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 <moel...@debian.org> Mon, 02 Aug 2010 12:06:32 +0200 + -- Thorsten Alteholz <deb...@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-packag...@lists.alioth.debian.org> -Uploaders: Steffen Moeller <moel...@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 <moel...@debian.org>, + Thorsten Alteholz <deb...@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 <moel...@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: _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit