J35P312/FluFFyPipe:latest
$ singularity pull shub://J35P312/FluFFyPipe:latest
Singularity Recipe
Bootstrap: docker
From: ubuntu:16.04
%environment
SHELL=/bin/bash
PATH=/opt/anaconda/bin:${PATH}
LC_ALL=C.UTF-8
%runscript
export PATH=/opt/anaconda/bin:${PATH}
%post
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 sudo libatlas3-base python3 python3-pip
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}
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda config --add channels r
#conda install -c bioconda wisecondorx=1.1.5
pip install -U git+https://github.com/CenterForMedicalGeneticsGhent/WisecondorX@v1.1.6
conda install -c bioconda samtools picard bioconductor-dnacopy
conda install -c bioconda bwa fastqc biobambam
conda install -c r r-doparallel r-foreach r-neuralnet r-glmnet r-data.table r-mass r-matrix r-jsonlite
pip install sklearn numpy scipy matplotlib pysam futures bottleneck cython
pip3 install multiqc
cd /bin/ && wget https://github.com/CenterForMedicalGeneticsGhent/PREFACE/archive/v0.1.1.zip && unzip v0.1.1.zip
cd /
cd /bin/ && git clone https://github.com/J35P312/AMYCNE.git && cd AMYCNE && python setup.py build_ext --inplace
git clone https://github.com/SciLifeLab/TIDDIT.git
mv TIDDIT/* /bin/
cd /bin/ && ./INSTALL.sh
chmod +x /bin/TIDDIT.py
cd /bin/ && git clone https://github.com/J35P312/FluFFyPipe.git
Collection
- Name: J35P312/FluFFyPipe
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/J35P312-FluFFyPipe-latest |
collection name | J35P312/FluFFyPipe |
branch | master |
tag | latest |
commit | 70e1216b11506828059c04dc0d80de221ed19bb8 |
version (container hash) | 7af3969aa82998a8ef1506f0d382ba6e |
build date | 2021-03-08T17:54:56.189Z |
size (MB) | 3740.0 |
size (bytes) | 1870495775 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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