package.computecanada.ca/yum/cc-cvmfs-public/prod/other/cvmfs-config-computecanada-${CC_STACK}.all.deb && \
     apt-get install -y ./cvmfs-config-computecanada-${CC_STACK}.all.deb && \
-    rm -f cvmfs-config-computecanada-${CC_STACK}.all.deb
-RUN apt-get install -y libpng-dev libjpeg-dev libtiff-dev && \
+    rm -f cvmfs-config-computecanada-${CC_STACK}.all.deb && \
+    apt-get install -y libpng-dev libjpeg-dev libtiff-dev && \
     apt-get install -y imagemagick pigz which zip unzip make gcc expect file dejagnu less tcl-dev cvmfs-config-computecanada cvmfs-fuse3 cvmfs-config-default && \
     apt-get clean all
 
 RUN mkdir /cvmfs-cache  && chmod 777 /cvmfs-cache  /cvmfs
 RUN mkdir /cvmfs/ref.mugqic /cvmfs/soft.mugqic /cvmfs/cvmfs-config.computecanada.ca
 
 # module
-RUN wget https://github.com/cea-hpc/modules/releases/download/v${MODULE_VERSION}/modules-${MODULE_VERSION}.tar.gz
-RUN tar xzf modules-${MODULE_VERSION}.tar.gz && \
+RUN wget https://github.com/cea-hpc/modules/releases/download/v${MODULE_VERSION}/modules-${MODULE_VERSION}.tar.gz && \
+    tar xzf modules-${MODULE_VERSION}.tar.gz && \
     rm modules-${MODULE_VERSION}.tar.gz \
     && cd  modules-${MODULE_VERSION}  && ./configure && make -j 7  && make install \
     && cd .. && rm -rf modules-${MODULE_VERSION} && rm -rf /usr/local/Modules/modulefiles/*

README.md

@@ -8,7 +8,7 @@ While you can use (GiaC) to debug GenPipes on your laptop, [GenPipes](https://bi
 
 ## Install a compatible container technology on your machine
 
-Follow installation procedure from the [Singularity install page](https://github.com/hpcng/singularity/blob/master/INSTALL.md) or the [Docker install page](https://docs.docker.com/get-docker/).
+Follow installation procedure from the [Apptainer install page](https://apptainer.org/docs/user/latest/quick_start.html#installation) or the [Docker install page](https://docs.docker.com/get-docker/).
 
 You can also [Read the GenPipes documentation](https://genpipes.readthedocs.io/).
 
@@ -35,14 +35,14 @@ You can now configure the `genpipes/resources/container/etc/wrapper.conf` file:
 # GEN_SHARED_CVMFS should have a sufficient amount of space to load full reference files
 export GEN_SHARED_CVMFS=$HOME/cvmfs
 BIND_LIST=
-GEN_CONTAINERTYPE=singularity
+GEN_CONTAINERTYPE=apptainer
 ```
 
 `GEN_SHARED_CVMFS` will hold a cache for GiaC [CVMFS](https://cernvm.cern.ch/portal/filesystem) system, it will hold the genomes and software being used by GenPipes. This folder will grow with GenPipes usage. You can delete it in between usage, but keep in mind that once deleted it will need to be rebuild by downloading data form the internet.
 
-`BIND_LIST` is a list of file system, separated by comma, you need GenPipes to have access to, by default, only your $HOME is mounted. For example if you are on an HPC system with a `/scratch` and `/data` space, you would have `BIND_LIST=/scratch,/data`. The string will be fed to Singularity `--bind` option, see `singularity --help` for more details.
+`BIND_LIST` is a list of file system, separated by comma, you need GenPipes to have access to, by default, only your $HOME is mounted. For example if you are on an HPC system with a `/scratch` and `/data` space, you would have `BIND_LIST=/scratch,/data`. The string will be fed to Singularity `--bind` option, see `apptainer --help` for more details.
 
-`GEN_CONTAINERTYPE` is the container to use, either `singularity` (default), `apptainer` or `docker`.
+`GEN_CONTAINERTYPE` is the container to use, either `apptainer` (default), `singularity`, `docker` or `podman`.
 
 You do not need any other setup on your machine.
 
@@ -62,10 +62,10 @@ https://genpipes.readthedocs.io/
 You can also run the `genpipes/resources/container/bin/container_wrapper.sh` command to get inside the container with the right configuration. You will then have access to all the GenPipes tools be able to run them directly inside the container, on a single host without the `--wrap` option.
 
 ## Whitout the wrapper
-### Using Singularity
+### Using Apptainer
 With `GEN_SHARED_CVMFS` being the cache directory on the host, `BIND_LIST` the file system to be accessed by genpipes, {IMAGE_PATH}/genpipes.sif the [latest sif file released](https://github.com/c3g/genpipes_in_a_container/releases/latest).
 ```
- singularity run \
+ apptainer run \
   --cleanenv \
   -S /var/run/cvmfs \
   -B ${GEN_SHARED_CVMFS}:/cvmfs-cache \
@@ -75,10 +75,10 @@ With `GEN_SHARED_CVMFS` being the cache directory on the host, `BIND_LIST` the f
   --fusemount "container:cvmfs2 ref.mugqic /cvmfs/ref.mugqic" \
   ${IMAGE_PATH}/genpipes.sif
 ```
-### Using Apptainer
+### Using Singularity
 With `GEN_SHARED_CVMFS` being the cache directory on the host, `BIND_LIST` the file system to be accessed by genpipes, {IMAGE_PATH}/genpipes.sif the [latest sif file released](https://github.com/c3g/genpipes_in_a_container/releases/latest).
 ```
- apptainer run \
+ singularity run \
   --cleanenv \
   -S /var/run/cvmfs \
   -B ${GEN_SHARED_CVMFS}:/cvmfs-cache \

container/wrapper_genpipes/etc/wrapper.conf.tpl

@@ -1,4 +1,4 @@
 # GEN_SHARED_CVMFS should have a sufficient amount of space to load full reference files
 export GEN_SHARED_CVMFS=$HOME/cvmfs
 BIND_LIST=
-GEN_CONTAINERTYPE=singularity
+GEN_CONTAINERTYPE=apptainer