[med-svn] r18830 - in trunk/packages/seqprep/trunk/debian: . tests
Andreas Tille
tille at moszumanska.debian.org
Fri Feb 20 14:35:03 UTC 2015
Author: tille
Date: 2015-02-20 14:35:03 +0000 (Fri, 20 Feb 2015)
New Revision: 18830
Added:
trunk/packages/seqprep/trunk/debian/README.test
trunk/packages/seqprep/trunk/debian/seqprep-data.docs
trunk/packages/seqprep/trunk/debian/seqprep-data.install
trunk/packages/seqprep/trunk/debian/seqprep.docs
trunk/packages/seqprep/trunk/debian/seqprep.install
trunk/packages/seqprep/trunk/debian/seqprep.manpages
trunk/packages/seqprep/trunk/debian/tests/
trunk/packages/seqprep/trunk/debian/tests/control
trunk/packages/seqprep/trunk/debian/tests/run-unit-test
Removed:
trunk/packages/seqprep/trunk/debian/docs
trunk/packages/seqprep/trunk/debian/install
trunk/packages/seqprep/trunk/debian/manpages
Modified:
trunk/packages/seqprep/trunk/debian/changelog
trunk/packages/seqprep/trunk/debian/control
trunk/packages/seqprep/trunk/debian/rules
Log:
Add autopkgtest
Added: trunk/packages/seqprep/trunk/debian/README.test
===================================================================
--- trunk/packages/seqprep/trunk/debian/README.test (rev 0)
+++ trunk/packages/seqprep/trunk/debian/README.test 2015-02-20 14:35:03 UTC (rev 18830)
@@ -0,0 +1,9 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+To run the unit tests for vsearch you need to install the data provided
+in vsearch-data. After installing this package simply run
+
+ sh run-unit-test
+
+in this directory.
Modified: trunk/packages/seqprep/trunk/debian/changelog
===================================================================
--- trunk/packages/seqprep/trunk/debian/changelog 2015-02-20 13:45:33 UTC (rev 18829)
+++ trunk/packages/seqprep/trunk/debian/changelog 2015-02-20 14:35:03 UTC (rev 18830)
@@ -1,7 +1,8 @@
seqprep (1.1-1) UNRELEASED; urgency=medium
* Initial Upload to Debian
-
+ Closes: #778838
+
-- Andreas Tille <tille at debian.org> Fri, 20 Feb 2015 13:49:15 +0100
seqprep (1.1-0biolinux1) trusty; urgency=medium
Modified: trunk/packages/seqprep/trunk/debian/control
===================================================================
--- trunk/packages/seqprep/trunk/debian/control 2015-02-20 13:45:33 UTC (rev 18829)
+++ trunk/packages/seqprep/trunk/debian/control 2015-02-20 14:35:03 UTC (rev 18830)
@@ -6,6 +6,7 @@
Priority: optional
Build-Depends: debhelper (>= 9),
python,
+ python-markdown,
ruby-ronn,
zlib1g-dev
Standards-Version: 3.9.6
@@ -29,3 +30,25 @@
It is always safest though to save the overlapping procedure for libraries
where you have some prior knowledge that a significant portion of the reads
will have some overlap.
+
+Package: seqprep-data
+Architecture: all
+Priority: extra
+Depends: ${misc:Depends},
+ seqprep
+Description: example data set for seqprep - only used for testing
+ SeqPrep is a program to merge paired end Illumina reads that are overlapping
+ into a single longer read. It may also just be used for its adapter trimming
+ feature without doing any paired end overlap. When an adapter sequence is
+ present, that means that the two reads must overlap (in most cases) so they
+ are forcefully merged. When reads do not have adapter sequence they must be
+ treated with care when doing the merging, so a much more specific approach is
+ taken. The default parameters were chosen with specificity in mind, so that
+ they could be ran on libraries where very few reads are expected to overlap.
+ It is always safest though to save the overlapping procedure for libraries
+ where you have some prior knowledge that a significant portion of the reads
+ will have some overlap.
+ .
+ This package is not needed for normal operation of seqprep. It simply
+ serves some test data as well as a test script.
