Author: alteholz Date: 2013-04-09 17:54:02 +0000 (Tue, 09 Apr 2013) New Revision: 13282
Added: trunk/packages/bagpipe/ trunk/packages/bagpipe/trunk/ trunk/packages/bagpipe/trunk/debian/ trunk/packages/bagpipe/trunk/debian/bagpipe.1 trunk/packages/bagpipe/trunk/debian/bagpipe.install trunk/packages/bagpipe/trunk/debian/bagpipe.manpages trunk/packages/bagpipe/trunk/debian/changelog trunk/packages/bagpipe/trunk/debian/compat trunk/packages/bagpipe/trunk/debian/control trunk/packages/bagpipe/trunk/debian/copyright trunk/packages/bagpipe/trunk/debian/rules trunk/packages/bagpipe/trunk/debian/script/ trunk/packages/bagpipe/trunk/debian/script/bagpipe trunk/packages/bagpipe/trunk/debian/source/ trunk/packages/bagpipe/trunk/debian/source/format trunk/packages/bagpipe/trunk/debian/watch Log: start of packaging Property changes on: trunk/packages/bagpipe/trunk/debian ___________________________________________________________________ Added: mergeWithUpstream + 1 Added: trunk/packages/bagpipe/trunk/debian/bagpipe.1 =================================================================== --- trunk/packages/bagpipe/trunk/debian/bagpipe.1 (rev 0) +++ trunk/packages/bagpipe/trunk/debian/bagpipe.1 2013-04-09 17:54:02 UTC (rev 13282) @@ -0,0 +1,150 @@ +.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.41.1. +.TH bagpipe "1" "April 2013" "bagpipe" "User Commands" +.SH NAME +bagpipe \- a pipeline for genetic association using HAPPY genome data +.SS "Usage:" +.IP +bagpipe configfile [\-action(s)] [\-option(s)=argument] +.PP +actions: scan, perm, perm_collate, nullsim, nullsim_collate, plot +.PP +options: locus_groups, outdir, scandir, plot_height, plot_width, +plot_scale, plot_type, plot_score, plot_tailprob memory, overwrite +.PP +Type 'bagpipe \fB\-h\fR' for summary usage +.PP +\&'bagpipe \fB\-\-help\fR' for detailed usage +.PP +\&'bagpipe \fB\-\-examples\fR' for examples +.PP +Requirements: +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 +.IP +1) a column SUBJECT.NAME giving the id of the animal in +the corresponding HAPPY data; +.IP +2) a column with the name of the phenotype as listed in the +Phenotype column of the model menu file; +.IP +3) columns corresponding to any covariates used in the +model menu formulae. +.PP +Key: +.IP +n \- an integer +.IP +d \- a decimal +.IP +s \- a string +.IP +b \- 1 for true and 0 for false. +.IP +xL \- a comma separated list of type x +.IP +locus.group \- either the name of a chromosome (eg, 1 or X) or a file of marker names. +.SS "Actions:" +.TP +scan +\- Genome scans +.TP +perm +\- Permutations +.TP +perm_collate +\- Calculate permutation thresholds +.TP +nullsim +\- Null simulations (not yet implemented) +.TP +nullsim_collate +\- Calculate null simulation thresholds (not yet implemented) +.TP +plot +\- Plot QTL scans to pdf file. +.TP +scanloci=sL +\- [Experimental] Scan individual loci, saving all fit information +.TP +posboot=sL +\- [Experimental] Perform k positional bootstraps between marker +.IP +intervals m1 and m2, where s=m1,m2,k +.SS "Settings:" +.TP +outdir +\- Directory for output. Default is ./ +.TP +scandir +\- Directory for output of scan data files within outdir (./) +.TP +locus_groups=sL +\- Run analyses on certain locus groups only [Default: do all in configfile] +.TP +save.at.loci=sL +\- [Experimental] Save model fit when scanning at specified loci. +.TP +tailprobs=dL +\- Calculate nullscan tail probabilities (ie, significance thresholds). +.IP +Eg, 0.05,0.01. [Default nL=0.001,0.01,0.05,0.1,0.2] +.SS "Plotting:" +.TP +plot_box +\- Draw box around each plot +.TP +plot_scale=s +\- Scale used for plot summary s={cM,bp,Mb} +.TP +plot_score=s +\- Specify locus score to plot s={LOD,modelcmp} +.TP +plot_type=s +\- s = {chromosomes,genome} +.IP +plot_tailprob=sL \- Include threshold lines as calculated by the *_collate options. +.IP +Each string s should have format <nullscantype>_<d>, where +nullscantype={perm,nullsim} and <d> is the tailprob looked up