[med-svn] [eagle] 01/01: Remove the test which creates a false positive in the autopkgtest by emitting some warnings. (Closes: #842356)

[Dylan Aïssi]

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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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