[med-svn] [trinityrnaseq] 01/01: 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 f471104799654dddd4131f9ec269cdddabdabce5
Author: Michael R. Crusoe <mcrusoe at msu.edu>
Date:   Sun Feb 1 12:04:26 2015 -0500

    Butterfly
---
 debian/copyright             | 2 +-
 debian/rules                 | 5 +++--
 debian/trinityrnaseq.install | 1 +
 3 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/debian/copyright b/debian/copyright
index 7448860..b6271c5 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 Butterfly/src/lib/collections-generic-4.01.jar Butterfly/src/lib/java-getopt-1.0.13.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 Butterfly/src/lib/Jaligner.jar
 
 Files: *
 Copyright: © 2011 The Broad Institute, Inc; © 2014 trinityrnaseq
diff --git a/debian/rules b/debian/rules
index 54510fc..50d104d 100755
--- a/debian/rules
+++ b/debian/rules
@@ -12,8 +12,9 @@ DH_VERBOSE := 1
 #GIT_TAG        := $(subst ~,_,$(VERSION))
 
 ROOT_DIR := $(shell dirname $(realpath $(lastword $(MAKEFILE_LIST))))
+BUTTERFLY_LIBDIR := ${ROOT_DIR}/../Butterfly/src/lib
 
-export CLASSPATH=/usr/share/java/collections15.jar:/usr/share/java/gnu-getopt.jar:${ROOT_DIR}'/../Butterfly/src/lib/jung*'
+export CLASSPATH=/usr/share/java/collections15.jar:/usr/share/java/gnu-getopt.jar:${BUTTERFLY_LIBDIR}/jung-algorithms-2.0.1.jar:${BUTTERFLY_LIBDIR}/jung-api-2.0.1.jar:${BUTTERFLY_LIBDIR}/jung-api-2.0.1.jar:${BUTTERFLY_LIBDIR}/jung-graph-impl-2.0.1.jar
 
 SOURCE_DIRECTORIES = Inchworm Chrysalis trinity-plugins/fastool trinity-plugins/parafly
 %:
@@ -26,9 +27,9 @@ override_dh_auto_configure:
 		--prefix=/usr/lib/trinityrnaseq/$${target}; done
 
 override_dh_auto_build:
+	jh_build -J Butterfly.jar Butterfly/src
 	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 \
diff --git a/debian/trinityrnaseq.install b/debian/trinityrnaseq.install
index 76e96ef..37108f8 100644
--- a/debian/trinityrnaseq.install
+++ b/debian/trinityrnaseq.install
@@ -1,4 +1,5 @@
 debian/bin/* /usr/bin
+Butterfly/Butterfly.jar /usr/lib/trinityrnaseq/Butterfly/
 trinity-plugins/fastool/fastool /usr/lib/trinityrnaseq/trinity-plugins/fastool/
 Chrysalis/TranscriptomeFromVaryK /usr/lib/trinityrnaseq/Chrysalis/
 Chrysalis/RunButterfly /usr/lib/trinityrnaseq/Chrysalis/

-- 
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