connor-lab/singularity-recipes:ariba
$ singularity pull shub://connor-lab/singularity-recipes:ariba
Singularity Recipe
Bootstrap: docker
From: centos:latest
%post
yum -y update
yum -y install epel-release
yum install -y bzip2 bzip2-devel gcc gcc-c++ git ncurses-devel make unzip xz-devel zlib-devel
yum install -y python36 python36-devel python36-setuptools
easy_install-3.6 pip
## MUMmer 4
curl -fsSL 'https://github.com/mummer4/mummer/releases/download/v4.0.0beta2/mummer-4.0.0beta2.tar.gz' | tar -xz -C /usr/local/bin
cd /usr/local/bin/mummer-4.0.0beta2 && ./configure && make install
## Bowtie2
curl -fsSL 'https://github.com/BenLangmead/bowtie2/releases/download/v2.3.4.3/bowtie2-2.3.4.3-linux-x86_64.zip' -o /usr/local/bin/bowtie2-2.3.4.3.zip
cd /usr/local/bin/ && unzip bowtie2-2.3.4.3.zip
find /usr/local/bin/bowtie2-2.3.4.3-linux-x86_64 -type f -executable -exec ln -s {} /usr/local/bin \;
## SPAdes
curl -fsSL 'http://cab.spbu.ru/files/release3.13.0/SPAdes-3.13.0-Linux.tar.gz' | tar -xz -C /usr/local/bin/
find /usr/local/bin/SPAdes* -name "spades.py" -type f -executable -exec ln -s {} /usr/local/bin \;
## CD-HIT
curl -fsSL 'https://github.com/weizhongli/cdhit/releases/download/V4.6.8/cd-hit-v4.6.8-2017-1208-source.tar.gz' | tar -xz -C /usr/local/bin
cd /usr/local/bin/cd-hit-v4.6.8-2017-1208 && make && make install
pip3 install ariba
%runscript
exec ariba "$@"
Collection
- Name: connor-lab/singularity-recipes
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/connor-lab-singularity-recipes-ariba |
collection name | connor-lab/singularity-recipes |
branch | master |
tag | ariba |
commit | a43cefa7f62c25a6726a49f5634f285ba75ea6a9 |
version (container hash) | 78e3c33a5b393288cefa4c703faf9e10 |
build date | 2019-02-07T11:31:15.361Z |
size (MB) | 1107 |
size (bytes) | 453885983 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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