[med-svn] [trinityrnaseq] 03/03: build Butterfly

[Michael Crusoe]

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

misterc-guest pushed a commit to branch master
in repository trinityrnaseq.

commit 4f7469d1ec99456f64d05340d3201e3be637b798
Author: Michael R. Crusoe <mcrusoe at msu.edu>
Date:   Sun Feb 1 10:23:43 2015 -0500

    build Butterfly
---
 debian/control   | 2 +-
 debian/copyright | 2 +-
 debian/rules     | 7 ++++++-
 3 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/debian/control b/debian/control
index acc8b75..8a51e66 100644
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,7 @@ Section: science
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Michael R. Crusoe
-Build-Depends: debhelper (>= 9), autotools-dev, jellyfish (>= 2.1.4)
+Build-Depends: debhelper (>= 9), autotools-dev, jellyfish (>= 2.1.4), libcollections15-java, javahelper, libgetopt-java
 Standards-Version: 3.9.5
 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/trinityrnaseq.git
 Vcs-Svn: git://anonscm.debian.org/debian-med/trinityrnaseq.git
diff --git a/debian/copyright b/debian/copyright
index d07940a..7448860 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,7 +1,7 @@
 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: trinityrnaseq
 Source: https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.2.tar.gz
-Exclude: trinity_plugins/jellyfish-2.1.4.tar.gz util/support_scripts/ExitTester.jar
+Exclude: trinity_plugins/jellyfish-2.1.4.tar.gz util/support_scripts/ExitTester.jar Butterfly/src/lib/collections-generic-4.01.jar Butterfly/src/lib/java-getopt-1.0.13.jar
 
 Files: *
 Copyright: © 2011 The Broad Institute, Inc; © 2014 trinityrnaseq
diff --git a/debian/rules b/debian/rules
index 2ad6f7e..54510fc 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,6 +1,6 @@
 #!/usr/bin/make -f
 
-#DH_VERBOSE := 1
+DH_VERBOSE := 1
 
 # some helpful variables - uncomment them if needed
 # shamelessly stolen from http://jmtd.net/log/awk/
@@ -11,6 +11,10 @@
 #DEBIAN_BRANCH  := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf)
 #GIT_TAG        := $(subst ~,_,$(VERSION))
 
+ROOT_DIR := $(shell dirname $(realpath $(lastword $(MAKEFILE_LIST))))
+
+export CLASSPATH=/usr/share/java/collections15.jar:/usr/share/java/gnu-getopt.jar:${ROOT_DIR}'/../Butterfly/src/lib/jung*'
+
 SOURCE_DIRECTORIES = Inchworm Chrysalis trinity-plugins/fastool trinity-plugins/parafly
 %:
 	dh $@ --parallel
@@ -24,6 +28,7 @@ override_dh_auto_configure:
 override_dh_auto_build:
 	for target in ${SOURCE_DIRECTORIES}; do dh_auto_build \
 		-O--sourcedirectory=$${target}; done
+	jh_build -J Butterfly.jar Butterfly/src
 
 override_dh_auto_clean:
 	for target in ${SOURCE_DIRECTORIES}; do dh_autotools-dev_restoreconfig \

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