connor-lab/singularity-recipes:variant_calling
$ singularity pull shub://connor-lab/singularity-recipes:variant_calling
Singularity Recipe
Bootstrap: docker
From: alpine:3.8
%post
apk update
apk upgrade
apk add git make
apk add bash curl gcc bzip2-dev libc-dev ncurses-dev openjdk8-jre-base xz-dev zlib-dev
apk add python2
curl -fsSL 'https://github.com/dkoboldt/varscan/releases/download/2.4.2/VarScan.v2.4.2.jar' -o /usr/local/bin/varscan.jar
curl -fsSL 'https://github.com/samtools/samtools/archive/1.1.tar.gz' | tar -xz -C /tmp/
curl -fsSL 'https://github.com/samtools/htslib/archive/1.1.tar.gz' | tar -xz -C /tmp && mv /tmp/htslib-1.1 /tmp/htslib
cd /tmp/htslib && make
cd /tmp/samtools-1.1 && make
curl -fsSL 'https://github.com/CSB5/lofreq/blob/master/dist/lofreq_star-2.1.3.1.tar.gz?raw=true' | tar -xz -C /tmp
cd /tmp/lofreq_star-2.1.3.1 && ./configure SAMTOOLS=/tmp/samtools-1.1 HTSLIB=/tmp/htslib && make install
curl -fsSL 'https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2' | tar -xj -C /tmp/
cd /tmp/samtools-1.9 && ./configure && make && make install
curl -fsSL 'https://github.com/samtools/bcftools/releases/download/1.9/bcftools-1.9.tar.bz2' | tar -xj -C /tmp/
cd /tmp/bcftools-1.9 && ./configure && make && make install
curl -fsSL 'https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2' | tar -xj -C /tmp/
cd /tmp/htslib-1.9 && ./configure && make && make install
rm -rf /tmp/samtools* /tmp/lofreq* /tmp/htslib* /tmp/bcftools*
%labels
Maintainer m-bull
Collection
- Name: connor-lab/singularity-recipes
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/connor-lab-singularity-recipes-variant_calling |
collection name | connor-lab/singularity-recipes |
branch | master |
tag | variant_calling |
commit | df99279f62163633d6d5fb465bb1a7321fbfe67b |
version (container hash) | 0b8a4a49fee524b9d825dad112af073a |
build date | 2019-02-07T19:57:01.368Z |
size (MB) | 261 |
size (bytes) | 119250975 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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