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prepare release See merge request tron/bnt_neoants/splice2neo!138
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FROM docker://rocker/r-ver:4.2.3 | ||
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MAINTAINER [email protected] | ||
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ENV SRC /usr/local/src | ||
ENV BIN /usr/local/bin | ||
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COPY DESCRIPTION /usr/local/src | ||
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RUN apt update && apt install -y \ | ||
build-essential \ | ||
libxml2-dev \ | ||
libcairo2-dev \ | ||
libgit2-dev \ | ||
default-libmysqlclient-dev \ | ||
libpq-dev \ | ||
libsasl2-dev \ | ||
libsqlite3-dev \ | ||
libssh2-1-dev \ | ||
libxtst6 \ | ||
libcurl4-openssl-dev \ | ||
libharfbuzz-dev \ | ||
libfribidi-dev \ | ||
libfreetype6-dev \ | ||
libpng-dev \ | ||
libtiff5-dev \ | ||
libjpeg-dev \ | ||
libbz2-dev \ | ||
unixodbc-dev \ | ||
tini \ | ||
git \ | ||
locales \ | ||
&& rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \ | ||
apt clean && \ | ||
apt autoremove -y && \ | ||
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 \ | ||
readr \ | ||
tibble \ | ||
dplyr \ | ||
magrittr \ | ||
argparse \ | ||
stringr \ | ||
tidyr \ | ||
purrr \ | ||
devtools \ | ||
remotes \ | ||
BiocManager \ | ||
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)' | ||
RUN Rscript -e 'library(remotes); remotes::install_version("MASS", version = "7.3-60", repos = "http://cran.us.r-project.org", Ncpus=8)' | ||
RUN Rscript -e 'BiocManager::install(c("BSgenome.Hsapiens.UCSC.hg19"), Ncpus=8)' | ||
RUN export SPLICE2NEO_VERSION=$(grep 'Version:' /usr/local/src/DESCRIPTION | awk '{print $2}') && \ | ||
Rscript -e "library(remotes); remotes::install_git('https://github.com/TRON-Bioinformatics/splice2neo.git', ref = 'v${SPLICE2NEO_VERSION}', Ncpus=8)" | ||
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RUN apt autoremove -y | ||
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# Remove build dependencies from container | ||
RUN apt remove -y \ | ||
build-essential \ | ||
libxml2-dev \ | ||
libcairo2-dev \ | ||
libgit2-dev \ | ||
default-libmysqlclient-dev \ | ||
libpq-dev \ | ||
libsasl2-dev \ | ||
libsqlite3-dev \ | ||
libssh2-1-dev \ | ||
libxtst6 \ | ||
libcurl4-openssl-dev \ | ||
libharfbuzz-dev \ | ||
libfribidi-dev \ | ||
libfreetype6-dev \ | ||
libpng-dev \ | ||
libtiff5-dev \ | ||
libjpeg-dev \ | ||
unixodbc-dev \ | ||
libbz2-dev \ | ||
git \ | ||
locales | ||
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WORKDIR / | ||
ENTRYPOINT ["tini", "--"] | ||
CMD [ "/bin/bash" ] |
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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. | ||
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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``` | ||
singularity build --fakeroot splice2neo.sif splice2neo.def | ||
``` | ||
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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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``` | ||
singularity exec -e -B `pwd` -B /path/to/your/inputs splice2neo.sif Rscript splice2neo.R | ||
``` | ||
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### Interactive usage | ||
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``` | ||
singularity shell -B `pwd` -B /path/to/your/inputs splice2neo.sif | ||
``` | ||
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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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``` | ||
podman build -t tronbioinformatics/splice2neo:"${TAG}" . | ||
``` |
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#!/bin/bash | ||
# | ||
# Maintainer: Johannes Hausmann <[email protected]> | ||
# Build OCI images for splice2neo | ||
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cp ../DESCRIPTION DESCRIPTION | ||
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export TAG=$(grep 'Version:' DESCRIPTION | awk '{print $2}') | ||
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podman build -t tronbioinformatics/splice2neo:"${TAG}" . | ||
#podman build -t tronbioinformatics/splice2neo:latest . | ||
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rm DESCRIPTION |
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Bootstrap: docker | ||
From: rocker/r-ver:4.2.3 | ||
Stage: spython-base | ||
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%files | ||
../DESCRIPTION /usr/local/src/ | ||
%labels | ||
MAINTAINER [email protected] | ||
%post | ||
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SRC=/usr/local/src | ||
BIN=/usr/local/bin | ||
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apt update && apt install -y \ | ||
build-essential \ | ||
libxml2-dev \ | ||
libcairo2-dev \ | ||
libgit2-dev \ | ||
default-libmysqlclient-dev \ | ||
libpq-dev \ | ||
libsasl2-dev \ | ||
libsqlite3-dev \ | ||
libssh2-1-dev \ | ||
libxtst6 \ | ||
libcurl4-openssl-dev \ | ||
libharfbuzz-dev \ | ||
libfribidi-dev \ | ||
libfreetype6-dev \ | ||
libpng-dev \ | ||
libtiff5-dev \ | ||
libjpeg-dev \ | ||
unixodbc-dev \ | ||
libbz2-dev \ | ||
git && \ | ||
apt clean && \ | ||
apt autoremove -y | ||
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install2.r --error --skipinstalled -n 8 \ | ||
readr \ | ||
tibble \ | ||
dplyr \ | ||
magrittr \ | ||
argparse \ | ||
stringr \ | ||
tidyr \ | ||
purrr \ | ||
devtools \ | ||
remotes \ | ||
BiocManager \ | ||
vroom | ||
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export SPLICE2NEO_VERSION=$(grep 'Version:' /usr/local/src/DESCRIPTION | awk '{print $2}') && \ | ||
R --no-save <<__EOF__ | ||
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BiocManager::install("BSgenome.Hsapiens.UCSC.hg38", Ncpus=8) | ||
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library(remotes) | ||
remotes::install_version("Matrix", version = "1.6-5", repos = "http://cran.us.r-project.org") | ||
remotes::install_version("MASS", version = "7.3-60", repos = "http://cran.us.r-project.org") | ||
remotes::install_git('https://github.com/TRON-Bioinformatics/splice2neo.git', ref = "v${SPLICE2NEO_VERSION}") | ||
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__EOF__ | ||
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apt autoremove -y | ||
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# Remove build dependencies from container | ||
apt remove -y \ | ||
build-essential \ | ||
libxml2-dev \ | ||
libcairo2-dev \ | ||
libgit2-dev \ | ||
default-libmysqlclient-dev \ | ||
libpq-dev \ | ||
libsasl2-dev \ | ||
libsqlite3-dev \ | ||
libssh2-1-dev \ | ||
libxtst6 \ | ||
libcurl4-openssl-dev \ | ||
libharfbuzz-dev \ | ||
libfribidi-dev \ | ||
libfreetype6-dev \ | ||
libpng-dev \ | ||
libtiff5-dev \ | ||
libjpeg-dev \ | ||
unixodbc-dev \ | ||
libbz2-dev | ||
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%environment | ||
export SRC=/usr/local/src | ||
export BIN=/usr/local/bin | ||
%runscript | ||
cd / | ||
exec tini -- /bin/bash "$@" | ||
%startscript | ||
cd / | ||
exec tini -- /bin/bash "$@" |
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