J35P312/FindSVSingularity:latest
$ singularity pull shub://J35P312/FindSVSingularity:latest
Singularity Recipe
Bootstrap: docker
From: ubuntu:16.04
%environment
SHELL=/bin/bash
PATH=/opt/anaconda/bin:${PATH}
LC_ALL=C.UTF-8
ROOTSYS=/opt/root/
LD_LIBRARY_PATH=/opt/root/lib
%runscript
echo "This is what happens when you run the container..."
export PATH=/opt/anaconda/bin:${PATH}
%post
echo "Hello from inside the container"
apt-get update
apt-get -y install wget git bzip2 build-essential gcc zlib1g-dev language-pack-en-base apt-transport-https make cmake unzip libncurses5-dev libncursesw5-dev
update-locale LC_ALL=en_US.UTF-8 LANG=en_US.UTF-8
cd /root/ && wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
cd /root/ && chmod 700 ./Miniconda2-latest-Linux-x86_64.sh
cd /root/ && bash ./Miniconda2-latest-Linux-x86_64.sh -b -p /opt/anaconda/
export PATH=/opt/anaconda/bin:${PATH}
cd /opt/ && wget https://root.cern.ch/download/root_v6.13.02.Linux-ubuntu16-x86_64-gcc5.4.tar.gz
cd /opt/ && tar -xvf root_v6.13.02.Linux-ubuntu16-x86_64-gcc5.4.tar.gz
export ROOTSYS=/opt/root
export PATH=$PATH:$ROOTSYS/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ROOTSYS/lib
cd /opt/ && wget https://github.com/abyzovlab/CNVnator/releases/download/v0.3.3/CNVnator_v0.3.3.zip
cd /opt && unzip CNVnator_v0.3.3.zip
cd /opt/CNVnator_v0.3.3/src/samtools/ && make
cd /opt/CNVnator_v0.3.3/src/ && make
cd /opt/ && wget https://github.com/SciLifeLab/TIDDIT/archive/TIDDIT-2.12.0.zip && unzip TIDDIT-2.12.0.zip
mv /opt/TIDDIT-TIDDIT-2.12.0 /opt/TIDDIT
cd /opt/TIDDIT && ./INSTALL.sh .
cd /opt/ && git clone https://github.com/J35P312/SVDB.git
cd /opt/SVDB && pip install -e .
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda install -c bioconda samtools vt
pip install genmod pyaml
Collection
- Name: J35P312/FindSVSingularity
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/J35P312-FindSVSingularity-latest |
collection name | J35P312/FindSVSingularity |
branch | master |
tag | latest |
commit | 25b0d9969bb41b21c770e17926bbd0f44ee1550f |
version (container hash) | 0a1809e9e8513d60c3ebf7f8637d3f7b |
build date | 2021-02-22T11:29:10.709Z |
size (MB) | 1531.0 |
size (bytes) | 695373855 |
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.