UMMS-Biocore/initialrun:latest
$ singularity pull shub://UMMS-Biocore/initialrun:latest
Singularity Recipe
BootStrap: docker
From: ubuntu:16.04
%labels
AUTHOR Onur Yukselen <onur.yukselen@umassmed.edu>
Version v1.0
%environment
PATH=$PATH:/bin:/sbin:/data/sratoolkit.2.9.6-1-ubuntu64/bin
export PATH
%post
apt-get update
apt-get -y upgrade
apt-get dist-upgrade
apt-get -y install unzip libsqlite3-dev libbz2-dev libssl-dev python python-dev \
python-pip git libxml2-dev software-properties-common wget tree vim sed \
subversion g++ gcc gfortran libcurl4-openssl-dev curl zlib1g-dev build-essential libffi-dev python-lzo
###################
## Python modules
###################
export LC_ALL=C
pip install --upgrade pip==9.0.3
pip install pysam
pip install numpy scipy biopython
### SRA-toolkit
mkdir /data && cd /data
mkdir -p /project /nl /share
wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.9.6-1/sratoolkit.2.9.6-1-ubuntu64.tar.gz
tar -xvzf sratoolkit.2.9.6-1-ubuntu64.tar.gz
###S3CMD
apt-get -y upgrade
apt-get -y install python-setuptools
wget http://netix.dl.sourceforge.net/project/s3tools/s3cmd/1.6.0/s3cmd-1.6.0.tar.gz
tar xvfz s3cmd-1.6.0.tar.gz
cd s3cmd-1.6.0
python setup.py install
Collection
- Name: UMMS-Biocore/initialrun
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/UMMS-Biocore-initialrun-latest |
collection name | UMMS-Biocore/initialrun |
branch | develop |
tag | latest |
commit | 3d21a88f9a191284f7440e4a206a49a558274aae |
version (container hash) | 716bdeb0eb417b3a1481aff894833d17 |
build date | 2019-06-13T14:46:43.408Z |
size (MB) | 1199 |
size (bytes) | 536502303 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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