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commit 5e61aa27eecd3019028ce2a51ff16a795b19ebc1 Author: Sascha Steinbiss <[email protected]> Date: Fri Jun 24 14:23:25 2016 +0000 add command line tool --- debian/control | 14 ++++++++++++ debian/patches/rename_tool.patch | 46 ++++++++++++++++++++++++++++++++++++++++ debian/patches/series | 1 + debian/rules | 2 +- debian/ssw-align.install | 1 + debian/ssw-align.links | 1 + 6 files changed, 64 insertions(+), 1 deletion(-) diff --git a/debian/control b/debian/control index 28f9d96..ff3e1f7 100644 --- a/debian/control +++ b/debian/control @@ -60,3 +60,17 @@ Description: Java bindings for libssw implementation of the Smith-Waterman algorithm using Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. + +Package: ssw-align +Architecture: any +Depends: ${shlibs:Depends}, + ${misc:Depends}, + libssw0 (= ${binary:Version}) +Description: Smith-Waterman aligner based on libssw + This package provides a command-line aligner based on the libssw library, + a fast SIMD accelerated implementation of the Smith-Waterman algorithm. + The input files can be in FASTA or FASTQ format. Both target and query files + can contain multiple sequences. Each sequence in the query file will be + aligned with all sequences in the target file. Output is provided in SAM or + BLAST-like text format. + diff --git a/debian/patches/rename_tool.patch b/debian/patches/rename_tool.patch new file mode 100644 index 0000000..e11ea26 --- /dev/null +++ b/debian/patches/rename_tool.patch @@ -0,0 +1,46 @@ +--- a/src/Makefile ++++ b/src/Makefile +@@ -4,9 +4,10 @@ + #CXXFLAGS := $(CFLAGS) + LOBJS = ssw.o + LCPPOBJS = ssw_cpp.o +-PROG = ssw_test ++PROG = ssw-align + SOVERS=.0 + LIB = libssw.so$(SOVERS) ++LLIB = libssw.so + STATICLIB = libssw.a + EXAMPLE = example_c + EXAMPLE_CPP = example_cpp +@@ -26,14 +27,18 @@ + $(LIB): ssw.c ssw.h ssw_cpp.h ssw_cpp.cpp + $(CXX) $(CPPFLAGS) $(CXXFLAGS) -fPIC -shared -rdynamic -Wl,-soname,$(LIB) -o $@ $^ $(LDFLAGS) + ++$(LLIB): $(LIB) ++ ln -s $< $@ ++ + $(STATICLIB): $(LOBJS) $(LCPPOBJS) + ar rcs $@ $^ + +-$(PROG): main.c kseq.h ++$(PROG): main.c kseq.h $(LLIB) ++ $(CC) $(CPPFLAGS) $(CFLAGS) -o $@ main.c kseq.h -L. -lssw -lm -lz + + $(EXAMPLE): example.c + +-$(PROG) $(EXAMPLE): $(LOBJS) ++$(EXAMPLE): $(LOBJS) + $(CC) -o $@ $(filter-out %.h,$^) $(CPPFLAGS) $(CFLAGS) -lm -lz $(LDFLAGS) + + $(EXAMPLE_CPP): example.cpp $(LOBJS) $(LCPPOBJS) +--- a/src/main.c ++++ b/src/main.c +@@ -294,7 +294,7 @@ + } + if (optind + 2 > argc) { + fprintf(stderr, "\n"); +- fprintf(stderr, "Usage: ssw_test [options] ... <target.fasta> <query.fasta>(or <query.fastq>)\n"); ++ fprintf(stderr, "Usage: %s [options] ... <target.fasta> <query.fasta>(or <query.fastq>)\n", argv[0]); + fprintf(stderr, "Options:\n"); + fprintf(stderr, "\t-m N\tN is a positive integer for weight match in genome sequence alignment. [default: 2]\n"); + fprintf(stderr, "\t-x N\tN is a positive integer. -N will be used as weight mismatch in genome sequence alignment. [default: 2]\n"); diff --git a/debian/patches/series b/debian/patches/series index ad20a84..d163b77 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,2 +1,3 @@ build_all_libs.patch hardening.patch +rename_tool.patch diff --git a/debian/rules b/debian/rules index 0ca3473..11e4357 100755 --- a/debian/rules +++ b/debian/rules @@ -9,7 +9,7 @@ PKG_VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[[:digit:]]*://' -e 's/-.* dh $@ override_dh_auto_clean: - rm -f debian/*install debian/*links + rm -f debian/libssw*install debian/libssw*links $(MAKE) -C src clean override_dh_auto_build: diff --git a/debian/ssw-align.install b/debian/ssw-align.install new file mode 100644 index 0000000..78a9739 --- /dev/null +++ b/debian/ssw-align.install @@ -0,0 +1 @@ +src/ssw-align usr/bin diff --git a/debian/ssw-align.links b/debian/ssw-align.links new file mode 100644 index 0000000..a936d36 --- /dev/null +++ b/debian/ssw-align.links @@ -0,0 +1 @@ +usr/bin/ssw-align usr/bin/ssw_test -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libssw.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
