[med-svn] [trinityrnaseq] 06/09: build the scaffold_iworm_contigs tool

[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 eee4160078124033c1a6695c0a0ecc761386dda8
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Fri Jan 15 05:01:30 2016 -0800

    build the scaffold_iworm_contigs tool
---
 debian/control                                          |  3 ++-
 .../patches/scaffold_iworm_contigs-Makefile-fix-clean   | 17 +++++++++++++++++
 debian/patches/series                                   |  1 +
 debian/rules                                            |  2 +-
 debian/trinityrnaseq.install                            |  1 +
 5 files changed, 22 insertions(+), 2 deletions(-)

diff --git a/debian/control b/debian/control
index f92f657..d47d008 100644
--- a/debian/control
+++ b/debian/control
@@ -14,7 +14,8 @@ Build-Depends: debhelper (>= 9),
                default-jdk,
                parafly,
                libjs-jquery,
-               jaligner
+               jaligner,
+               libhts-dev
 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
diff --git a/debian/patches/scaffold_iworm_contigs-Makefile-fix-clean b/debian/patches/scaffold_iworm_contigs-Makefile-fix-clean
new file mode 100644
index 0000000..b966e01
--- /dev/null
+++ b/debian/patches/scaffold_iworm_contigs-Makefile-fix-clean
@@ -0,0 +1,17 @@
+Author: Michael R. Crusoe <crusoe at ucdavis.edu>
+Description: removes link to zlib; add hardening flags; makes clean target
+resiliant
+--- trinityrnaseq.orig/trinity-plugins/scaffold_iworm_contigs/Makefile
++++ trinityrnaseq/trinity-plugins/scaffold_iworm_contigs/Makefile
+@@ -2,9 +2,9 @@
+ prefix = ../htslib
+ 
+ ScaffoldIwormContigs:
+-	$(CXX) -I$(prefix) -L$(prefix) ScaffoldIwormContigs.cpp error_checker.cpp -lhts -lz -o scaffold_iworm_contigs
++	$(CXX) $(LDFLAGS) -I$(prefix) -L$(prefix) ScaffoldIwormContigs.cpp error_checker.cpp -lhts -o scaffold_iworm_contigs
+ 
+ clean:
+-	rm scaffold_iworm_contigs
++	rm -f scaffold_iworm_contigs
+ 
+ 
diff --git a/debian/patches/series b/debian/patches/series
index 4701ce1..68d9373 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -10,3 +10,4 @@ fix-jsquery
 fix_system_paths
 hardening
 reproducible-build
+scaffold_iworm_contigs-Makefile-fix-clean
diff --git a/debian/rules b/debian/rules
index af0b1d0..2d46e5a 100755
--- a/debian/rules
+++ b/debian/rules
@@ -5,7 +5,7 @@ DH_VERBOSE := 1
 JDIR=/usr/share/java
 export CLASSPATH=${JDIR}/commons-collections4.jar:${JDIR}/gnu-getopt.jar:${JDIR}/jung-algorithms.jar:${JDIR}/jung-api.jar:${JDIR}/jung-graph-impl.jar:${JDIR}/jaligner.jar
 export JAVA_HOME=/usr/lib/jvm/default-java
-SOURCE_DIRECTORIES = Inchworm Chrysalis trinity-plugins/*Fastool* trinity-plugins/slclust
+SOURCE_DIRECTORIES = Inchworm Chrysalis trinity-plugins/*Fastool* trinity-plugins/slclust trinity-plugins/scaffold_iworm_contigs
 BASEDIR=debian/trinityrnaseq/usr/lib/trinityrnaseq
 EXBASEDIR=debian/trinityrnaseq-examples/usr/share/trinityrnaseq
 
diff --git a/debian/trinityrnaseq.install b/debian/trinityrnaseq.install
index 8bfb7b0..2d0d964 100644
--- a/debian/trinityrnaseq.install
+++ b/debian/trinityrnaseq.install
@@ -2,6 +2,7 @@ debian/bin/* /usr/bin
 Analysis /usr/lib/trinityrnaseq/
 trinity-plugins/*Fastool*/fastool /usr/lib/trinityrnaseq/trinity-plugins/fastool/
 trinity-plugins/slclust/bin/slclust /usr/lib/trinityrnaseq/trinity-plugins/slclust/bin/
+trinity-plugins/scaffold_iworm_contigs/scaffold_iworm_contigs /usr/lib/trinityrnaseq/trinity-plugins/scaffold_iworm_contigs/
 Chrysalis/TranscriptomeFromVaryK /usr/lib/trinityrnaseq/Chrysalis/
 Chrysalis/RunButterfly /usr/lib/trinityrnaseq/Chrysalis/
 Chrysalis/ReadsToTranscripts_MPI_chang /usr/lib/trinityrnaseq/Chrysalis/

-- 
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