iferres/Singularity_recipes:panx
$ singularity pull shub://iferres/Singularity_recipes:panx
Singularity Recipe
Bootstrap: docker
From: ubuntu:16.04
%post
apt update
apt install -y wget bzip2 git
#install conda
wget https://repo.continuum.io/miniconda/Miniconda2-4.5.12-Linux-x86_64.sh -O /opt/miniconda.sh
bash /opt/miniconda.sh -b -p /opt/miniconda
export PATH="/opt/miniconda/bin:$PATH"
conda config --add channels bioconda
#install panx
git clone https://github.com/neherlab/pan-genome-analysis.git
cd pan-genome-analysis
git checkout 4684a0becb450cf7cc8fede9a02c2193bc41801e
conda install python=2.7.13 python-dateutil>=2.5.0 biopython numpy scipy pandas ete2 diamond fasttree mafft mcl raxml treetime
#conda env create -f panX-environment.yml
#~/miniconda2/bin/conda env create -f panX-environment.yml
#source activate panX
%runscript
#export PATH=/root/miniconda2/bin/:$PATH
#. activate panX && /pan-genome-analysis/panX.py
/pan-genome-analysis/panX.py "$@"
%environment
export PATH="/opt/miniconda/bin:$PATH"
Collection
- Name: iferres/Singularity_recipes
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/iferres-Singularity_recipes-panx |
collection name | iferres/Singularity_recipes |
branch | master |
tag | panx |
commit | 0ce3b25e13f331f88b5441bc2aa8e441193c13d1 |
version (container hash) | 5bfbcf39482daa689cd33c1a7a11175a |
build date | 2019-10-18T09:36:42.529Z |
size (MB) | 4036 |
size (bytes) | 1830215711 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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