[med-svn] [eagle] 01/01: Remove the test which creates a false positive in the autopkgtest by emitting some warnings. (Closes: #842356)
Dylan Aïssi
bob.dybian-guest at moszumanska.debian.org
Sun Oct 30 23:06:56 UTC 2016
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bob.dybian-guest pushed a commit to branch master
in repository eagle.
commit 9d1f5e632b89ea69b348327bc7a30973f82acbbc
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date: Sun Oct 30 23:30:59 2016 +0100
Remove the test which creates a false positive in the autopkgtest by emitting some warnings. (Closes: #842356)
---
debian/bio-eagle-examples.install | 2 +-
debian/changelog | 7 +++++++
debian/rules | 5 -----
debian/tests/run-sample-analysis | 15 ++++++---------
4 files changed, 14 insertions(+), 15 deletions(-)
diff --git a/debian/bio-eagle-examples.install b/debian/bio-eagle-examples.install
index 784167d..4e0822b 100644
--- a/debian/bio-eagle-examples.install
+++ b/debian/bio-eagle-examples.install
@@ -1,2 +1,2 @@
-example/examples.tar.xz /usr/share/doc/bio-eagle/examples/
+example/* /usr/share/doc/bio-eagle/examples/
tables /usr/share/doc/bio-eagle/examples/
diff --git a/debian/changelog b/debian/changelog
index 5c786bb..dce74ca 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+bio-eagle (2.3-3) unstable; urgency=medium
+
+ * Remove the test which creates a false positive in the autopkgtest
+ by emitting some warnings. (Closes: #842356)
+
+ -- Dylan Aïssi <bob.dybian at gmail.com> Sun, 30 Oct 2016 23:26:33 +0100
+
bio-eagle (2.3-2) unstable; urgency=medium
* Add a comment in the description about the renaming.
diff --git a/debian/rules b/debian/rules
index 65e44fc..9ed8893 100755
--- a/debian/rules
+++ b/debian/rules
@@ -5,11 +5,6 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
%:
dh $@ --sourcedirectory=src
-override_dh_install:
- cd $(CURDIR)/example/ && \
- tar Jcvf examples.tar.xz * --sort=name --mode=go=rX,u+rw,a-s --owner=root --group=root --numeric-owner
- dh_install
-
override_dh_installchangelogs:
dh_installchangelogs debian/upstream.changelog
diff --git a/debian/tests/run-sample-analysis b/debian/tests/run-sample-analysis
index 96b6419..af8e86f 100755
--- a/debian/tests/run-sample-analysis
+++ b/debian/tests/run-sample-analysis
@@ -2,7 +2,7 @@
# http://dep.debian.net/deps/dep8/
# Autopkgtest: Test if (bio-)eagle run analysis correctly
# Author: Dylan Aïssi <bob.dybian at gmail.com>
-# Last-Update: 2016-09-17
+# Last-Update: 2016-10-30
pkg=bio-eagle
if [ "$ADTTMP" = "" ] ; then
@@ -11,7 +11,11 @@ fi
cd $ADTTMP
cp -a /usr/share/doc/${pkg}/examples/* $ADTTMP
-tar Jxvf $ADTTMP/examples.tar.xz
+gunzip EUR_test.bed.gz
+gunzip EUR_test.bim.gz
+gunzip EUR_test.fam.gz
+gunzip phased.sample.gz
+gunzip ref.bcf.gz
# From upstream run_example.sh
bio-eagle \
@@ -37,12 +41,5 @@ bio-eagle \
--numThreads=4 \
--v1fast
-# From upstream run_example_ref.sh
-bio-eagle \
- --vcfRef=ref.bcf \
- --vcfTarget=target.vcf.gz \
- --geneticMapFile=tables/genetic_map_hg19_example.txt.gz \
- --outPrefix=target.phased
-
rm -rf $ADTTMP/*
--
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