monaghaa/rnaseq2:latest
$ singularity pull shub://monaghaa/rnaseq2:latest
Singularity Recipe
BootStrap: docker
From: ubuntu:20.10
##################################
#notes from andy:
#I didn't check to see if any genomics databases were needed
#these can generally be installed outside the container
#but sometimes they need environment variables to be set
##################################
%post
# install some system deps
apt-get -y update
apt-get -y install locales curl bzip2 less unzip git wget vim ant default-jdk
# this is a X11 dep
apt-get -y install libxext6
# tools to open PDF and HTML files
#apt-get -y install firefox xpdf
# some extra devel libs
apt-get -y install zlib1g-dev libssl-dev libpng-dev uuid-dev
# other
locale-gen en_US.UTF-8
apt-get clean
# download and install miniconda3
curl -sSL -O https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -p /opt/miniconda3 -b
rm -fr Miniconda3-latest-Linux-x86_64.sh
export PATH=/opt/miniconda3/bin:$PATH
conda update -n base conda
conda config --add channels conda-forge
conda config --add channels bioconda
# install some dependencies to build R packages
# apt-get -y install build-essential gfortran
# install some bioinfo tools from Bioconda
conda create -y -n rnaseq2 -c bioconda cutadapt fastqc hisat2 samtools rsem bowtie2 trimmomatic
#create a runscript so that conda is correctly invoked in bash
echo '#!/bin/bash' >/opt/runscript
echo '. "/opt/miniconda3/etc/profile.d/conda.sh"' >>/opt/runscript
echo 'conda activate rnaseq2' >>/opt/runscript
echo '$@' >>/opt/runscript
%runscript
bash /opt/runscript "$@"
%environment
export LANG=en_US.UTF-8
export LANGUAGE=en_US:en
export LC_ALL=en_US.UTF-8
export XDG_RUNTIME_DIR=""
Collection
- Name: monaghaa/rnaseq2
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/monaghaa-rnaseq2-latest |
collection name | monaghaa/rnaseq2 |
branch | master |
tag | latest |
commit | d70d306423d97790d5c35c9c91a07684386b4a8f |
version (container hash) | d508fbfd67e32c3b8019cc357d23c0ae |
build date | 2020-11-19T18:42:25.751Z |
size (MB) | 3376.0 |
size (bytes) | 1753530399 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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