[med-svn] [probabel] 03/04: Add patch with man-page for probabel.pl. Fixes another lintian warning.

[Lennart Karssen]

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lckarssen-guest pushed a commit to branch master
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commit cabee88e87445e2e3248ad7cf9a6d31be4f4ede4
Author: L.C. Karssen <lennart at karssen.org>
Date:   Fri Dec 13 01:36:37 2013 +0100

    Add patch with man-page for probabel.pl. Fixes another lintian warning.
---
 debian/patches/man-page-probabel.pl | 82 +++++++++++++++++++++++++++++++++++++
 1 file changed, 82 insertions(+)

diff --git a/debian/patches/man-page-probabel.pl b/debian/patches/man-page-probabel.pl
new file mode 100644
index 0000000..9c06320
--- /dev/null
+++ b/debian/patches/man-page-probabel.pl
@@ -0,0 +1,82 @@
+Description: Add man-page for probabel.pl
+ This patch will be sent upstream.
+Forwarded: TODO
+Author: Lennart C. Karssen <lennart at karssen.org>
+Last-Update: 2013-12-12
+
+--- /dev/null
++++ b/doc/probabel.pl.1
+@@ -0,0 +1,73 @@
++.TH probabel.pl 1 "12 December 2013"
++.SH NAME
++probabel.pl \- Wrapper around the three ProbABEL binaries, simplifying their use
++.SH SYNOPSIS
++.B probabel.pl
++.BI "" "CHROM-START CHROM-STOP METHOD COHORT MODEL PHENOTYPE [OTHER_OPTIONS]"
++.SH DESCRIPTION
++.B probabel.pl
++is a wrapper around the three ProbABEL binaries: \fBpalinear\fR,
++\fBpalogist\fR, and \fBpacoxph\fR.
++.PP
++It is designed to simplify runnig of a Genome-Wide Association Study
++(GWAS) by saving the user's precious time in two ways:
++.PP
++1) it runs the regression analysis of all chromosomes from \fICHROM-START\fR to
++\fICHROM-STOP\fR.
++.PP
++2) In contrast to the three binaries mentioned above,
++with \fBprobabel.pl\fR the user doesn't need to specify the locations
++of the required genetic data files. Their location is centrally
++managed in a configuration file (\fI/etc/probabel_config.cfg\fR by default).
++
++.SH OPTIONS
++.SS Required command line options
++.TP
++.I CHROM-START
++Number of the chromosome to start the analysis at.
++.TP
++.I CHROM-END
++Number of the chromosome to end the analysis at.
++.PP
++Note that analysis of a single chromosome can be run by specifying the
++same number for \fICHROM-START\fR and \fICHROM-STOP\fR. In fact, this
++is the way to run analysis for the X or Y chromosome
++.TP
++.I METHOD
++Which regression method to use, can be one of \fIlinear\fR,
++\fIlogistic,\fR or \fIcoxph\fR.
++
++.TP
++.I COHORT
++The name of the cohort as defined in the
++\fI/etc/probabel_config.cfg\fR file. Using the cohort identifier from
++the config file the three actual ProbABEL binaries know where to find
++the genotypic information files (dosage files and/or probability
++files).
++.TP
++.I MODEL
++The genetic model to be used. Can be either \fB--additive\fR for the
++additive model (requires genotype data in dosage form), or
++\fB--allmodels\fR to run all genetic models: additive, recessive,
++dominant, over-dominant and 2df.
++.TP
++.I PHENOTYPE
++The name of the phenotype file, without its extension (which should be
++\fI.PHE\fR!).
++
++.SS Other options
++Any options listed after the (mandatory) previous ones will be passed
++on to the underlying binary: \fBpalinear\fR, \fBpalogist\fR or
++\fBpacoxph\fR, depending on the \fIMETHOD\fR.
++.PP
++The most commonly used option is the \fB\-o\fR option, followed by a
++file name, this specifies the beginning of the file name for the
++output files.
++
++.SS Additional options
++.B "\-h, \-\-help"
++Get additional help on how to run \fBprobabel.pl\fR. In this case none of
++the other options needs to be specified.
++
++.SH EXAMPLES
++probabel.pl 1 22 linear "My_Large_Cohort" --additive my_phenotype

-- 
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