Commit 5b17dbd6 authored by jacqueslagnel's avatar jacqueslagnel
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# 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"
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.
# 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
# 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
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
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