NIH-HPC/singularity-examples:rnaseq
$ singularity pull shub://NIH-HPC/singularity-examples:rnaseq
Singularity Recipe
BootStrap: docker
From: continuumio/miniconda: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
%runscript
#!/bin/bash
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# this text will 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: $(samtools --version | head -n1)"
}
arg="${1:-none}"
case "$arg" in
none) usage; exit 1;;
help) usage; exit 0;;
list) tools; exit 0;;
# just try to execute it then
*) $@;;
esac
%environment
export PATH="/opt/conda/bin:/usr/local/bin:/usr/bin:/bin:"
unset CONDA_DEFAULT_ENV
export ANACONDA_HOME=/opt/conda
Collection
- Name: NIH-HPC/singularity-examples
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/NIH-HPC-singularity-examples-rnaseq |
collection name | NIH-HPC/singularity-examples |
branch | master |
tag | rnaseq |
commit | 2ccdc4a334b5e669dd6eab2099623f8b0d5f5af8 |
version (container hash) | ec8aa7a15c3ab3ad4d76e03b78f9f4dd |
build date | 2019-10-21T11:22:01.848Z |
size (MB) | 1284 |
size (bytes) | 446349343 |
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.