[med-svn] [Git][med-team/nanook][master] 3 commits: Add test and reference data

[Pranav Ballaney]

Pranav Ballaney pushed to branch master at Debian Med / nanook


Commits:
54ed425d by Pranav Ballaney at 2020-06-28T04:53:02+05:30
Add test and reference data

- - - - -
59b3abc6 by Pranav Ballaney at 2020-06-28T04:53:25+05:30
Add autopkgtests

- - - - -
a76719c5 by Pranav Ballaney at 2020-06-28T04:53:57+05:30
Install docs

- - - - -


9 changed files:

- + debian/README.test
- debian/changelog
- + debian/docs
- + debian/examples
- + debian/tests/README.test_data
- + debian/tests/control
- + debian/tests/data.tar.gz
- + debian/tests/ref.tar.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 +1,18 @@
+nanook (1.33+dfsg-2) UNRELEASED; urgency=medium
+
+  [ Hervé Ménager ]
+  * correct bio.tools and scicrunch refs
+
+  [ Steffen Moeller ]
+  * d/u/metadata: yamllint
+
+  [ Pranav Ballaney ]
+  * Add test and reference data
+  * Add autopkgtests
+  * Install docs
+
+ -- Pranav Ballaney <ballaneypranav at gmail.com>  Sun, 28 Jun 2020 04:53:32 +0530
+
 nanook (1.33+dfsg-1) unstable; urgency=medium
 
   * New upstream version


=====================================
debian/docs
=====================================
@@ -0,0 +1,4 @@
+README.md
+debian/README*
+debian/tests/run-unit-test
+debian/tests/README*


=====================================
debian/examples
=====================================
@@ -0,0 +1 @@
+debian/tests/*
\ No newline at end of file


=====================================
debian/tests/README.test_data
=====================================
@@ -0,0 +1,5 @@
+data.tar.gz is a subset of the data available at 
+https://opendata.earlham.ac.uk/opendata/nanook/nanook_ecoli_500.tar.gz
+
+ref.tar.gz contains results obtained by processing this data as described at
+https://nanook.readthedocs.io/en/latest/tutorial.html
\ No newline at end of file


=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr


=====================================
debian/tests/data.tar.gz
=====================================
Binary files /dev/null and b/debian/tests/data.tar.gz differ


=====================================
debian/tests/ref.tar.gz
=====================================
Binary files /dev/null and b/debian/tests/ref.tar.gz differ


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,35 @@
+#!/bin/bash
+set -e
+
+pkg=nanook
+
+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}"
+
+tar xf data.tar.gz
+tar xf ref.tar.gz
+#do_stuff_to_test_package#
+cd data/nanook_ecoli_500/references
+lastdb -Q 0 ecoli_dh10b_cs ecoli_dh10b_cs.fasta
+cd ..
+nanook extract -s N79596_dh10b_8kb_11022015
+nanook align -s N79596_dh10b_8kb_11022015 -r references/ecoli_dh10b_cs.fasta
+nanook analyse -s N79596_dh10b_8kb_11022015 -r references/ecoli_dh10b_cs.fasta -passonly
+
+cd ../..
+for file in ref/*; do
+  if [[ -f $file ]]; then
+    output=data${file#ref}
+    diff $file $output
+  fi
+done



View it on GitLab: https://salsa.debian.org/med-team/nanook/-/compare/bc7d23084567260e3f9bc5c74724cbb5c3060948...a76719c53704128eb1d149d16c857844a5be8490

-- 
View it on GitLab: https://salsa.debian.org/med-team/nanook/-/compare/bc7d23084567260e3f9bc5c74724cbb5c3060948...a76719c53704128eb1d149d16c857844a5be8490
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200627/1db001dc/attachment-0001.html>