Pranav Ballaney pushed to branch master at Debian Med / gasic
Commits: a1b7dda5 by Pranav Ballaney at 2020-05-09T04:36:57+05:30 Add autopkgtest template - - - - - a54f060c by Pranav Ballaney at 2020-05-10T02:50:12+05:30 Install examples - - - - - 507482db by Pranav Ballaney at 2020-05-10T02:50:28+05:30 Add autopkgtests - - - - - d72532ed by Pranav Ballaney at 2020-05-10T02:53:33+05:30 Install docs and update changelog - - - - - 18 changed files: - + debian/README.test - debian/changelog - debian/docs - debian/examples - + debian/tests/control - + debian/tests/data/README.test_data - + debian/tests/data/genomes/dwv.fasta-e.gz - + debian/tests/data/genomes/dwv.fasta.fai.gz - + debian/tests/data/genomes/dwv.fasta.gz - + debian/tests/data/genomes/vdv-1-dwv-5.fasta.fai.gz - + debian/tests/data/genomes/vdv-1-dwv-9.fasta.fai.gz - + debian/tests/data/genomes/vdv1.fasta.fai.gz - + debian/tests/data/genomes/vdv1.fasta.gz - + debian/tests/data/genomes/vdv1dwv5.fasta.gz - + debian/tests/data/genomes/vdv1dwv9.fasta.gz - + debian/tests/data/names.gz - + debian/tests/data/reads/SRR059298_subset.fastq.gz - + debian/tests/run-unit-test Changes: ===================================== debian/README.test ===================================== @@ -0,0 +1,8 @@ +Notes on how this package can be tested. +──────────────────────────────────────── + +This package can be tested by running the provided test: + + sh run-unit-test + +in order to confirm its integrity. ===================================== debian/changelog ===================================== @@ -1,3 +1,14 @@ +gasic (0.0.r19-6) UNRELEASED; urgency=medium + + [ Steffen Moeller ] + * d/u/metadata: fixed yaml + + [ Pranav Ballaney ] + * Install examples + * Add autopkgtests + + -- Pranav Ballaney <[email protected]> Sun, 10 May 2020 02:52:45 +0530 + gasic (0.0.r19-5) unstable; urgency=medium * Use 2to3 to port to Python3 ===================================== debian/docs ===================================== @@ -1,2 +1,5 @@ doc/MANUAL README +debian/README.test +debian/tests/data/README.test_data +debian/tests/run-unit-test \ No newline at end of file ===================================== debian/examples ===================================== @@ -1,2 +1,3 @@ doc/example_script.py debian/README.example +debian/tests/data/* \ No newline at end of file ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr ===================================== debian/tests/data/README.test_data ===================================== @@ -0,0 +1,10 @@ +Files: genomes/* +Source: https://github.com/seqan/knime_seqan_workflows/blob/master/metagenomics_gasic_workflow/bee_example.zip + +Files: reads/* +Source: https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR059298 +The file SRR059298_subset.fastq contains the first 400000 lines +from the fastq file obtained from the above source. + +Files: names +This was written by Pranav Ballaney <[email protected]> for the tests. \ No newline at end of file ===================================== debian/tests/data/genomes/dwv.fasta-e.gz ===================================== Binary files /dev/null and b/debian/tests/data/genomes/dwv.fasta-e.gz differ ===================================== debian/tests/data/genomes/dwv.fasta.fai.gz ===================================== Binary files /dev/null and b/debian/tests/data/genomes/dwv.fasta.fai.gz differ ===================================== debian/tests/data/genomes/dwv.fasta.gz ===================================== Binary files /dev/null and b/debian/tests/data/genomes/dwv.fasta.gz differ ===================================== debian/tests/data/genomes/vdv-1-dwv-5.fasta.fai.gz ===================================== Binary files /dev/null and b/debian/tests/data/genomes/vdv-1-dwv-5.fasta.fai.gz differ ===================================== debian/tests/data/genomes/vdv-1-dwv-9.fasta.fai.gz ===================================== Binary files /dev/null and b/debian/tests/data/genomes/vdv-1-dwv-9.fasta.fai.gz differ ===================================== debian/tests/data/genomes/vdv1.fasta.fai.gz ===================================== Binary files /dev/null and b/debian/tests/data/genomes/vdv1.fasta.fai.gz differ ===================================== debian/tests/data/genomes/vdv1.fasta.gz ===================================== Binary files /dev/null and b/debian/tests/data/genomes/vdv1.fasta.gz differ ===================================== debian/tests/data/genomes/vdv1dwv5.fasta.gz ===================================== Binary files /dev/null and b/debian/tests/data/genomes/vdv1dwv5.fasta.gz differ ===================================== debian/tests/data/genomes/vdv1dwv9.fasta.gz ===================================== Binary files /dev/null and b/debian/tests/data/genomes/vdv1dwv9.fasta.gz differ ===================================== debian/tests/data/names.gz ===================================== Binary files /dev/null and b/debian/tests/data/names.gz differ ===================================== debian/tests/data/reads/SRR059298_subset.fastq.gz ===================================== Binary files /dev/null and b/debian/tests/data/reads/SRR059298_subset.fastq.gz differ ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,30 @@ +#!/bin/bash +set -e + +pkg=gasic + +export LC_ALL=C.UTF-8 +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + # Double quote below to expand the temporary directory variable now versus + # later is on purpose. + # shellcheck disable=SC2064 + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}" + +cd "${AUTOPKGTEST_TMP}" + +gunzip -r * + +cd genomes + +bowtie-build dwv.fasta dwv.fasta +bowtie-build vdv1.fasta vdv1.fasta +bowtie-build vdv1dwv9.fasta vdv1dwv9.fasta +bowtie-build vdv1dwv5.fasta vdv1dwv5.fasta + +cd .. + +run_mappers names reads/SRR059298_subset.fastq -i ./genomes/%s.fasta -o ./SAM/mapped_%s.sam -m bowtie View it on GitLab: https://salsa.debian.org/med-team/gasic/-/compare/22206cfd7982de4ab38e1bc947ee38bcf68657ba...d72532ed7b70713f43233bc7b2087b6b622507b5 -- View it on GitLab: https://salsa.debian.org/med-team/gasic/-/compare/22206cfd7982de4ab38e1bc947ee38bcf68657ba...d72532ed7b70713f43233bc7b2087b6b622507b5 You're receiving this email because of your account on salsa.debian.org.
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