[med-svn] [trinityrnaseq] 01/02: parafly, transdecoder, and JUNG have been split out

Mon Feb 16 05:13:59 UTC 2015

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

commit f044b705f81669ab46e3e84a27cc64961478150a
Author: Michael R. Crusoe <mcrusoe at msu.edu>
Date:   Fri Feb 13 11:12:44 2015 -0500

    parafly, transdecoder, and JUNG have been split out
---
 debian/control               |  7 +++++--
 debian/copyright             |  4 +++-
 debian/patches/series        |  1 +
 debian/patches/update-paths  | 36 ++++++++++++++++++++++++++++++++++++
 debian/rules                 |  9 ++++-----
 debian/trinityrnaseq.install |  2 +-
 6 files changed, 50 insertions(+), 9 deletions(-)

diff --git a/debian/control b/debian/control
index 4cc931d..9292f9f 100644
--- a/debian/control
+++ b/debian/control
@@ -6,10 +6,11 @@ Priority: optional
 Build-Depends: debhelper (>= 9),
                autotools-dev,
                jellyfish (>= 2.1.4),
-               libcollections15-java,
+               libjung-java,
                javahelper,
                libgetopt-java,
-               default-jdk
+               default-jdk,
+               parafly
 Standards-Version: 3.9.6
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/trinityrnaseq.git
 Vcs-Git: git://anonscm.debian.org/debian-med/trinityrnaseq.git
@@ -24,6 +25,7 @@ Depends: ${shlibs:Depends},
          python,
          libwww-perl,
          default-jre-headless,
+         libjung-java,
          samtools,
          jellyfish,
          r-base-core,
@@ -31,6 +33,7 @@ Depends: ${shlibs:Depends},
          rsem,
          express,
          trimmomatic,
+         transdecoder
 Suggests: collectl
 Description: RNA-Seq De novo Assembly
  Trinity represents a novel method for the efficient and robust de novo
diff --git a/debian/copyright b/debian/copyright
index ee4832c..610f394 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -8,11 +8,13 @@ Files-Excluded: trinity-plugins/jellyfish-*.tar.gz
  Butterfly/prev_vers
  trinity-plugins/rsem*.tar.gz
  trinity-plugins/Trimmomatic*
+ trinity-plugins/parafly*
+ trinity-plugins/TransDecoder*
 
 Files: *
 Copyright: © 2011 The Broad Institute, Inc; © 2014 trinityrnaseq
 Comment: trinity-plugins/slclust is from http://sourceforge.net/projects/slclust/
-Comment: trinity-plugins/GAL_0.2.1 is from http://www.sequenceontology.org/software/GAL_Code/
+ trinity-plugins/GAL_0.2.1 is from http://www.sequenceontology.org/software/GAL_Code/
 License: BSD-3-clause
  All rights reserved.
  .
diff --git a/debian/patches/series b/debian/patches/series
index 5cf7b6f..c8d6b30 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
 chrysalis-make-tweak
 noExitTester
 jellyfish-path
+update-paths
diff --git a/debian/patches/update-paths b/debian/patches/update-paths
new file mode 100644
index 0000000..2d06b21
--- /dev/null
+++ b/debian/patches/update-paths
@@ -0,0 +1,36 @@
+--- trinityrnaseq.orig/util/support_scripts/trinity_install_tests.sh
++++ trinityrnaseq/util/support_scripts/trinity_install_tests.sh
+@@ -6,7 +6,7 @@
+ echo ' '
+ echo "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
+ 
+-if [ -e "trinity-plugins/jellyfish/jellyfish" ]
++if [ -e "/usr/bin/jellyfish" ]
+ then
+ 	echo "JellyFish:               has been Installed Properly"
+ else
+@@ -52,7 +52,7 @@
+ else
+ 	echo "fastool Installation appears to have FAILED"
+ fi
+-if [ -e "trinity-plugins/parafly/bin/ParaFly" ]
++if [ -e "/usr/bin/ParaFly" ]
+ then
+ 	echo "parafly:                 has been Installed Properly"
+ else
+--- trinityrnaseq.orig/Trinity
++++ trinityrnaseq/Trinity
+@@ -38,10 +38,10 @@
+ my $BUTTERFLY_DIR = "$ROOTDIR/Butterfly";
+ my $JELLYFISH_DIR = "/usr";
+ my $FASTOOL_DIR = "$ROOTDIR/trinity-plugins/fastool";
+-my $COLLECTL_DIR = "$ROOTDIR/trinity-plugins/collectl/bin";
++my $COLLECTL_DIR = "/usr/bin";
+ my $COREUTILS_DIR = "$ROOTDIR/trinity-plugins/coreutils/bin";
+-my $PARAFLY = "$ROOTDIR/trinity-plugins/parafly/bin/ParaFly";
+-my $TRIMMOMATIC = "$ROOTDIR/trinity-plugins/Trimmomatic/trimmomatic.jar";
++my $PARAFLY = "/usr/bin/ParaFly";
++my $TRIMMOMATIC = "/usr/share/java/trimmomatic.jar";
+ my $TRIMMOMATIC_DIR = "$ROOTDIR/trinity-plugins/Trimmomatic";
+ 
+ #&version_check();
diff --git a/debian/rules b/debian/rules
index 592e483..c23cf4a 100755
--- a/debian/rules
+++ b/debian/rules
@@ -11,12 +11,10 @@ DH_VERBOSE := 1
 #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))))
-BUTTERFLY_LIBDIR := ${ROOT_DIR}/../Butterfly/src/lib
+JAVALIBDIR := /usr/share/java
+export CLASSPATH=${JAVALIBDIR}/collections15.jar:/usr/share/java/gnu-getopt.jar:${JAVALIBDIR}/jung-algorithms.jar:${JAVALIBDIR}/jung-apijar:${JAVALIBDIR}/jung-graph-impl.jar
 
-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-code
+SOURCE_DIRECTORIES = Inchworm Chrysalis trinity-plugins/*Fastool*
 
 BASEDIR=debian/trinityrnaseq/usr/lib/trinityrnaseq
 
@@ -38,6 +36,7 @@ override_dh_auto_clean:
 	for target in ${SOURCE_DIRECTORIES}; do dh_autotools-dev_restoreconfig \
 		-O--sourcedirectory=$${target}; dh_auto_clean \
 		--sourcedirectory=$${target}; done
+	rm Chrysalis/Makefile_auto
 
 override_dh_auto_install:
 	for target in ${SOURCE_DIRECTORIES}; do dh_auto_install \
diff --git a/debian/trinityrnaseq.install b/debian/trinityrnaseq.install
index ad9e5c0..161c278 100644
--- a/debian/trinityrnaseq.install
+++ b/debian/trinityrnaseq.install
@@ -1,7 +1,7 @@
 debian/bin/* /usr/bin
 Analysis /usr/lib/trinityrnaseq/
 Butterfly/Butterfly.jar /usr/lib/trinityrnaseq/Butterfly/
-trinity-plugins/fastool/fastool /usr/lib/trinityrnaseq/trinity-plugins/fastool/
+trinity-plugins/*Fastool*/fastool /usr/lib/trinityrnaseq/trinity-plugins/fastool/
 Chrysalis/TranscriptomeFromVaryK /usr/lib/trinityrnaseq/Chrysalis/
 Chrysalis/RunButterfly /usr/lib/trinityrnaseq/Chrysalis/
 Chrysalis/ReadsToTranscripts_MPI_chang /usr/lib/trinityrnaseq/Chrysalis/

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

