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franla23franla23
committedOct 23, 2024·
Merge branch 'add_container_manifest' into 'dev'
Add initial container support See merge request tron/bnt_neoants/splice2neo!136
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v0.6.12
2 parents 0d3df77 + 09b003c commit ef24d98

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‎Docker/Dockerfile

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FROM docker://rocker/r-ver:4.2.3
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MAINTAINER johannes.hausmann@tron-mainz.de
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ENV SRC /usr/local/src
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ENV BIN /usr/local/bin
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COPY DESCRIPTION /usr/local/src
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RUN apt update && apt install -y \
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build-essential \
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libxml2-dev \
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libcairo2-dev \
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libgit2-dev \
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default-libmysqlclient-dev \
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libpq-dev \
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libsasl2-dev \
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libsqlite3-dev \
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libssh2-1-dev \
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libxtst6 \
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libcurl4-openssl-dev \
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libharfbuzz-dev \
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libfribidi-dev \
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libfreetype6-dev \
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libpng-dev \
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libtiff5-dev \
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libjpeg-dev \
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libbz2-dev \
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unixodbc-dev \
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tini \
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git \
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locales \
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&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
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apt clean && \
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apt autoremove -y && \
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rm -rf /var/lib/{apt,dpkg,cache,log}/
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RUN locale-gen en_US.UTF-8
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RUN install2.r --error --skipinstalled -n 8 \
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readr \
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tibble \
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dplyr \
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magrittr \
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argparse \
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stringr \
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tidyr \
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purrr \
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devtools \
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remotes \
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BiocManager \
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vroom
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RUN Rscript -e 'library(remotes); remotes::install_version("Matrix", version = "1.6-5", repos = "http://cran.us.r-project.org", Ncpus=8)'
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RUN Rscript -e 'library(remotes); remotes::install_version("MASS", version = "7.3-60", repos = "http://cran.us.r-project.org", Ncpus=8)'
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RUN Rscript -e 'BiocManager::install(c("BSgenome.Hsapiens.UCSC.hg19"), Ncpus=8)'
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RUN export SPLICE2NEO_VERSION=$(grep 'Version:' /usr/local/src/DESCRIPTION | awk '{print $2}') && \
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Rscript -e "library(remotes); remotes::install_git('https://github.com/TRON-Bioinformatics/splice2neo.git', ref = 'v${SPLICE2NEO_VERSION}', Ncpus=8)"
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RUN apt autoremove -y
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# Remove build dependencies from container
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RUN apt remove -y \
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build-essential \
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libxml2-dev \
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libcairo2-dev \
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libgit2-dev \
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default-libmysqlclient-dev \
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libpq-dev \
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libsasl2-dev \
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libsqlite3-dev \
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libssh2-1-dev \
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libxtst6 \
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libcurl4-openssl-dev \
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libharfbuzz-dev \
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libfribidi-dev \
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libfreetype6-dev \
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libpng-dev \
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libtiff5-dev \
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libjpeg-dev \
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unixodbc-dev \
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libbz2-dev \
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git \
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locales
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WORKDIR /
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ENTRYPOINT ["tini", "--"]
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CMD [ "/bin/bash" ]

‎Docker/README.md

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# Container support
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We provide a Singularity and a Docker image that contains all software pre-installed for running the splice2neo analysis.
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However, singularity is our preferred method for running splice2neo as it allows unprivileged users to run the application in a container.
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## Singularity
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To use the the singularity image, you have to first build it from the definition file. Please make sure you have `fakeroot` permissions or ask your sysadmin to build the image.
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```
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singularity build --fakeroot splice2neo.sif splice2neo.def
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```
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To run the analysis, bind your input directory into the container. The container ships the HG19 version of BSgenome.
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### Script usage
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```
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singularity exec -e -B `pwd` -B /path/to/your/inputs splice2neo.sif Rscript splice2neo.R
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```
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### Interactive usage
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```
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singularity shell -B `pwd` -B /path/to/your/inputs splice2neo.sif
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```
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Within the container you can now open a R-Session and execute the commands.
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## Docker / podman
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We use podman to build and manage our Docker images. Podman is API compatible with Docker and provides unprivileged execution of images.
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```
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podman build -t tronbioinformatics/splice2neo:"${TAG}" .
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```

