[med-svn] [qualimap] 02/03: Follow Emmanuel Borg's hint to rather patch pom.xml than fiddling around with maven .rules

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository qualimap.

commit 95986f6e8ea9348f4392bcb2a9c6f6c86e0c543d
Author: Andreas Tille <tille at debian.org>
Date:   Thu Nov 26 18:33:16 2015 +0100

    Follow Emmanuel Borg's hint to rather patch pom.xml than fiddling around with maven .rules
---
 debian/maven.rules           |  9 ++++-----
 debian/patches/adapt_pom.xml | 25 +++++++++++++++++++++++++
 debian/patches/series        |  1 +
 3 files changed, 30 insertions(+), 5 deletions(-)

diff --git a/debian/maven.rules b/debian/maven.rules
index 911d808..e3d429f 100644
--- a/debian/maven.rules
+++ b/debian/maven.rules
@@ -1,11 +1,10 @@
 
 junit junit jar s/4\..*/4.x/ * *
-org.bioinfo.ngs qualimap jar * * *
-org.bioinfo.ngs qualimap jar s/.*/debian/ * *
-net.sf picard jar s/.*/fake/ * *
-net.sf samtools jar s/.*/fake/ * *
+org.bioinfo ngs jar s/.*/fake/ * *
+#replaced by quilt patch###net.sf.picard picard jar s/.*/fake/ * *
+#replaced by quilt patch###net.sf.samtools samtools jar s/.*/fake/ * *
 com.miglayout s/miglayout/miglayout-swing/ * s/.*/debian/ * *
-# if the uppder does not help, try this
+# if the upper does not help, try this
 # com.miglayout s/miglayout/miglayout-core/ * s/.*/debian/ * *
 # it just depends where the classes qualimap suspects in miglayout war provided
 # Emmanuel thinks also this could work as alternative
diff --git a/debian/patches/adapt_pom.xml b/debian/patches/adapt_pom.xml
new file mode 100644
index 0000000..92e8017
--- /dev/null
+++ b/debian/patches/adapt_pom.xml
@@ -0,0 +1,25 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 17 Nov 2015 14:47:59 +0100
+Description: Due to missing Maven support in picard-tools we need to
+ announce where to find the according classes.  This patch was created
+ according to a hint by Emmanuel Bourg at the debian-java list at
+ .
+   https://lists.debian.org/debian-java/2015/11/msg00069.html
+
+--- a/pom.xml
++++ b/pom.xml
+@@ -60,12 +60,14 @@
+        		<groupId>net.sf.picard</groupId>
+         	<artifactId>picard</artifactId>
+            	<version>1.70</version>
++                <systemPath>/usr/share/java/picard.jar</systemPath>
+        	</dependency>
+         <dependency>
+ 			<groupId>net.sf.samtools</groupId>
+             <artifactId>samtools</artifactId>
+             <version>1.70</version>
+             <scope>compile</scope>
++            <systemPath>/usr/share/java/sam.jar</systemPath>
+         </dependency>
+        	<dependency>
+            	<groupId>com.miglayout</groupId>
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..83ea553
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+adapt_pom.xml

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/qualimap.git