[med-svn] [Git][med-team/gasic][master] 4 commits: Add autopkgtest template

[Pranav Ballaney]

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 <ballaneypranav at gmail.com>  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 <ballaneypranav at gmail.com> for the tests.
\ No newline at end of file


=====================================
debian/tests/data/genomes/dwv.fasta-e.gz
=====================================
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=====================================
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

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