[med-svn] [Git][med-team/jaligner][master] 5 commits: Install example and reference data

[Pranav Ballaney]

Pranav Ballaney pushed to branch master at Debian Med / jaligner


Commits:
36fe8b76 by Pranav Ballaney at 2020-07-03T08:12:49+05:30
Install example and reference data

- - - - -
a1f25fdf by Pranav Ballaney at 2020-07-03T08:16:30+05:30
Install docs

- - - - -
4cce27a5 by Pranav Ballaney at 2020-07-03T08:16:36+05:30
Add autopkgtests

- - - - -
ead4e864 by Pranav Ballaney at 2020-07-03T08:17:02+05:30
Add Pranav Ballaney to Uploaders

- - - - -
01a98951 by Pranav Ballaney at 2020-07-03T08:19:54+05:30
Include reference binary

- - - - -


9 changed files:

- + debian/README.test
- debian/control
- + debian/docs
- + debian/examples
- debian/source/include-binaries
- + debian/tests/README.test_data
- + debian/tests/control
- + debian/tests/references.tar.xz
- + 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/control
=====================================
@@ -1,7 +1,8 @@
 Source: jaligner
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Tim Booth <tbooth at ceh.ac.uk>,
-           Michael R. Crusoe <michael.crusoe at gmail.com>
+           Michael R. Crusoe <michael.crusoe at gmail.com>,
+           Pranav Ballaney <ballaneypranav at gmail.com>
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 11~),


=====================================
debian/docs
=====================================
@@ -0,0 +1,4 @@
+README*
+debian/README*
+debian/tests/README*
+debian/tests/run-unit-test
\ No newline at end of file


=====================================
debian/examples
=====================================
@@ -0,0 +1,2 @@
+src/jaligner/example/sequences/*
+debian/tests/reference*
\ No newline at end of file


=====================================
debian/source/include-binaries
=====================================
@@ -7,3 +7,4 @@ debian/images/open.gif
 debian/images/paste.gif
 debian/images/print.gif
 debian/images/save.gif
+debian/tests/references.tar.xz
\ No newline at end of file


=====================================
debian/tests/README.test_data
=====================================
@@ -0,0 +1,3 @@
+references.tar.xz contains output files produced by running jaligner on 
+p53_human and p53_mouse, which come with the jaligner package. 
+The jaligner command is provided in run-unit-test.
\ No newline at end of file


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


=====================================
debian/tests/references.tar.xz
=====================================
Binary files /dev/null and b/debian/tests/references.tar.xz differ


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,29 @@
+#!/bin/bash
+set -e
+
+pkg=jaligner
+
+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 *
+tar -xf references.tar.xz
+ls  -R
+#do_stuff_to_test_package#
+matrices=$(ls /usr/share/jaligner/jaligner/matrix/matrices)
+
+for matrix in $matrices;
+do
+    jaligner p53_human.fasta p53_mouse.fasta ${matrix} 10 0.5 > result.${matrix}.txt
+    diff reference.${matrix}.txt result.${matrix}.txt
+done



View it on GitLab: https://salsa.debian.org/med-team/jaligner/-/compare/ef763cb7d2ae2ab81acf0f9d25e5516f1f098358...01a98951682a3f5f013daa2a8723b74f89b1cb45

-- 
View it on GitLab: https://salsa.debian.org/med-team/jaligner/-/compare/ef763cb7d2ae2ab81acf0f9d25e5516f1f098358...01a98951682a3f5f013daa2a8723b74f89b1cb45
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