[med-svn] [libssw] 02/07: add manpage

[Sascha Steinbiss]

This is an automated email from the git hooks/post-receive script.

satta pushed a commit to branch master
in repository libssw.

commit c7cc0bb0d16394601802d4231a38e81a7d158e3e
Author: Sascha Steinbiss <satta at debian.org>
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

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