[med-svn] r5096 - in trunk/packages/bagphenotype/trunk/debian: . patches

Mon Aug 2 13:53:16 UTC 2010

Author: moeller
Date: 2010-08-02 13:53:14 +0000 (Mon, 02 Aug 2010)
New Revision: 5096

Added:
   trunk/packages/bagphenotype/trunk/debian/bagphenotype.pl.1
   trunk/packages/bagphenotype/trunk/debian/copyright
   trunk/packages/bagphenotype/trunk/debian/manpages
Removed:
   trunk/packages/bagphenotype/trunk/debian/bagphenotype.debhelper.log
Modified:
   trunk/packages/bagphenotype/trunk/debian/
   trunk/packages/bagphenotype/trunk/debian/control
   trunk/packages/bagphenotype/trunk/debian/patches/series
Log:
bagphenotype has just become usable.



Property changes on: trunk/packages/bagphenotype/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
   + 1

Deleted: trunk/packages/bagphenotype/trunk/debian/bagphenotype.debhelper.log
===================================================================

--- trunk/packages/bagphenotype/trunk/debian/bagphenotype.debhelper.log	2010-08-02 12:38:13 UTC (rev 5095)
+++ trunk/packages/bagphenotype/trunk/debian/bagphenotype.debhelper.log	2010-08-02 13:53:14 UTC (rev 5096)
@@ -1,32 +0,0 @@
-dh_installdirs
-dh_installdirs
-dh_installdocs
-dh_installexamples
-dh_installman
-dh_installinfo
-dh_installmenu
-dh_installcron
-dh_installinit
-dh_installdebconf
-dh_installemacsen
-dh_installcatalogs
-dh_installpam
-dh_installlogrotate
-dh_installlogcheck
-dh_installchangelogs
-dh_installudev
-dh_lintian
-dh_install
-dh_link
-dh_installmime
-dh_strip
-dh_compress
-dh_fixperms
-dh_makeshlibs
-dh_installdeb
-dh_perl
-dh_shlibdeps
-dh_gencontrol
-dh_link
-dh_md5sums
-dh_builddeb

Added: trunk/packages/bagphenotype/trunk/debian/bagphenotype.pl.1
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/bagphenotype.pl.1	                        (rev 0)
+++ trunk/packages/bagphenotype/trunk/debian/bagphenotype.pl.1	2010-08-02 13:53:14 UTC (rev 5096)
@@ -0,0 +1,234 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.38.2.
+.TH BAGPHENOTYPE.PL "1" "August 2010" "bagphenotype.pl " "User Commands"
+.SH NAME
+bagphenotype.pl \- manual page for bagphenotype.pl 
+.SH DESCRIPTION
+.SS "Usage:"
+.IP
+bagphenotype configfile [options ...]
+.SS "Requirements:"
+.IP
+Config file: a file of configuration parameters
+.IP
+HAPPY genome cache: a directory containing cached HAPPY matrices
+Phenotype file: a tab delimited table with phenotype and covariate
+.IP
+values for each animal. The table must include
+1) a column SUBJECT.NAME giving the id of the animal in
+the corresponding HAPPY data;
+2) a column with the name of the phenotype as listed in the
+Phenotype column of the model menu file;
+3) columns corresponding to any covariates used in the
+model menu formulae.
+.SH OPTIONS
+.TP
+outdir
+\- Directory for output. Default is ./
+.TP
+scandir
+\- Directory for output of scan data files within outdir (./)
+.TP
+peakdir
+\- Directory for thresholds, peaks and rma
+.TP
+gscan
+\- Genome scans
+.TP
+perm
+\- Permutations
+.TP
+null
+\- Null simulations
+.TP
+thresholds
+\- Define thresholds for additive and/or full models
+.IP
+as for example
+.IP
+thresholds=5a,4a,6f,5.5f
+.IP
+to mean 5 and 4 as high and low additive thresholds
+and 6 and 5.5 as high and low full thresholds
+.TP
+peaks
+\- Define peaks from genome scans based on
+.IP
+permutation or null simulation thresholds (see config)
+peak.separation (where 0 => choose all markers)
+.TP
+plot
+\- Plot single QTL model scans
+.TP
+plotpeaks
+\- Plot peaks chosen along with peak separation
+.IP
+and peak.ci.radius for each peak (from config)
+.TP
+plotsummary
+\- Plot summary of single and multiple QTL models
+.TP
+plot_height
+\- Notional height of plotsummary output in inches
+.TP
+plot_scale
+\- Scale used for plot summary, can be cM, bp, or Mb
+.TP
+plot_width
+\- Notional width of plotsummary output in inches
+.TP
+rma
+\- Resample model averaging of defined peaks
+.TP
+boot
+\- Positional bootstrap within peak.ci.radius of each peak
+.IP
+with rmip > rmip.thresh (from config)
+.TP
+cleanup
+\- Delete Rout files that do not report errors or warnings
+.TP
+dryrun
+\- Print commands but do not execute them
+.IP
+exploremodel \- Which model to explore with perm/null/rma/boot.
+.IP
+Default is both
+.TP
+memory
+\- Use memory where possible rather than disk access
+.IP
+[default is 1 = true]
+.IP
+nomenuconfig \- Write the complete config file for a phenotype
+.IP
+ie, incorporating all the information from the menu file
+but minus the menu file
+.SS "Example:"
+.IP
+Genome scans only
+.IP
+bagphenotype configfile \fB\-\-gscan\fR=\fI1\fR
+.IP
+Write commands to screen but do not execute
+.IP
+bagphenotype configfile \fB\-\-gscan\fR=\fI1\fR \fB\-\-dryrun\fR=\fI1\fR
+.SS "Usage:"
+.IP
+bagphenotype configfile [options ...]
+.SS "Requirements:"
+.IP
+Config file: a file of configuration parameters
+.IP
+HAPPY genome cache: a directory containing cached HAPPY matrices
+Phenotype file: a tab delimited table with phenotype and covariate
+.IP
+values for each animal. The table must include
+1) a column SUBJECT.NAME giving the id of the animal in
+the corresponding HAPPY data;
+2) a column with the name of the phenotype as listed in the
+Phenotype column of the model menu file;
+3) columns corresponding to any covariates used in the
+model menu formulae.
+.TP
+outdir
+\- Directory for output. Default is ./
+.TP
+scandir
+\- Directory for output of scan data files within outdir (./)
+.TP
+peakdir
+\- Directory for thresholds, peaks and rma
+.TP
+gscan
+\- Genome scans
+.TP
+perm
+\- Permutations
+.TP
+null
+\- Null simulations
+.TP
+thresholds
+\- Define thresholds for additive and/or full models
+.IP
+as for example
+.IP
+thresholds=5a,4a,6f,5.5f
+.IP
+to mean 5 and 4 as high and low additive thresholds
+and 6 and 5.5 as high and low full thresholds
+.TP
+peaks
+\- Define peaks from genome scans based on
+.IP
+permutation or null simulation thresholds (see config)
+peak.separation (where 0 => choose all markers)
+.TP
+plot
+\- Plot single QTL model scans
+.TP
+plotpeaks
+\- Plot peaks chosen along with peak separation
+.IP
+and peak.ci.radius for each peak (from config)
+.TP
+plotsummary
+\- Plot summary of single and multiple QTL models
+.TP
+plot_height
+\- Notional height of plotsummary output in inches
+.TP
+plot_scale
+\- Scale used for plot summary, can be cM, bp, or Mb
+.TP
+plot_width
+\- Notional width of plotsummary output in inches
+.TP
+rma
+\- Resample model averaging of defined peaks
+.TP
+boot
+\- Positional bootstrap within peak.ci.radius of each peak
+.IP
+with rmip > rmip.thresh (from config)
+.TP
+cleanup
+\- Delete Rout files that do not report errors or warnings
+.TP
+dryrun
+\- Print commands but do not execute them
+.IP
+exploremodel \- Which model to explore with perm/null/rma/boot.
+.IP
+Default is both
+.TP
+memory
+\- Use memory where possible rather than disk access
+.IP
+[default is 1 = true]
+.IP
+nomenuconfig \- Write the complete config file for a phenotype
+.IP
+ie, incorporating all the information from the menu file
+but minus the menu file
+.SS "Example:"
+.IP
+Genome scans only
+.IP
+bagphenotype configfile \fB\-\-gscan\fR=\fI1\fR
+.IP
+Write commands to screen but do not execute
+.IP
+bagphenotype configfile \fB\-\-gscan\fR=\fI1\fR \fB\-\-dryrun\fR=\fI1\fR
+.SH "SEE ALSO"
+The full documentation for
+.B bagphenotype.pl
+is maintained as a Texinfo manual.  If the
+.B info
+and
+.B bagphenotype.pl
+programs are properly installed at your site, the command
+.IP
+.B info bagphenotype.pl
+.PP
+should give you access to the complete manual.

Modified: trunk/packages/bagphenotype/trunk/debian/control
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/control	2010-08-02 12:38:13 UTC (rev 5095)
+++ trunk/packages/bagphenotype/trunk/debian/control	2010-08-02 13:53:14 UTC (rev 5096)
@@ -11,6 +11,6 @@
 
 Package: bagphenotype
 Architecture: all
-Depends: ${shlibs:Depends}, r-other-valdar-bagphenotype.library, libcarp-assert-perl, r-base-core, libgetopt-long-descriptive-perl, perl
+Depends: ${misc:Depends}, r-other-valdar-bagphenotype.library, libcarp-assert-perl, r-base-core, perl
 Description: CLI for the bagphenotype R package
  mapping QTLs in populations descended from known founders

Added: trunk/packages/bagphenotype/trunk/debian/copyright
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/bagphenotype/trunk/debian/copyright	2010-08-02 13:53:14 UTC (rev 5096)
@@ -0,0 +1,32 @@
+X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
+X-Debianized-By: Steffen Moeller moeller at debian.org
+X-Debinized-Date: Mon, 02 Aug 2010 15:40:15 +0200
+X-Source-Downloaded-From: http://www.unc.edu/~wvaldar/software/bagphenotype/distrib/
+Upstream Authors: William Valdar
+
+Files: debian/*
+Copyright: © 2010 Steffen Moeller <moeller at debian.org>
+License: GPL-3
+
+Files: *
+Copyright: © 2010 William Valdar
+License: GPL-3
+
+
+License: GPL-3
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This package is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+On Debian systems, the complete text of the GNU General
+Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".

Added: trunk/packages/bagphenotype/trunk/debian/manpages
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/manpages	                        (rev 0)
+++ trunk/packages/bagphenotype/trunk/debian/manpages	2010-08-02 13:53:14 UTC (rev 5096)
@@ -0,0 +1 @@
+debian/bagphenotype.pl.1

Modified: trunk/packages/bagphenotype/trunk/debian/patches/series
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/patches/series	2010-08-02 12:38:13 UTC (rev 5095)
+++ trunk/packages/bagphenotype/trunk/debian/patches/series	2010-08-02 13:53:14 UTC (rev 5096)
@@ -1 +1,2 @@
 bagphenotype_default_path.patch
+usage_to_stdout.patch


