ffineis/nurcs-singularity:biobakery

$ singularity pull shub://ffineis/nurcs-singularity:biobakery

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=2018080115480830195"
	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-*
	echo 'export PATH='$PATH:/home/linuxbrew/.linuxbrew/bin:$(pwd):$(pwd)/utils >> $SINGULARITY_ENVIRONMENT
	chmod 755 /home/linuxbrew

%test

	export PATH=/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: ffineis/nurcs-singularity
• License: None

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