[med-svn] r9991 - in trunk/packages/bagphenotype/trunk/debian: . patches

Thorsten Alteholz alteholz at alioth.debian.org
Tue Mar 13 18:40:55 UTC 2012 

Author: alteholz
Date: 2012-03-13 18:40:55 +0000 (Tue, 13 Mar 2012)
New Revision: 9991

Added:
   trunk/packages/bagphenotype/trunk/debian/bagphenotype.1
Removed:
   trunk/packages/bagphenotype/trunk/debian/debhelper.log
Modified:
   trunk/packages/bagphenotype/trunk/debian/bagphenotype.install
   trunk/packages/bagphenotype/trunk/debian/changelog
   trunk/packages/bagphenotype/trunk/debian/control
   trunk/packages/bagphenotype/trunk/debian/manpages
   trunk/packages/bagphenotype/trunk/debian/patches/bagphenotype_default_path.patch
   trunk/packages/bagphenotype/trunk/debian/patches/series
   trunk/packages/bagphenotype/trunk/debian/rules
Log:
some cleanup, but I think this is for historical reasons only

Added: trunk/packages/bagphenotype/trunk/debian/bagphenotype.1
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/bagphenotype.1	                        (rev 0)
+++ trunk/packages/bagphenotype/trunk/debian/bagphenotype.1	2012-03-13 18:40:55 UTC (rev 9991)
@@ -0,0 +1,234 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.38.2.
+.TH BAGPHENOTYPE "1" "August 2010" "bagphenotype " "User Commands"
+.SH NAME
+bagphenotype \- mapping QTLs in populations descended from known founders
+.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
+is maintained as a Texinfo manual.  If the
+.B info
+and
+.B bagphenotype
+programs are properly installed at your site, the command
+.IP
+.B info bagphenotype
+.PP
+should give you access to the complete manual.

Modified: trunk/packages/bagphenotype/trunk/debian/bagphenotype.install
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/bagphenotype.install	2012-03-13 18:35:50 UTC (rev 9990)
+++ trunk/packages/bagphenotype/trunk/debian/bagphenotype.install	2012-03-13 18:40:55 UTC (rev 9991)
@@ -1,2 +1,2 @@
-lib/*	usr/share/bagphenotype
-bagphenotype.pl	usr/bin
+bagphenotype/lib/*	usr/share/bagphenotype
+bagphenotype/bagphenotype	usr/bin

Modified: trunk/packages/bagphenotype/trunk/debian/changelog
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/changelog	2012-03-13 18:35:50 UTC (rev 9990)
+++ trunk/packages/bagphenotype/trunk/debian/changelog	2012-03-13 18:40:55 UTC (rev 9991)
@@ -2,8 +2,9 @@
 
   * Initial release.
 
-  [ Thorsten Alteholz ]
   * debian/rules: target get-orig-source added
   * debian/watch: fixed
+  * debian/rules: moved to dh
+  * debian/bagphenotype.install: path fixed
 
- -- Steffen Moeller <moeller at debian.org>  Mon, 02 Aug 2010 12:06:32 +0200
+ -- Thorsten Alteholz <debian at alteholz.de>  Sat, 10 Mar 2012 18:06:32 +0100

Modified: trunk/packages/bagphenotype/trunk/debian/control
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/control	2012-03-13 18:35:50 UTC (rev 9990)
+++ trunk/packages/bagphenotype/trunk/debian/control	2012-03-13 18:40:55 UTC (rev 9991)
@@ -2,12 +2,13 @@
 Section: perl
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Steffen Moeller <moeller at debian.org>
-Build-Depends: debhelper (>= 5.0.0), cdbs, r-base-dev, r-cran-g.data (>= 2.0)
-Standards-Version: 3.9.1.0
-Homepage: http://www.unc.edu/~wvaldar/bagphenotype.html
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/bagphenotype/bagphenotype/debian/?rev=0&sc=0
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/bagphenotype/bagphenotype/trunk/
+Uploaders: Steffen Moeller <moeller at debian.org>,
+ Thorsten Alteholz <debian at alteholz.de>
+Build-Depends: debhelper (>= 9.0.0), r-base-dev, r-cran-g.data (>= 2.0)
+Standards-Version: 3.9.3.0
+Homepage: http://valdarlab.unc.edu/bagphenotype.html
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/bagphenotype/bagphenotype/debian/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/bagphenotype/bagphenotype/trunk/
 
 Package: bagphenotype
 Architecture: all

Deleted: trunk/packages/bagphenotype/trunk/debian/debhelper.log
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/debhelper.log	2012-03-13 18:35:50 UTC (rev 9990)
+++ trunk/packages/bagphenotype/trunk/debian/debhelper.log	2012-03-13 18:40:55 UTC (rev 9991)
@@ -1 +0,0 @@
-dh_installdirs

Modified: trunk/packages/bagphenotype/trunk/debian/manpages
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/manpages	2012-03-13 18:35:50 UTC (rev 9990)
+++ trunk/packages/bagphenotype/trunk/debian/manpages	2012-03-13 18:40:55 UTC (rev 9991)
@@ -1 +1 @@
-debian/bagphenotype.pl.1
+debian/bagphenotype.1

Modified: trunk/packages/bagphenotype/trunk/debian/patches/bagphenotype_default_path.patch
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/patches/bagphenotype_default_path.patch	2012-03-13 18:35:50 UTC (rev 9990)
+++ trunk/packages/bagphenotype/trunk/debian/patches/bagphenotype_default_path.patch	2012-03-13 18:40:55 UTC (rev 9991)
@@ -1,7 +1,10 @@
+Description: introduce default path for BAGPHENOTYPE_LIBS
+Author: Steffen Moeller <moeller at debian.org>
+
 Index: bagphenotype-0.20100316/bagphenotype.pl
 ===================================================================
---- bagphenotype-0.20100316.orig/bagphenotype.pl	2010-08-02 14:31:44.511364778 +0200
-+++ bagphenotype-0.20100316/bagphenotype.pl	2010-08-02 14:36:01.613238056 +0200
+--- bagphenotype-0.20100316.orig/bagphenotype/bagphenotype.pl	2010-08-02 14:31:44.511364778 +0200
++++ bagphenotype-0.20100316/bagphenotype/bagphenotype.pl	2010-08-02 14:36:01.613238056 +0200
 @@ -21,7 +21,14 @@
  {
  	unless ($ENV{'BAGPHENOTYPE_LIBS'})

Modified: trunk/packages/bagphenotype/trunk/debian/patches/series
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/patches/series	2012-03-13 18:35:50 UTC (rev 9990)
+++ trunk/packages/bagphenotype/trunk/debian/patches/series	2012-03-13 18:40:55 UTC (rev 9991)
@@ -1,2 +1,2 @@
 bagphenotype_default_path.patch
-usage_to_stdout.patch
+#usage_to_stdout.patch

Modified: trunk/packages/bagphenotype/trunk/debian/rules
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/rules	2012-03-13 18:35:50 UTC (rev 9990)
+++ trunk/packages/bagphenotype/trunk/debian/rules	2012-03-13 18:40:55 UTC (rev 9991)
@@ -1,8 +1,14 @@
 #!/usr/bin/make -f
 
-include /usr/share/cdbs/1/rules/debhelper.mk
+%:
+	dh $@
 
-clean::
+override_dh_install:
+	cp bagphenotype/bagphenotype.pl bagphenotype/bagphenotype
+	dh_install
+
+override_dh_clean:
+	dh_clean
 	$(RM) -r debian/stamp-*
 
 get-orig-source:

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