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


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
We cannot guarantee that all containers will still exist on GitHub.