mbhall88/Singularity_recipes:mykrobe
$ singularity pull shub://mbhall88/Singularity_recipes:mykrobe
Singularity Recipe
Bootstrap: debootstrap
OSVersion: bionic
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
%environment
export PATH=/usr/local/bin:$PATH
export LC_ALL=C.UTF-8
export LANG=C.UTF-8
%post
apt-get update
apt-get install -y software-properties-common wget build-essential zlib1g-dev git
apt-add-repository universe
apt-get update
export LC_ALL=C.UTF-8
export LANG=C.UTF-8
# ========================
# INSTALL Mykrobe
# ========================
VERSION=0.7.0
URL=https://github.com/Mykrobe-tools/mykrobe/archive/v"$VERSION".tar.gz
apt-get install -y python3-pip mongodb
wget "$URL" -O - | tar -xzf -
cd mykrobe*
wget https://bit.ly/2H9HKTU -O - | tar -vxzf -
rm -fr src/mykrobe/data
mv mykrobe-data src/mykrobe/data
pip3 install .
# %test
pip3 install pytest
mykrobe --help
mykrobe predict --help
mykrobe variants --help
mykrobe genotype --help
cd /mykrobe*
# only run tests that dont require mongodb
pytest tests/metagenomics_tests \
tests/predict_tests \
tests/stats_tests \
tests/typer_tests
Collection
- Name: mbhall88/Singularity_recipes
- License: MIT License
View on Datalad
Metrics
key | value |
---|---|
id | /containers/mbhall88-Singularity_recipes-mykrobe |
collection name | mbhall88/Singularity_recipes |
branch | master |
tag | mykrobe |
commit | 54c141a214e113dfa7366affc7afcdcbf819508b |
version (container hash) | 09da57a12121bfa7c57cdd5183d9b815 |
build date | 2019-10-29T05:50:16.554Z |
size (MB) | 1240 |
size (bytes) | 577699871 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
Feedback
Was this page helpful?
Glad to hear it! Please tell us how we can improve.
Sorry to hear that. Please tell us how we can improve.