+
Deleted: trunk/packages/seqprep/trunk/debian/docs
===================================================================
--- trunk/packages/seqprep/trunk/debian/docs 2015-02-20 13:45:33 UTC (rev 18829)
+++ trunk/packages/seqprep/trunk/debian/docs 2015-02-20 14:35:03 UTC (rev 18830)
@@ -1 +0,0 @@
-README.md
Deleted: trunk/packages/seqprep/trunk/debian/install
===================================================================
--- trunk/packages/seqprep/trunk/debian/install 2015-02-20 13:45:33 UTC (rev 18829)
+++ trunk/packages/seqprep/trunk/debian/install 2015-02-20 14:35:03 UTC (rev 18830)
@@ -1 +0,0 @@
-seqprep /usr/bin
Deleted: trunk/packages/seqprep/trunk/debian/manpages
===================================================================
--- trunk/packages/seqprep/trunk/debian/manpages 2015-02-20 13:45:33 UTC (rev 18829)
+++ trunk/packages/seqprep/trunk/debian/manpages 2015-02-20 14:35:03 UTC (rev 18830)
@@ -1 +0,0 @@
-debian/*.1
Modified: trunk/packages/seqprep/trunk/debian/rules
===================================================================
--- trunk/packages/seqprep/trunk/debian/rules 2015-02-20 13:45:33 UTC (rev 18829)
+++ trunk/packages/seqprep/trunk/debian/rules 2015-02-20 14:35:03 UTC (rev 18830)
@@ -8,11 +8,11 @@
dh_auto_build
cp SeqPrep seqprep
ronn -r --manual=seqprep --organization='Cancer Therapeutics Innovation Group' debian/seqprep.1.ronn
+ markdown_py -f README.html README.md
override_dh_clean:
dh_clean
rm -f seqprep
- rm -rf Test/info Test/out
rm -f debian/*.1
override_dh_auto_test:
@@ -20,3 +20,10 @@
cd Test && mkdir -p out info && \
bash -xc 'gzcat(){ zcat "$$@" ; } ; . RUNTEST.sh'
[ `cat Test/info/pe_*.txt | md5sum | cut -b -10` = 8bc8e0787e ]
+ # remove output dirs right after testing to make sure the files
+ # will not be included in the data package
+ rm -rf Test/info Test/out
+
+override_dh_install:
+ dh_install
+ sed -i 's#../SeqPrep#/usr/bin/seqprep#' $(CURDIR)/debian/seqprep-data/usr/share/doc/seqprep/examples/RUNTEST.sh
Added: trunk/packages/seqprep/trunk/debian/seqprep-data.docs
===================================================================
--- trunk/packages/seqprep/trunk/debian/seqprep-data.docs (rev 0)
+++ trunk/packages/seqprep/trunk/debian/seqprep-data.docs 2015-02-20 14:35:03 UTC (rev 18830)
@@ -0,0 +1,2 @@
+debian/README.test
+debian/tests/run-unit-test
Added: trunk/packages/seqprep/trunk/debian/seqprep-data.install
===================================================================
--- trunk/packages/seqprep/trunk/debian/seqprep-data.install (rev 0)
+++ trunk/packages/seqprep/trunk/debian/seqprep-data.install 2015-02-20 14:35:03 UTC (rev 18830)
@@ -0,0 +1 @@
+Test/* usr/share/doc/seqprep/examples
Added: trunk/packages/seqprep/trunk/debian/seqprep.docs
===================================================================
--- trunk/packages/seqprep/trunk/debian/seqprep.docs (rev 0)
+++ trunk/packages/seqprep/trunk/debian/seqprep.docs 2015-02-20 14:35:03 UTC (rev 18830)
@@ -0,0 +1 @@
+README.html
Added: trunk/packages/seqprep/trunk/debian/seqprep.install
===================================================================
--- trunk/packages/seqprep/trunk/debian/seqprep.install (rev 0)
+++ trunk/packages/seqprep/trunk/debian/seqprep.install 2015-02-20 14:35:03 UTC (rev 18830)
@@ -0,0 +1 @@
+seqprep /usr/bin
Added: trunk/packages/seqprep/trunk/debian/seqprep.manpages
===================================================================
--- trunk/packages/seqprep/trunk/debian/seqprep.manpages (rev 0)
+++ trunk/packages/seqprep/trunk/debian/seqprep.manpages 2015-02-20 14:35:03 UTC (rev 18830)
@@ -0,0 +1 @@
+debian/*.1
Added: trunk/packages/seqprep/trunk/debian/tests/control
===================================================================
--- trunk/packages/seqprep/trunk/debian/tests/control (rev 0)
+++ trunk/packages/seqprep/trunk/debian/tests/control 2015-02-20 14:35:03 UTC (rev 18830)
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
Added: trunk/packages/seqprep/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/seqprep/trunk/debian/tests/run-unit-test (rev 0)
+++ trunk/packages/seqprep/trunk/debian/tests/run-unit-test 2015-02-20 14:35:03 UTC (rev 18830)
@@ -0,0 +1,19 @@
+#!/bin/sh -e
+
+pkg=seqprep
+if [ "$ADTTMP" = "" ] ; then
+ ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+cp -a /usr/share/doc/${pkg}/examples/* .
+# sed -i 's#../SeqPrep#/usr/bin/seqprep#' RUNTEST.sh
+mkdir -p out info && \
+bash -xc 'gzcat(){ zcat "$@" ; } ; . RUNTEST.sh'
+if [ `cat info/pe_*.txt | md5sum | cut -b -10` = 8bc8e0787e ] ; then
+ echo "Test OK"
+else
+ echo "Test failed"
+ exit 1
+fi
+
+rm -f $ADTTMP/*
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