‎Docker/build_docker.sh

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#!/bin/bash
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#
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# Maintainer: Johannes Hausmann <johannes.hausmann@posteo.de>
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# Build OCI images for splice2neo
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cp ../DESCRIPTION DESCRIPTION
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export TAG=$(grep 'Version:' DESCRIPTION | awk '{print $2}')
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podman build -t tronbioinformatics/splice2neo:"${TAG}" .
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#podman build -t tronbioinformatics/splice2neo:latest .
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rm DESCRIPTION

‎Docker/splice2neo.def

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Bootstrap: docker
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From: rocker/r-ver:4.2.3
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Stage: spython-base
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%files
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../DESCRIPTION /usr/local/src/
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%labels
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MAINTAINER johannes.hausmann@tron-mainz.de
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%post
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SRC=/usr/local/src
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BIN=/usr/local/bin
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apt update && apt install -y \
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build-essential \
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libxml2-dev \
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libcairo2-dev \
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libgit2-dev \
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default-libmysqlclient-dev \
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libpq-dev \
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libsasl2-dev \
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libsqlite3-dev \
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libssh2-1-dev \
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libxtst6 \
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libcurl4-openssl-dev \
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libharfbuzz-dev \
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libfribidi-dev \
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libfreetype6-dev \
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libpng-dev \
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libtiff5-dev \
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libjpeg-dev \
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unixodbc-dev \
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libbz2-dev \
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git && \
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apt clean && \
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apt autoremove -y
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install2.r --error --skipinstalled -n 8 \
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readr \
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tibble \
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dplyr \
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magrittr \
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argparse \
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stringr \
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tidyr \
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purrr \
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devtools \
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remotes \
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BiocManager \
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vroom
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export SPLICE2NEO_VERSION=$(grep 'Version:' /usr/local/src/DESCRIPTION | awk '{print $2}') && \
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R --no-save <<__EOF__
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BiocManager::install("BSgenome.Hsapiens.UCSC.hg38", Ncpus=8)
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library(remotes)
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remotes::install_version("Matrix", version = "1.6-5", repos = "http://cran.us.r-project.org")
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remotes::install_version("MASS", version = "7.3-60", repos = "http://cran.us.r-project.org")
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remotes::install_git('https://github.com/TRON-Bioinformatics/splice2neo.git', ref = "v${SPLICE2NEO_VERSION}")
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__EOF__
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apt autoremove -y
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# Remove build dependencies from container
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apt remove -y \
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build-essential \
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libxml2-dev \
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libcairo2-dev \
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libgit2-dev \
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default-libmysqlclient-dev \
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libpq-dev \
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libsasl2-dev \
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libsqlite3-dev \
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libssh2-1-dev \
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libxtst6 \
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libcurl4-openssl-dev \
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libharfbuzz-dev \
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libfribidi-dev \
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libfreetype6-dev \
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libpng-dev \
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libtiff5-dev \
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libjpeg-dev \
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unixodbc-dev \
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libbz2-dev
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%environment
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export SRC=/usr/local/src
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export BIN=/usr/local/bin
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%runscript
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cd /
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exec tini -- /bin/bash "$@"
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%startscript
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cd /
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exec tini -- /bin/bash "$@"

‎README.md

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[![](https://img.shields.io/badge/devel%20version-0.6.6-blue.svg)](https://github.com/TRON-Bioinformatics/splice2neo)
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[![](https://img.shields.io/badge/lifecycle-experimental-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
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[![](https://img.shields.io/github/last-commit/TRON-Bioinformatics/splice2neo.svg)](https://github.com/TRON-Bioinformatics/splice2neo/commits/dev)
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[![Docker](https://img.shields.io/badge/docker-%230db7ed.svg?style=for-the-badge&logo=docker&logoColor=white)](https://hub.docker.com/r/tronbioinformatics/splice2neo/tags)
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<!-- badges: end -->
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Documentation: <https://tron-bioinformatics.github.io/splice2neo/>

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