GodloveD/rnaseq:latest
$ singularity pull shub://GodloveD/rnaseq:latest
Singularity Recipe
BootStrap: docker
From: continuumio/miniconda3:latest
IncludeCmd: yes
%post
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# this will install all necessary packages and prepare the container
apt-get -y update
apt-get -y install make gcc zlib1g-dev libncurses5-dev
wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 \
&& tar -xjf samtools-1.3.1.tar.bz2 \
&& cd samtools-1.3.1 \
&& make \
&& make prefix=/usr/local install
export PATH=/opt/conda/bin:$PATH
conda install --yes -c bioconda \
star=2.5.2b \
sailfish=0.10.1 \
fastqc=0.11.5 \
kallisto=0.43.0 \
subread=1.5.0.post3
conda clean --index-cache --tarballs --packages --yes
mkdir /gpfs /spin1 /gs2 /gs3 /gs4 /gs5 /gs6 /data /scratch /fdb /lscratch
cat > /singularity <<'EORUNSCRIPT'
#!/bin/bash
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# this text will get copied to /singularity and will run whenever the container
# is called as an executable
function usage() {
cat <<EOF
NAME
rnaseq - rnaseq pipeline tools 0.1
SYNOPSIS
rnaseq tool [tool options]
rnaseq list
rnaseq help
DESCRIPTION
Singularity container with tools to build rnaseq pipeline.
EOF
}
function tools() {
echo "conda: $(which conda)"
echo "---------------------------------------------------------------"
conda list
echo "---------------------------------------------------------------"
echo "samtools: $(samtools --version | head -n1)"
}
export PATH="/opt/conda/bin:/usr/local/bin:/usr/bin:/bin:"
unset CONDA_DEFAULT_ENV
export ANACONDA_HOME=/opt/conda
arg="${1:-none}"
case "$arg" in
none) usage; exit 1;;
help) usage; exit 0;;
list) tools; exit 0;;
# just try to execute it then
*) $@;;
esac
EORUNSCRIPT
chmod 755 /singularity
Collection
- Name: GodloveD/rnaseq
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/GodloveD-rnaseq-latest |
collection name | GodloveD/rnaseq |
branch | master |
tag | latest |
commit | ce0ab3b6a95492b235c7e485b900b1a2f364d406 |
version (container hash) | 80e3bb9959cf161069f4fb72d30fa7d0 |
build date | 2019-09-22T19:47:11.831Z |
size (MB) | 1324 |
size (bytes) | 480903199 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
Feedback
Was this page helpful?
Glad to hear it! Please tell us how we can improve.
Sorry to hear that. Please tell us how we can improve.