nuitrcs/biobakery:latest
$ singularity pull shub://nuitrcs/biobakery:latest
Singularity Recipe
Bootstrap: docker
From: biobakery/biobakery
%setup
%post
apt-get update
apt-get install -y wget git locales
#MC issue with locale (LC_ALL, LANGUAGE), to get it right:
locale-gen "en_US.UTF-8"
dpkg-reconfigure locales
export LANGUAGE="en_US.UTF-8"
echo 'LANGUAGE="en_US.UTF-8"' >> /etc/default/locale
echo 'LC_ALL="en_US.UTF-8"' >> /etc/default/locale
# install USEARCH. See https://github.com/CHPC-UofU/Singularity-bioBakery/blob/master/Singularity.
# TODO: change license
USEARCH_URL="https://drive5.com/cgi-bin/upload3.py?license=2018091412560519949"
wget -O /usr/local/bin/usearch $USEARCH_URL
chmod 111 /usr/local/bin/usearch
# install missing biobakery tools not installed in the biobakery/biobakery Docker image
# Note: `brew install metaphlan2` fails on biom package install (gcc compiler issue; not remedied by installing gcc-5)
pip install numpy
pip install pandas biopython scipy matplotlib h5py biom-format
cd /opt
curl https://bitbucket.org/biobakery/metaphlan2/get/default.zip --output metaphlan2.zip
unzip metaphlan2.zip
cd biobakery-metaphlan2-*
chmod 755 /home/linuxbrew
cd /opt
wget http://github.com/bbuchfink/diamond/releases/download/v0.9.22/diamond-linux64.tar.gz
tar xzf diamond-linux64.tar.gz
echo 'export PATH=/opt:$PATH:/home/linuxbrew/.linuxbrew/bin:$(pwd):$(pwd)/utils' >> $SINGULARITY_ENVIRONMENT
%test
export PATH=/opt:/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/bin:/usr/local/sbin:/home/linuxbrew/.linuxbrew/bin:/opt/biobakery-metaphlan2-*:/opt/biobakery-metaphlan2-*/utils
mkdir ~/test_output
# graphlan tests
graphlan_annotate.py /opt/hmptree.xml ~/test_output/hmptree.annot.xml --annot /opt/annot.txt
# humann2 tests
humann2_test
# kneaddata tests
kneaddata -i /home/linuxbrew/.linuxbrew/Cellar/kneaddata/0.6.1/libexec/lib/python2.7/site-packages/kneaddata/tests/data/demo.fastq --output ~/test_output/kneaddata_output
# halla tests
halla -X /opt/X_16_100.txt -Y /opt/Y_16_100.txt --output ~/test_output/halla_output
# ppanini tests
# note: ppanini has "unittest.loader.ModuleImportFailure" tests that are designed to fail, I think for compatitibility purposes?
ppanini_test
# shortbred tests
shortbred_identify.py --goi /home/linuxbrew/.linuxbrew/Cellar/biobakery_demos/1.6/libexec/lib/python2.7/site-packages/biobakery_demos/data/shortbred/input/input_prots.faa --ref /home/linuxbrew/.linuxbrew/Cellar/biobakery_demos/1.6/libexec/lib/python2.7/site-packages/biobakery_demos/data/shortbred/input/ref_prots.faa --markers mytestmarkers.faa --tmp ~/test_output/shortbred_output
# (shortbred clean up)
rm mytestmarkers.faa
# metaphlan tests
mkdir ~/test_output/metaphlan2_output
cd ~/test_output/metaphlan2_output
curl -O https://bitbucket.org/biobakery/biobakery/raw/tip/demos/biobakery_demos/data/metaphlan2/input/SRS014476-Supragingival_plaque.fasta.gz
metaphlan2.py SRS014476-Supragingival_plaque.fasta.gz --input_type fasta > SRS014476-Supragingival_plaque_profile.txt
# (clean up from tests)
cd ~
rm -rf ~/test_output
%files
singularity_logo.txt /opt
test_files/annot.txt /opt
test_files/hmptree.xml /opt
test_files/X_16_100.txt /opt
test_files/Y_16_100.txt /opt
%runscript
cat /opt/singularity_logo.txt
%environment
Collection
- Name: nuitrcs/biobakery
- License: MIT License
View on Datalad
Metrics
key | value |
---|---|
id | /containers/nuitrcs-biobakery-latest |
collection name | nuitrcs/biobakery |
branch | master |
tag | latest |
commit | 4bcf87dda7ebd777c361036f25c192a35fdee31e |
version (container hash) | 9e29950e4a08359f000dfb6ccb4a555b |
build date | 2021-01-29T17:33:21.612Z |
size (MB) | 11524 |
size (bytes) | 5632598047 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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