[med-svn] [sga] 01/02: Add manpages

[Andreas Tille]

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

tille pushed a commit to branch debian/unstable
in repository sga.

commit 5097b6d7848bfcf2cb73acd108433454f5dbb91c
Author: Andreas Tille <tille at debian.org>
Date:   Fri Sep 9 22:10:10 2016 +0200

    Add manpages
---
 debian/manpages    |  1 +
 debian/rules       |  1 +
 debian/sga-align.1 | 22 ++++++++++++++++++++++
 debian/sga-astat.1 | 32 ++++++++++++++++++++++++++++++++
 4 files changed, 56 insertions(+)

diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1
diff --git a/debian/rules b/debian/rules
index 51d91ea..209e538 100755
--- a/debian/rules
+++ b/debian/rules
@@ -34,6 +34,7 @@ override_dh_installexamples:
 	    src/examples/sga-celegans.sh > debian/$(pkg)/usr/share/doc/$(pkg)/examples/sga-celegans.sh
 
 override_dh_installman:
+	dh_installman
 	mkdir -p $(mandir)
 	PATH=/usr/lib/abyss:${PATH} \
 	help2man \
diff --git a/debian/sga-align.1 b/debian/sga-align.1
new file mode 100644
index 0000000..bb84fc1
--- /dev/null
+++ b/debian/sga-align.1
@@ -0,0 +1,22 @@
+.TH SGA-ALIGN "1" "September 2016" "sga-align 0.10.15" "User Commands"
+.SH NAME
+sga-aligm \- align reads to contigs
+.SH SYNOPSIS
+.B sga-align
+\fI[options]\fR \fI<contigs file> <input files>\fR
+.SH DESCRIPTION
+The major goal of SGA is to be very memory efficient, which is achieved by
+using a compressed representation of DNA sequence reads.
+.P
+SGA is a de novo assembler for DNA sequence reads. It is based on Gene Myers'
+string graph formulation of assembly and uses the FM-index/Burrows-Wheeler
+transform to efficiently find overlaps between sequence reads.
+.SH OPTIONS
+.TP
+--name=STR
+Use STR as the basename for the output files.
+.TP
+-t,--threads=N
+Use N threads when running bwa.
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/sga-astat.1 b/debian/sga-astat.1
new file mode 100644
index 0000000..2dfae47
--- /dev/null
+++ b/debian/sga-astat.1
@@ -0,0 +1,32 @@
+.TH SGA-ASTAT "1" "September 2016" "sga-astat 0.10.15" "User Commands"
+.SH NAME
+sga-astat \- Compute Myers' a-statistic for a set of contigs using the read alignments in in.bam
+.SH SYNOPSIS
+.B sga-astat
+\fI[options]\fR \fI<in.bam>\fR
+.SH DESCRIPTION
+The major goal of SGA is to be very memory efficient, which is achieved by
+using a compressed representation of DNA sequence reads.
+.P
+SGA is a de novo assembler for DNA sequence reads. It is based on Gene Myers'
+string graph formulation of assembly and uses the FM-index/Burrows-Wheeler
+transform to efficiently find overlaps between sequence reads.
+.SH OPTIONS
+.TP
+-m=INT
+only compute a-stat for contigs at least INT bases in length
+.TP
+-b=INT
+use the longest INT contigs to perform the initial estimate
+of the arrival rate (default: 20)
+.TP
+-n=INT
+perform INT bootstrap iterations of the estimate
+.TP
+-g=INT
+use INT as the genome size instead of estimating it
+.TP
+--no-duplicates
+do not use duplicate reads to calculate statistics
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sga.git