connor-lab/singularity-recipes:mykrobe-atlas
$ singularity pull shub://connor-lab/singularity-recipes:mykrobe-atlas
Singularity Recipe
Bootstrap: docker
From: centos:latest
%post
yum -y update
yum -y install epel-release
yum -y install gcc gcc-c++ git make wget zlib-devel
yum -y install python34 python34-devel python34-pip
curl -fsSL 'https://repo.mongodb.org/yum/redhat/mongodb-org-3.0.repo' -o /etc/yum.repos.d/mongodb-org-3.0.repo
yum install -y mongodb-org
cd /usr/local/bin
git clone --recursive -b geno_kmer_count https://github.com/phelimb/mccortex mccortex-geno_kmer_count
cd mccortex-geno_kmer_count && make clean && make
ln -s /usr/local/bin/mccortex-geno_kmer_count/bin/mccortex31 /usr/local/bin/
cd /usr/local/bin
git clone https://github.com/Mykrobe-tools/mykrobe-atlas-cli.git mykrobe-latest
cd mykrobe-latest
wget -O mykrobe-data.tar.gz http://s3.climb.ac.uk/mykrobe/mykrobe-data.tgz && tar -zxvf mykrobe-data.tar.gz && rm -fr src/mykrobe/data && mv mykrobe-data src/mykrobe/data
pip3.4 install .
curl -fsSL 'https://raw.githubusercontent.com/iqbal-lab/Mykrobe-predictor/master/scripts/json_to_tsv.py' -o /usr/local/bin/json_to_tsv.py
chmod +x /usr/local/bin/json_to_tsv.py
ln -s /usr/local/bin/mccortex31 /usr/bin/
%labels
Maintainer m-bull
Version mykrobe-atlas-latest
Collection
- Name: connor-lab/singularity-recipes
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/connor-lab-singularity-recipes-mykrobe-atlas |
collection name | connor-lab/singularity-recipes |
branch | master |
tag | mykrobe-atlas |
commit | d5710c095065a9aa78f89c03835bd96ff0ae8d01 |
version (container hash) | 5dce8dfe995489ef77b0ffa74bed2cb4 |
build date | 2019-06-17T19:35:29.690Z |
size (MB) | 1006 |
size (bytes) | 409239583 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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