[med-svn] [Git][med-team/macs][master] Added a new test directory for autopkgtest along with some sample data

[Aikaterini Kalou]

Aikaterini Kalou pushed to branch master at Debian Med / macs


Commits:
2cc4ef8c by kkalou-guest at 2018-02-19T00:14:51+02:00
Added a new test directory for autopkgtest along with some sample data

- - - - -


7 changed files:

- + README.test
- + debian/examples/aluY.chr1.bed
- + debian/examples/gerp.chr1.bed
- + debian/macs-example-data.install
- + debian/macs.examples
- + debian/tests/control
- + debian/tests/run-unit-test


Changes:

=====================================
README.test
=====================================
--- /dev/null
+++ b/README.test
@@ -0,0 +1,12 @@
+otes on how this package can be tested.
+
+
+This package can be tested by executing
+
+   sh run-unit-test
+
+in order to confirm its integrity.
+
+Notes : the sample data are recovered from; https://github.com/arq5x/  They are both ‘.BED’ 
+file extensions. However the macs package install instructions is
+using the ‘BAM’ extension format. If anyone has any recommendation on where to find sample data in this format it will be much appreciated :)


=====================================
debian/examples/aluY.chr1.bed
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/examples/gerp.chr1.bed
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/macs-example-data.install
=====================================
--- /dev/null
+++ b/debian/macs-example-data.install
@@ -0,0 +1,4 @@
+debian/examples/aluY.chr1.bed	usr/share/doc/macs/examples
+debian/examples/gerp.chr1.bed	usr/share/doc/macs/examples
+debian/README.test		usr/share/doc/macs
+debian/tests/run-unit-test	usr/share/doc/macs


=====================================
debian/macs.examples
=====================================
--- /dev/null
+++ b/debian/macs.examples
@@ -0,0 +1,3 @@
+examples/*
+debian/examples/*
+release/common/*.tree


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


=====================================
debian/tests/run-unit-test
=====================================
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,18 @@
+#!/bin/bash
+set -e
+set -x
+
+pkg="macs"
+
+
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+  trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP
+
+cd $AUTOPKGTEST_TMP
+
+macs2 callpeak -t aluY.chr1.bed --nomodel -g hs -n test -B -q 0.01
+macs2 callpeak -t gerp.chr1.bed --nomodel --broad -g hs --broad-cutoff 0.1



View it on GitLab: https://salsa.debian.org/med-team/macs/commit/2cc4ef8c16c90241faae96bb59042278d910b357

---
View it on GitLab: https://salsa.debian.org/med-team/macs/commit/2cc4ef8c16c90241faae96bb59042278d910b357
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