in the +corresponding thresh file. Eg, s=perm_0.05 plots the 0.05 threshold +calculated by permutation. +.TP +plot_height=d +\- Notional height of plotsummary output in inches +.TP +plot_width=d +\- Notional width of plotsummary output in inches +.SS "Performance:" +.TP +cleanup +\- Delete Rout files that do not report errors or warnings +.TP +dryrun +\- Print commands but do not execute them +.TP +memory=d +\- Store marker matrices in memory upto n Mb [default n=0] +.TP +nomenuconfig +\- Write the complete config file for an analysis +.IP +ie, incorporating all the information from the menu file +but minus the menu file +.TP +overwrite=b +\- Overwrite existing analysis files [Default overwrite=0] +.SS "Help:" +.TP +examples +\- Give examples +.TP +example_config +\- Write an example config file to config.example +.SS "Web" +.TP +More information can be found at: +http://valdarlab.unc.edu/software/bagpipe/_build/html/bagpipe.html Added: trunk/packages/bagpipe/trunk/debian/bagpipe.install =================================================================== --- trunk/packages/bagpipe/trunk/debian/bagpipe.install (rev 0) +++ trunk/packages/bagpipe/trunk/debian/bagpipe.install 2013-04-09 17:54:02 UTC (rev 13282) @@ -0,0 +1,3 @@ +debian/script/bagpipe usr/bin +bagpipe/bagpipe.pl usr/share/bagpipe +bagpipe/lib/* usr/share/perl5/Bagpipe Added: trunk/packages/bagpipe/trunk/debian/bagpipe.manpages =================================================================== --- trunk/packages/bagpipe/trunk/debian/bagpipe.manpages (rev 0) +++ trunk/packages/bagpipe/trunk/debian/bagpipe.manpages 2013-04-09 17:54:02 UTC (rev 13282) @@ -0,0 +1 @@ +debian/bagpipe.1 Added: trunk/packages/bagpipe/trunk/debian/changelog =================================================================== --- trunk/packages/bagpipe/trunk/debian/changelog (rev 0) +++ trunk/packages/bagpipe/trunk/debian/changelog 2013-04-09 17:54:02 UTC (rev 13282) @@ -0,0 +1,6 @@ +bagpipe (2012.02.15-1) UNRELEASED; urgency=low + + * initial version (Closes: #XXXXXX) + + -- Thorsten Alteholz <deb...@alteholz.de> Tue, 09 Apr 2013 18:00:07 +0200 + Added: trunk/packages/bagpipe/trunk/debian/compat =================================================================== --- trunk/packages/bagpipe/trunk/debian/compat (rev 0) +++ trunk/packages/bagpipe/trunk/debian/compat 2013-04-09 17:54:02 UTC (rev 13282) @@ -0,0 +1 @@ +9 Added: trunk/packages/bagpipe/trunk/debian/control =================================================================== --- trunk/packages/bagpipe/trunk/debian/control (rev 0) +++ trunk/packages/bagpipe/trunk/debian/control 2013-04-09 17:54:02 UTC (rev 13282) @@ -0,0 +1,45 @@ +Source: bagpipe +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> +Uploaders: Thorsten Alteholz <deb...@alteholz.de> +Build-Depends: debhelper (>= 9) +Standards-Version: 3.9.4 +Homepage: http://valdarlab.unc.edu/software/bagpipe/_build/html/bagpipe.html +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/bagpipe/trunk/ +Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/bagpipe/trunk/ + +Package: bagpipe +Architecture: all +Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends} +Description: genomewide LD mapping + Bagpipe is a program for performing genomewide linkage disequilibrium + mapping of quantitative trait loci in populations whose genome structure + can be accommodated in the HAPPY framework [Mott00]. This includes most + diploid crosses where the founders of the individuals have known genotypes. + . + * Bagpipe is a simplified and streamlined version of Bagphenotype that + does not currently include resample model averaging (RMA) capabilities. + * Bagpipe can help fit single locus regression models (with or without + random effects) to marker intervals whose genetic ancestry is inferred + using the HAPPY software. + * Bagpipe cannot help you decide what is a sensible model to fit. + * Bagpipe does not currently accommodate populations with significant + population structure, except through the specification of simple random + intercepts based on unpatterned covariance matrices. + * Bagpipe is named after the Scottish wind instrument "the bagpipes" and + after Bagphenotype, which in turn was a PIPEline for BAGging-based + multiple QTL analysis of phenoTYPEs. Bagphenotype was in turn based + on software written by Richard Mott and William Valdar to analyze + heterogeneous stock mice in [Valdar06]. + * Bagpipe is experimental software, is provided free of charge subject to + copyleft restrictions, and comes with no guarantees whatsoever. + . + [Mott00] Mott R, Talbot CJ, Turri MG, Collins AC, Flint, J (2000) + A method for fine mapping quantitative trait loci in outbred animal + stocks. Proceedings of the National Academy of Sciences of the United + States of America, 97(23), 12649-54. + [Valdar06] Valdar W, Solberg LC, Gaugier D, Burnett S, Klenerman P, + Cookson WO, Taylor M, Rawlins JNP, Mott R, Flint J (2006) + Genome-wide genetic association of complex traits in outbred mice. + Nature Genetics 38(8):879-87. PMID:16832355 Added: trunk/packages/bagpipe/trunk/debian/copyright =================================================================== --- trunk/packages/bagpipe/trunk/debian/copyright (rev 0) +++ trunk/packages/bagpipe/trunk/debian/copyright 2013-04-09 17:54:02 UTC (rev 13282) @@ -0,0 +1,27 @@ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: bagpipe +Source: http://valdarlab.unc.edu/software/bagpipe/_build/html/bagpipe.html + +Files: * +Copyright: 2012 William Valda +License: GPL3+ + bagpipe 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. + . + bagpipe 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 bagpipe. If not, see <http://www.gnu.org/licenses/>. + . + On Debian systems, the complete text of the GNU General + Public License version 2 can be found in "/usr/share/common-licenses/GPL-3". + +Files: debian/* +Copyright: 2013 Thorsten Alteholz <deb...@alteholz.de> +License: GPL3+ + see above Added: trunk/packages/bagpipe/trunk/debian/rules =================================================================== --- trunk/packages/bagpipe/trunk/debian/rules (rev 0) +++ trunk/packages/bagpipe/trunk/debian/rules 2013-04-09 17:54:02 UTC (rev 13282) @@ -0,0 +1,16 @@ +#!/usr/bin/make -f + +# DH_VERBOSE := 1 + +%: + dh $@ + +override_dh_auto_install: + dh_auto_install + ls -lR +# dh_installchangelogs README + +get-orig-source: + mkdir -p ../tarballs + uscan --verbose --force-download --destdir=../tarballs + Property changes on: trunk/packages/bagpipe/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/bagpipe/trunk/debian/script/bagpipe =================================================================== --- trunk/packages/bagpipe/trunk/debian/script/bagpipe (rev 0) +++ trunk/packages/bagpipe/trunk/debian/script/bagpipe 2013-04-09 17:54:02 UTC (rev 13282) @@ -0,0 +1,4 @@ +#!/bin/bash + +export BAGPIPE_LIBS=/usr/share/perl5/Bagpipe +/usr/share/bagpipe/bagpipe.pl $@ Property changes on: trunk/packages/bagpipe/trunk/debian/script/bagpipe ___________________________________________________________________ Added: svn:executable + * Added: trunk/packages/bagpipe/trunk/debian/source/format =================================================================== --- trunk/packages/bagpipe/trunk/debian/source/format (rev 0) +++ trunk/packages/bagpipe/trunk/debian/source/format 2013-04-09 17:54:02 UTC (rev 13282) @@ -0,0 +1 @@ +3.0 (quilt) Added: trunk/packages/bagpipe/trunk/debian/watch =================================================================== --- trunk/packages/bagpipe/trunk/debian/watch (rev 0) +++ trunk/packages/bagpipe/trunk/debian/watch 2013-04-09 17:54:02 UTC (rev 13282) @@ -0,0 +1,4 @@ +version=3 +opts="uversionmangle=s/_/./g" \ + http://valdarlab.unc.edu/software/bagpipe/_build/html/bagpipe.html http://valdarlab.unc.edu/software/bagpipe/install/bagpipe_([\d_]+)\.tar\.gz + _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit