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commit c7cc0bb0d16394601802d4231a38e81a7d158e3e Author: Sascha Steinbiss <[email protected]> Date: Fri Jun 24 14:40:36 2016 +0000 add manpage --- debian/control | 1 + debian/extra-man-info.txt | 16 ++++++++++++++++ debian/patches/rename_tool.patch | 2 +- debian/rules | 10 +++++++++- debian/ssw-align.links | 1 + debian/ssw-align.manpages | 1 + 6 files changed, 29 insertions(+), 2 deletions(-) diff --git a/debian/control b/debian/control index ff3e1f7..7aba6c8 100644 --- a/debian/control +++ b/debian/control @@ -7,6 +7,7 @@ Build-Depends: debhelper (>= 9), default-jdk-headless, javahelper, dh-autoreconf, + help2man, zlib1g-dev Standards-Version: 3.9.8 Testsuite: autopkgtest diff --git a/debian/extra-man-info.txt b/debian/extra-man-info.txt new file mode 100644 index 0000000..b7c8692 --- /dev/null +++ b/debian/extra-man-info.txt @@ -0,0 +1,16 @@ +[DESCRIPTION] + +This command line tool uses SSW, a fast SIMD optimized alignment library, +to perform alignments on input files. + +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. If the target file has N +sequences and the query file has M sequences, the results will have M*N alignments. + +[OUTPUT FORMATS] + +The software can output SAM format or BLAST like format results. +For a specification of the SAM format, please see +http://samtools.sourceforge.net/SAM1.pdf. The additional optional field +"ZS" indicates the suboptimal alignment score. diff --git a/debian/patches/rename_tool.patch b/debian/patches/rename_tool.patch index e11ea26..2125fb2 100644 --- a/debian/patches/rename_tool.patch +++ b/debian/patches/rename_tool.patch @@ -24,7 +24,7 @@ -$(PROG): main.c kseq.h +$(PROG): main.c kseq.h $(LLIB) -+ $(CC) $(CPPFLAGS) $(CFLAGS) -o $@ main.c kseq.h -L. -lssw -lm -lz ++ $(CC) $(CPPFLAGS) $(CFLAGS) -o $@ main.c kseq.h -L. -lssw -lm -lz $(LDFLAGS) $(EXAMPLE): example.c diff --git a/debian/rules b/debian/rules index 11e4357..9ba2f1a 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/libssw*install debian/libssw*links + rm -f debian/libssw*install debian/libssw*links debian/ssw-align.1 $(MAKE) -C src clean override_dh_auto_build: @@ -19,6 +19,14 @@ override_dh_auto_install: debian/libssw0.install debian/libssw-dev.install debia mv src/ssw.jar src/ssw-$(PKG_VERSION).jar dh_auto_install +override_dh_installman: + LD_LIBRARY_PATH=`pwd`/src help2man --version-string=' ' --help-option=' ' \ + -I debian/extra-man-info.txt \ + -N -n 'fast Smith-Waterman aligner' \ + --no-discard-stderr src/ssw-align \ + | fgrep -v ERROR > debian/ssw-align.1 + dh_installman + override_dh_auto_test: src/example_c src/example_cpp diff --git a/debian/ssw-align.links b/debian/ssw-align.links index a936d36..861b6ff 100644 --- a/debian/ssw-align.links +++ b/debian/ssw-align.links @@ -1 +1,2 @@ usr/bin/ssw-align usr/bin/ssw_test +usr/share/man/man1/ssw-align.1.gz usr/share/man/man1/ssw_test.1.gz diff --git a/debian/ssw-align.manpages b/debian/ssw-align.manpages new file mode 100644 index 0000000..eaf1983 --- /dev/null +++ b/debian/ssw-align.manpages @@ -0,0 +1 @@ +debian/ssw-align.1 -- 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
