connor-lab/singularity-recipes:iva
$ singularity pull shub://connor-lab/singularity-recipes:iva
Singularity Recipe
Bootstrap: docker
From: alpine:3.8
%environment
PATH=$PATH:/usr/local/bin/MUMmer3.23
export PATH
%post
apk update
apk upgrade
apk add bash bzip2-dev g++ gcc libc-dev make ncurses-dev openjdk8-jre-base perl xz-dev zlib-dev
apk add python3 python3-dev py3-pip
wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 -O /tmp/samtools.tar.bz2
cd /tmp
tar xvjf samtools.tar.bz2
cd samtools-1.9 && ./configure && make && make install
wget 'https://downloads.sourceforge.net/project/smalt/smalt-0.7.6-static.tar.gz' -O /tmp/smalt-0.7.6-static.tar.gz
cd /tmp && tar xvzf smalt-0.7.6-static.tar.gz
cd smalt-0.7.6 && ./configure && make && make install
wget https://github.com/refresh-bio/KMC/releases/download/v3.1.0/KMC3.1.0.linux.tar.gz -O /tmp/KMC3.1.0.linux.tar.gz
cd /tmp && tar xvzf KMC3.1.0.linux.tar.gz
mv kmc* /usr/local/bin
wget https://github.com/tcsh-org/tcsh/archive/cvs2git-20170131.tar.gz -O /tmp/cvs2git-20170131.tar.gz
cd /tmp && tar xvzf cvs2git-20170131.tar.gz
cd tcsh-cvs2git-20170131 && ./configure && make && make install
ln -s /usr/local/bin/tcsh /usr/local/bin/csh
wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip -O /usr/local/bin/Trimmomatic-0.38.zip
cd /usr/local/bin && unzip Trimmomatic-0.38.zip
ln -s /usr/local/bin/Trimmomatic-0.38/trimmomatic-0.38.jar /usr/local/bin
wget https://downloads.sourceforge.net/project/mummer/mummer/3.23/MUMmer3.23.tar.gz -O /usr/local/bin/MUMmer3.23.tar.gz
cd /usr/local/bin && tar xvzf MUMmer3.23.tar.gz
cd MUMmer3.23 && make && make install
export PATH=$PATH:/usr/local/bin/MUMmer3.23
pip3 install iva
Collection
- Name: connor-lab/singularity-recipes
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/connor-lab-singularity-recipes-iva |
collection name | connor-lab/singularity-recipes |
branch | master |
tag | iva |
commit | 2583535411903625da9ca664dd7548537bbbc2da |
version (container hash) | f53dc752c20f00359f831145524bf66c |
build date | 2019-02-07T15:45:22.876Z |
size (MB) | 676 |
size (bytes) | 187789343 |
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.