[med-svn] r20784 - in trunk/packages/maq/trunk/debian: . mans

Wed Dec 16 14:34:14 UTC 2015

Author: tille
Date: 2015-12-16 14:34:14 +0000 (Wed, 16 Dec 2015)
New Revision: 20784

Added:
   trunk/packages/maq/trunk/debian/mans/
   trunk/packages/maq/trunk/debian/mans/farm-run.pl.1
   trunk/packages/maq/trunk/debian/mans/maq.pl.1
   trunk/packages/maq/trunk/debian/mans/maq_eval.pl.1
   trunk/packages/maq/trunk/debian/mans/maq_plot.pl.1
Modified:
   trunk/packages/maq/trunk/debian/changelog
   trunk/packages/maq/trunk/debian/rules
Log:
Add missing manpages


Modified: trunk/packages/maq/trunk/debian/changelog
===================================================================

--- trunk/packages/maq/trunk/debian/changelog	2015-12-16 13:35:32 UTC (rev 20783)
+++ trunk/packages/maq/trunk/debian/changelog	2015-12-16 14:34:14 UTC (rev 20784)
@@ -2,6 +2,7 @@
 
   * moved debian/upstream to debian/upstream/metadata
   * cme fix dpkg-control
+  * Add missing manpages
 
  -- Andreas Tille <tille at debian.org>  Wed, 16 Dec 2015 14:34:18 +0100
 

Added: trunk/packages/maq/trunk/debian/mans/farm-run.pl.1
===================================================================
--- trunk/packages/maq/trunk/debian/mans/farm-run.pl.1	                        (rev 0)
+++ trunk/packages/maq/trunk/debian/mans/farm-run.pl.1	2015-12-16 14:34:14 UTC (rev 20784)
@@ -0,0 +1,16 @@
+.TH FARM-RUN.PL "1" "December 2015" "farm-run.pl 0.7.1" "User Commands"
+.SH NAME
+farm-run.pl \- helps running maq jobs in batch mode
+.SH SYNOPSIS
+.B farm-run.pl
+[\fI\,-OPTIONS \/\fR[\fI\,-MORE_OPTIONS\/\fR]] [\fI\,--\/\fR] [\fI\,PROGRAM_ARG1 \/\fR...]
+.SH DESCRIPTION
+This script needs a config file that can be created using maq.pl(1).
+.SH OPTIONS
+.PP
+With arguments: \fB\-R\fR \fB\-c\fR \fB\-q\fR
+.PP
+Options may be merged together.  \fB\-\-\fR stops processing of options.
+Space is not required between options and their arguments.
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

Added: trunk/packages/maq/trunk/debian/mans/maq.pl.1
===================================================================
--- trunk/packages/maq/trunk/debian/mans/maq.pl.1	                        (rev 0)
+++ trunk/packages/maq/trunk/debian/mans/maq.pl.1	2015-12-16 14:34:14 UTC (rev 20784)
@@ -0,0 +1,45 @@
+.TH MAQ.PL "1" "December 2015" "maq.pl 0.7.1" "User Commands"
+.SH NAME
+maq.pl \- helper script for maq
+.SH SYNOPSIS
+.B maq.pl
+\fI\,<command> \/\fR[\fI\,options\/\fR] \fI\,<input> \/\fR[...]
+.SH DESCRIPTION
+helper script for maq
+.P
+Version: 0.4.7
+.SH OPTIONS.
+.TP
+\fIeasyrun\fR
+simple pipeline for small dataset
+.TP
+\fIdemo\fR
+demonstration of maq functionalities (for SE only)
+.TP
+\fISNPfilter\fR
+filter SNPs
+.TP
+\fIstatmap\fR
+extract statistics from the error output of 'maq map'
+.TP
+\fIchrpt2snp\fR
+convert dbSNP's chr_rpt file to .snp file
+.TP
+\fIucsc2snp\fR
+convert UCSC's SNP dump to .snp file
+.TP
+\fIfastq2bfq\fR
+convert fastq in batch
+.TP
+\fIcat2pair\fR
+convert paired end reads format
+.TP
+\fIsv\fR
+call structural variations
+.TP
+\fIindelpe\fR
+post\-processing indelpe output
+.SH AUTHOR
+The program was written by Heng Li <lh3 at sanger.ac.uk>.
+.P
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

Added: trunk/packages/maq/trunk/debian/mans/maq_eval.pl.1
===================================================================
--- trunk/packages/maq/trunk/debian/mans/maq_eval.pl.1	                        (rev 0)
+++ trunk/packages/maq/trunk/debian/mans/maq_eval.pl.1	2015-12-16 14:34:14 UTC (rev 20784)
@@ -0,0 +1,24 @@
+.TH MAQ_EVAL.PL "1" "December 2015" "maq_eval.pl 0.7.1" "User Commands"
+.SH NAME
+maq_eval.pl \- evaluate Maq SNPs/indels
+.SH SYNOPSIS
+.B maq_eval.pl
+\fI\,<command> <arguments>\/\fR
+.SH DESCRIPTION
+evaluate Maq SNPs/indels
+.P
+Version: 0.1.11
+.SH OPTIONS
+.TP
+\fIsub\fR
+evaluate substitutions
+.TP
+\fIgeno\fR
+evaluate genotyping results
+.TP
+\fIindelpe\fR
+evaluate indelpe results
+.SH AUTHOR
+The program was written by Heng Li <lh3 at sanger.ac.uk>.
+.P
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

Added: trunk/packages/maq/trunk/debian/mans/maq_plot.pl.1
===================================================================
--- trunk/packages/maq/trunk/debian/mans/maq_plot.pl.1	                        (rev 0)
+++ trunk/packages/maq/trunk/debian/mans/maq_plot.pl.1	2015-12-16 14:34:14 UTC (rev 20784)
@@ -0,0 +1,18 @@
+.TH MAQ_PLOT.PL "1" "December 2015" "maq_plot.pl 0.7.1" "User Commands"
+.SH NAME
+maq_plot.pl \- plot pairs along the chromosome
+.SH SYNOPSIS
+.B maq_plot.pl
+\fI\,<command> <arguments>\/\fR
+.SH OPTIONS
+.TP
+\fIabpair\fR
+plot abnormal pairs along the chromosome
+.TP
+\fIdepth\fR
+depth plot
+.TP
+\fImixed\fR
+mixed plot
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

Modified: trunk/packages/maq/trunk/debian/rules
===================================================================
--- trunk/packages/maq/trunk/debian/rules	2015-12-16 13:35:32 UTC (rev 20783)
+++ trunk/packages/maq/trunk/debian/rules	2015-12-16 14:34:14 UTC (rev 20784)
@@ -12,3 +12,9 @@
 
 override_dh_compress:
 	dh_compress --exclude=.pdf
+
+override_dh_installman:
+	dh_installman
+	# when installing via debian/manpages the .pl is stripped and the
+	# files will end up in /usr/share/man/pl/man1
+	cp -a debian/mans/*.1 debian/maq/usr/share/man/man1


