[med-svn] [artemis] 06/08: Add patch to allow jar files to be built without 3rd-party files

[Afif Elghraoui]

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

afif-guest pushed a commit to branch master
in repository artemis.

commit 29b652fc81566ab586e4eada8691ad2f6b41f709
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Thu Oct 22 04:26:14 2015 -0700

    Add patch to allow jar files to be built without 3rd-party files
---
 debian/patches/jar-rules.patch | 64 ++++++++++++++++++++++++++++++++++++++++++
 debian/patches/series          |  1 +
 2 files changed, 65 insertions(+)

diff --git a/debian/patches/jar-rules.patch b/debian/patches/jar-rules.patch
new file mode 100644
index 0000000..4750841
--- /dev/null
+++ b/debian/patches/jar-rules.patch
@@ -0,0 +1,64 @@
+Description: Leave out removed files when building jar files
+ The recipe to build the jar files looks for some files
+ that have been excluded from the source distribution (lib/*).
+ Their absence causes "can not stat" errors, so any reference to
+ them is removed here.
+Author: Afif Elghraoui <afif at ghraoui.name>
+Forwarded: not-needed
+Last-Update: 2015-10-22
+--- artemis.orig/Makefile
++++ artemis/Makefile
+@@ -290,29 +290,7 @@
+ 	mkdir jar_build
+ 	rm -f artemis.jar
+ 	cd jar_build; \
+-	if [ ! -d org ]; then \
+-	  for fileJar in ../lib/*.jar; do \
+-	    jar xvf $$fileJar; \
+-	    rm -rf META-INF/MANIFEST.MF; \
+-	  done; \
+-          for fileJar in ../lib/j2ssh/*.jar; do \
+-            jar xvf $$fileJar; \
+-            rm -rf META-INF/MANIFEST.MF; \
+-          done; \
+-          for fileJar in ../lib/ibatis/*.jar; do \
+-            jar xvf $$fileJar; \
+-            rm -rf META-INF/MANIFEST.MF; \
+-          done; \
+-          for fileJar in ../lib/batik/*.jar; do \
+-            jar xvf $$fileJar; \
+-            rm -rf META-INF/MANIFEST.MF; \
+-          done; \
+-          for fileJar in ../lib/picard/*.jar; do \
+-            jar xvf $$fileJar; \
+-            rm -rf META-INF/MANIFEST.MF; \
+-          done; \
+-        fi; \
+-	cp -R ../lib/LICENSE.Apache ../uk ../org ../nsdb ../type ../seqdb ../etc ../images ../lib/j2ssh/j2ssh.properties \
++	cp -R ../uk ../org ../nsdb ../type ../seqdb ../etc ../images \
+ 	      ../images/PSUlogo.gif ../images/icon.gif ../README ../artemis_sqlmap .
+ 	find jar_build -name '*.java' -print | xargs rm -f
+ 	find jar_build -name '.svn' -print | xargs rm -rf
+@@ -320,18 +298,18 @@
+ 	rm -rf META-INF/MANIFEST.MF; \
+ 	echo "Main-Class: uk.ac.sanger.artemis.components.ArtemisMain\nPermissions: all-permissions" > manifest-art; \
+ 	jar cmf manifest-art artemis.jar META-INF/services images/PSUlogo.gif images/icon.gif README etc \
+-	                     artemis_sqlmap org uk com net nsdb type seqdb LICENSE.Apache j2ssh.properties; \
++	                     artemis_sqlmap org uk com net nsdb type seqdb; \
+         echo "Main-Class: uk.ac.sanger.artemis.circular.DNADraw\nPermissions: all-permissions" > manifest-circular; \
+         jar cmf manifest-circular DNAPlotter.jar images/PSUlogo.gif README etc \
+-                             uk org/gmod org/w3c org/apache org/biojava/bio/ com/ibatis/common/jdbc/ net/sf/samtools/ LICENSE.Apache j2ssh.properties; \
++                             uk org/gmod org/w3c org/apache org/biojava/bio/ com/ibatis/common/jdbc/ net/sf/samtools/; \
+ 	echo "Main-Class: uk.ac.sanger.artemis.components.alignment.BamView\nPermissions: all-permissions" > manifest-bamview; \
+ 	jar cmf manifest-bamview BamView.jar META-INF/services etc uk org/apache org/biojava org/biojavax org/gmod org/w3c net/sf com/ibatis; \
+ 	echo "Main-Class: uk.ac.sanger.artemis.components.ActMain\nPermissions: all-permissions" > manifest-act; \
+ 	jar cmf manifest-act act.jar META-INF/services images/PSUlogo.gif images/icon.gif README etc \
+-	                     artemis_sqlmap org uk com net nsdb type seqdb LICENSE.Apache j2ssh.properties; \
++	                     artemis_sqlmap org uk com net nsdb type seqdb; \
+ 	rm -f etc/log4j.properties; \
+ 	jar cmf manifest-art artemis_mac.jar images/PSUlogo.gif images/icon.gif README \
+-	        uk org/gmod nsdb type seqdb LICENSE.Apache artemis_sqlmap
++	        uk org/gmod nsdb type seqdb artemis_sqlmap
+ 
+ clean :
+ 	-rm -rf *.html artemis.jar seqdb nsdb type resources uk/ac/sanger/jcon/ jar_build tar_build  artemis_compiled.tar
diff --git a/debian/patches/series b/debian/patches/series
index eefb4e0..80fd47f 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 class-path.patch
+jar-rules.patch
 CRAMReferenceSequenceFile.patch

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