[med-svn] [bagpipe] 01/06: start of packaging
Andreas Tille
tille at debian.org
Sat Dec 2 08:23:42 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository bagpipe.
commit 5c7d8c42edcf91de51d5bc746936654121428b2e
Author: Thorsten Alteholz <alteholz at debian.org>
Date: Tue Apr 9 17:54:02 2013 +0000
start of packaging
---
debian/bagpipe.1 | 150 ++++++++++++++++++++++++++++++++++++++++++++++++
debian/bagpipe.install | 3 +
debian/bagpipe.manpages | 1 +
debian/changelog | 6 ++
debian/compat | 1 +
debian/control | 45 +++++++++++++++
debian/copyright | 27 +++++++++
debian/rules | 16 ++++++
debian/script/bagpipe | 4 ++
debian/source/format | 1 +
debian/watch | 4 ++
11 files changed, 258 insertions(+)
diff --git a/debian/bagpipe.1 b/debian/bagpipe.1
new file mode 100644
index 0000000..73219c7
--- /dev/null
+++ b/debian/bagpipe.1
@@ -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
diff --git a/debian/bagpipe.install b/debian/bagpipe.install
new file mode 100644
index 0000000..7bb8044
--- /dev/null
+++ b/debian/bagpipe.install
@@ -0,0 +1,3 @@
+debian/script/bagpipe usr/bin
+bagpipe/bagpipe.pl usr/share/bagpipe
+bagpipe/lib/* usr/share/perl5/Bagpipe
diff --git a/debian/bagpipe.manpages b/debian/bagpipe.manpages
new file mode 100644
index 0000000..752cbb0
--- /dev/null
+++ b/debian/bagpipe.manpages
@@ -0,0 +1 @@
+debian/bagpipe.1
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..dc8b2c6
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,6 @@
+bagpipe (2012.02.15-1) UNRELEASED; urgency=low
+
+ * initial version (Closes: #XXXXXX)
+
+ -- Thorsten Alteholz <debian at alteholz.de> Tue, 09 Apr 2013 18:00:07 +0200
+
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..aa8ecd9
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,45 @@
+Source: bagpipe
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Thorsten Alteholz <debian at 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
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..9a1044f
--- /dev/null
+++ b/debian/copyright
@@ -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 <debian at alteholz.de>
+License: GPL3+
+ see above
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..6d852ff
--- /dev/null
+++ b/debian/rules
@@ -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
+
diff --git a/debian/script/bagpipe b/debian/script/bagpipe
new file mode 100755
index 0000000..3f5b7c2
--- /dev/null
+++ b/debian/script/bagpipe
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+export BAGPIPE_LIBS=/usr/share/perl5/Bagpipe
+/usr/share/bagpipe/bagpipe.pl $@
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..76ff926
--- /dev/null
+++ b/debian/watch
@@ -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
+
--
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