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commit 8a403c31aacabb4db85d5d94bc34006a2f682362 Author: Andreas Tille <[email protected]> Date: Tue May 2 13:42:45 2017 +0200 Add manpage --- debian/configManta.1 | 80 +++++++++++++++++++++++++++++++++++++++++++++++++++ debian/createmanpages | 22 ++++++++++++++ debian/manpages | 1 + 3 files changed, 103 insertions(+) diff --git a/debian/configManta.1 b/debian/configManta.1 new file mode 100644 index 0000000..ca9d119 --- /dev/null +++ b/debian/configManta.1 @@ -0,0 +1,80 @@ +.TH CONFIGMANTA "1" "May 2017" "configManta 1.0.2" "User Commands" +.SH NAME +configManta \- configure the Manta SV analysis pipeline +.SH SYNOPSIS +.B configManta.py +[\fI\,options\/\fR] +.SH DESCRIPTION +This script configures the Manta SV analysis pipeline. +You must specify a BAM or CRAM file for at least one sample. +.PP +Configuration will produce a workflow run script which +can execute the workflow on a single node or through +sge and resume any interrupted execution. +.SH OPTIONS +.TP +\fB\-\-version\fR +show program's version number and exit +.TP +\fB\-h\fR, \fB\-\-help\fR +show this help message and exit +.TP +\fB\-\-config\fR=\fI\,FILE\/\fR +provide a configuration file to override defaults in +global config file +(\fI\,/usr/share/manta/configManta.py.ini\/\fP) +.TP +\fB\-\-allHelp\fR +show all extended/hidden options +.IP +.SS Workflow options +.TP +\fB\-\-bam\fR=\fI\,FILE\/\fR, \fB\-\-normalBam\fR=\fI\,FILE\/\fR +Normal sample BAM or CRAM file. May be specified more +than once, multiple inputs will be treated as each BAM +file representing a different sample. [optional] (no +default) +.TP +\fB\-\-tumorBam\fR=\fI\,FILE\/\fR, \fB\-\-tumourBam\fR=\fI\,FILE\/\fR +Tumor sample BAM or CRAM file. Only up to one tumor +bam file accepted. [optional] (no default) +.TP +\fB\-\-exome\fR +Set options for WES input: turn off depth filters +.TP +\fB\-\-rna\fR +Set options for RNA\-Seq input: turn off depth filters +and don't treat anomalous reads as SV evidence when +the proper\-pair bit is set. +.TP +\fB\-\-unstrandedRNA\fR +Set if RNA\-Seq input is unstranded: Allows splicejunctions on either strand +.TP +\fB\-\-referenceFasta\fR=\fI\,FILE\/\fR +samtools\-indexed reference fasta file [required] +.TP +\fB\-\-runDir\fR=\fI\,DIR\/\fR +Run script and run output will be written to this +directory [required] (default: MantaWorkflow) +.SS Extended options: +.PP +These options are either unlikely to be reset after initial site +configuration or only of interest for workflow development/debugging. +They will not be printed here if a default exists unless \fB\-\-allHelp\fR is +specified +.TP +\fB\-\-scanSizeMb\fR=\fI\,INT\/\fR +Maximum sequence region size (in megabases) scanned by +each task during SV Locus graph generation. (default: +12) +.TP +\fB\-\-region\fR=\fI\,REGION\/\fR +Limit the analysis to a region of the genome for +debugging purposes. If this argument is provided +multiple times all specified regions will be analyzed +together. All regions must be non\-overlapping to get a +meaningful result. Examples: '\-\-region chr20' (whole +chromosome), '\-\-region chr2:100\-2000 \fB\-\-region\fR +chr3:2500\-3000' (two regions)' +.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/createmanpages b/debian/createmanpages new file mode 100755 index 0000000..b8ed6b4 --- /dev/null +++ b/debian/createmanpages @@ -0,0 +1,22 @@ +#!/bin/sh +MANDIR=debian +mkdir -p $MANDIR + +VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'` + +AUTHOR=".SH AUTHOR\nThis manpage was written by $DEBFULLNAME for the Debian distribution and +can be used for any other usage of the program. +" + +progname=configManta +help2man --no-info --no-discard-stderr --help-option=" --allHelp" \ + --name='configure the Manta SV analysis pipeline' \ + --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1 +echo $AUTHOR >> $MANDIR/${progname}.1 + +cat <<EOT +Please enhance the help2man output. +The following web page might be helpful in doing so: + http://liw.fi/manpages/ +EOT + 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/manta.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
