aseetharam/mikado:latest
$ singularity pull shub://aseetharam/mikado:latest
Singularity Recipe
Bootstrap: docker
From: conda/miniconda3-centos7
%test
export PATH="/usr/local/bin:$PATH:/usr/local/conda/bin/"
python --version
python -c "import numpy"
mikado --help
%files
environment.yml /
%environment
export PYTHONDONTWRITEBYTECODE=true
%post
### Install your packages ###
export PYTHONDONTWRITEBYTECODE=true
conda env update --prune -n base -f /environment.yml && conda clean -afy
yum -y install git wget zlib1g-dev gcc gcc-c++ && yum clean all
git clone https://github.com/EI-CoreBioinformatics/mikado.git /usr/local/src/mikado
cd /usr/local/src/mikado
python3 setup.py bdist_wheel && pip install --prefix /usr/local dist/*whl
echo '#!/bin/bash' >> /usr/local/bin/show_commit_hash
chash=$(git log | head -n1 | cut -f 2 -d " ")
echo -e "echo ${chash}" >> /usr/local/bin/show_commit_hash
chmod 775 /usr/local/bin/show_commit_hash
chmod -R 775 /usr/local/src/mikado/util/*
for TOOL in /usr/local/src/mikado/util/*
do
script=$(basename ${TOOL}) && cp ${TOOL} /usr/local/bin/${script}
done
cd /usr/local/src;
rm -rf mikado;
%apprun snakemake
snakemake "@"
%apprun mikado
mikado "@"
%apprun daijin
daijin "@"
%apprun prodigal
prodigal "@"
%apprun samtools
samtools "@"
%apprun diamond
diamond "@"
Collection
- Name: aseetharam/mikado
- License: GNU Lesser General Public License v3.0
View on Datalad
Metrics
key | value |
---|---|
id | /containers/aseetharam-mikado-latest |
collection name | aseetharam/mikado |
branch | master |
tag | latest |
commit | afeb6f104f8ba655eb9fbb290a7e8a9714f563c9 |
version (container hash) | e967ae3bfaf0ad6e57998063e13f303d |
build date | 2020-10-25T10:03:18.619Z |
size (MB) | 1323.0 |
size (bytes) | 396939295 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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