maxemil/PhyloMagnet:latest
$ singularity pull shub://maxemil/PhyloMagnet:latest
Singularity Recipe
Bootstrap:docker
From:continuumio/miniconda3:4.6.14
%labels
MAINTAINER Max Emil Schön <max-emil.schon@icm.uu.se>
DESCRIPTION Singularity image containing all requirements for the PhyloMagnet pipeline
VERSION 0.7
%environment
PATH=/opt/conda/envs/PhyloMagnet-0.7/bin:$PATH
export PATH
%files
environment.yml /
%post
apt-get update
apt-get install -y procps libxtst6
apt-get clean -y
####### parapa #########
cd /usr/local/bin
wget https://cme.h-its.org/exelixis/resource/download/software/papara_nt-2.5-static_x86_64.tar.gz
tar -xvf papara_nt-2.5-static_x86_64.tar.gz
rm papara_nt-2.5-static_x86_64.tar.gz
mv papara_static_x86_64 papara
/opt/conda/bin/conda env create -f /environment.yml
/opt/conda/bin/conda clean -a
%test
VERSION="0.7"
/opt/conda/envs/PhyloMagnet-$VERSION/opt/megan-6.12.3/tools/daa-meganizer -h
/opt/conda/envs/PhyloMagnet-$VERSION/opt/megan-6.12.3/tools/gc-assembler -h
/opt/conda/envs/PhyloMagnet-$VERSION/bin/trimal --version
/opt/conda/envs/PhyloMagnet-$VERSION/bin/mafft --version
/opt/conda/envs/PhyloMagnet-$VERSION/bin/diamond version
/opt/conda/envs/PhyloMagnet-$VERSION/bin/fastq-dump --version
which /opt/conda/envs/PhyloMagnet-$VERSION/bin/FastTree
/opt/conda/envs/PhyloMagnet-$VERSION/bin/iqtree -h
/opt/conda/envs/PhyloMagnet-$VERSION/bin/python3 --version
/opt/conda/envs/PhyloMagnet-$VERSION/bin/raxml-ng -version
/opt/conda/envs/PhyloMagnet-$VERSION/bin/epa-ng --version
/opt/conda/envs/PhyloMagnet-$VERSION/bin/gappa --help
/opt/conda/envs/PhyloMagnet-$VERSION/bin/prank -version
/opt/conda/envs/PhyloMagnet-$VERSION/bin/python3 -c "import ete3"
/usr/local/bin/papara
Collection
- Name: maxemil/PhyloMagnet
- License: Other
View on Datalad
Metrics
key | value |
---|---|
id | /containers/maxemil-PhyloMagnet-latest |
collection name | maxemil/PhyloMagnet |
branch | master |
tag | latest |
commit | c742de49e22fb820924d6b32311b501f6ab47d27 |
version (container hash) | 33bf1df183c46c2464fa00cfdd8b2fde |
build date | 2021-04-07T12:42:12.051Z |
size (MB) | 3042.0 |
size (bytes) | 974110751 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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