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commit eee4160078124033c1a6695c0a0ecc761386dda8 Author: Michael R. Crusoe <[email protected]> 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 <[email protected]> +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/ -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/trinityrnaseq.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
