Initial commit

.gitlab-ci.yml

+# recipe for building singularity image and deploy it on the registery for transdecoder version 5.5.0
+image:
+   name: quay.io/singularity/singularity:v3.4.0
+   entrypoint: [""]
+
+stages:
+ - build
+ - deploy
+
+# Build Singularity container transdecoder_v5.5.0.sif
+singularity-image:
+   stage: build
+   script:
+       - singularity build transdecoder_v5.5.0.sif Singularity.transdecoder_v5.5.0
+   artifacts:
+      paths:
+       - transdecoder_v5.5.0.sif
+# Push the image transdecoder_v5.5.0.sif on the registry
+deploy:
+   stage: deploy
+   script:
+       - singularity push --docker-username "${CI_REGISTRY_USER}" --docker-password "${CI_REGISTRY_PASSWORD}" transdecoder_v5.5.0.sif oras://"$CI_REGISTRY_IMAGE"/"$CI_PROJECT_NAME":"$CI_COMMIT_TAG"

LICENSE

+MIT License
+
+Copyright (c) 2020 Jacques Lagnel
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

+# transdecoder Singularity container
+Bionformatics package transdecoder<br>
+TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. Developer docs: https://github.com/TransDecoder/TransDecoder
+https://transdecoder.github.io
+transdecoder Version: 5.5.0<br>
+
+Singularity container based on the recipe: Singularity.transdecoder_v5.5.0
+
+Package installation using Miniconda3 V4.7.12<br>
+
+image singularity (V>=3.3) is automaticly built (gitlab-ci) and pushed on the registry using the .gitlab-ci.yml <br>
+
+can be pull (singularity version >=3.3) with:<br>
+singularity pull transdecoder_v5.5.0.sif oras://registry.forgemia.inra.fr/gafl/singularity/transdecoder_v5.5.0/transdecoder_v5.5.0:latest
+
+

Singularity.transdecoder_v5.5.0

+# distribution based on: debian 9.8
+Bootstrap:docker
+From:debian:9.8-slim
+
+# container for transdecoder v5.5.0
+# Build:
+# sudo singularity build transdecoder_v5.5.0.sif Singularity.transdecoder_v5.5.0
+
+%environment
+export LC_ALL=C
+export LC_NUMERIC=en_GB.UTF-8
+export PATH="/opt/miniconda/bin:$PATH"
+
+#%labels
+#COPYRIGHT INRAe GAFL 2020
+#AUTHOR Jacques Lagnel
+#VERSION 1.1
+#LICENSE MIT
+#DATE_MODIF MYDATEMODIF
+#transdecoder (v5.5.0)
+
+%help
+Container for transdecoder
+TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. Developer docs: https://github.com/TransDecoder/TransDecoder
+https://transdecoder.github.io
+
+Version: 5.5.0
+Package installation using Miniconda3 V4.7.12
+All packages are in /opt/miniconda/bin & are in PATH
+Default runscript: TransDecoder.LongOrfs
+
+Usage:
+    transdecoder_v5.5.0.sif --help
+    or:
+    singularity exec transdecoder_v5.5.0.sif TransDecoder.LongOrfs --help
+
+
+%runscript
+    #default runscript: TransDecoder.LongOrfs passing all arguments from cli: $@
+    exec /opt/miniconda/bin/TransDecoder.LongOrfs "$@"
+
+%post
+
+    #essential stuff but minimal
+    apt update
+    #for security fixe:
+    #apt upgrade -y
+    apt install -y wget bzip2
+
+    #install conda
+    cd /opt
+    rm -fr miniconda
+
+    #miniconda3: get miniconda3 version 4.7.12
+    wget https://repo.continuum.io/miniconda/Miniconda3-4.7.12-Linux-x86_64.sh -O miniconda.sh
+
+    #install conda
+    bash miniconda.sh -b -p /opt/miniconda
+    export PATH="/opt/miniconda/bin:$PATH"
+    #add channels
+    conda config --add channels defaults
+    conda config --add channels bioconda
+    conda config --add channels conda-forge
+
+    #install transdecoder
+    
+    conda install -y -c bioconda transdecoder=5.5.0
+
+    #cleanup
+    conda clean -y --all
+    rm -f /opt/miniconda.sh
+    apt autoremove --purge
+    apt clean
+

run_git.sh

+git init
+git remote rm origin
+git remote add origin git@forgemia.inra.fr:gafl/singularity/transdecoder.git
+git add .
+git commit -m "Initial commit"
+git remote -v
+git push -u origin master