update Planemo, Linux, Python, Singularity

.gitlab-ci.yml

@@ -11,7 +11,7 @@ build docker-planemo:
   stage: build
   
   variables:
-    IMAGE_TAG: $CI_REGISTRY/record/docker-planemo/docker-planemo-singularity:0.74.8
+    IMAGE_TAG: $CI_REGISTRY/record/docker-planemo/docker-planemo-singularity:0.74.9
   
   script:
     - docker info

Dockerfile

-FROM python:3.6.12
+FROM python:3.9.12-bullseye
 
 LABEL maintainer "Patrick Chabrier <patrick.chabrier@inrae.fr>"
 
 ENV DEBIAN_FRONTEND noninteractive
 
-RUN wget -O- http://neuro.debian.net/lists/xenial.us-ca.full | tee /etc/apt/sources.list.d/neurodebian.sources.list \
-    && apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9 \
-    && apt-get update
+# Installation de singularity-ce en 3.9.2
 
-RUN apt-get install -y singularity-container
+RUN apt-get update \
+    && apt-get install -y \ 
+    build-essential \ 
+    uuid-dev \ 
+    libgpgme-dev \ 
+    squashfs-tools \ 
+    libseccomp-dev \ 
+    wget \ 
+    pkg-config \ 
+    git \ 
+    cryptsetup-bin
 
-RUN pip install git+https://github.com/galaxyproject/planemo.git@0.74.8
+
+RUN VERSION=1.17.6 OS=linux ARCH=amd64 \
+    && wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz \ 
+    && tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz \ 
+    && rm go$VERSION.$OS-$ARCH.tar.gz
+    
+RUN echo 'export GOPATH=${HOME}/go' >> ~/.bashrc \ 
+    && echo 'export PATH=/usr/local/go/bin:${PATH}:${GOPATH}/bin' >> ~/.bashrc \ 
+    && . ~/.bashrc
+
+RUN export VERSION=3.9.2 \ 
+    && wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-ce-${VERSION}.tar.gz \ 
+    && tar -xzf singularity-ce-${VERSION}.tar.gz \
+    && cd singularity-ce-${VERSION}
+
+RUN pwd \
+    && export VERSION=3.9.2 \ 
+    && cd singularity-ce-${VERSION} \
+    && . ~/.bashrc \
+    && . ./mconfig \ 
+    && make -C ./builddir \ 
+    && make -C ./builddir install
+
+RUN pip install git+https://github.com/galaxyproject/planemo.git@0.74.9
 
 ENV GALAXY_TEST_UPLOAD_ASYNC false
 ENV GALAXY_TEST_DEFAULT_INTERACTOR api