Author: moeller
Date: 2010-08-02 12:38:13 +0000 (Mon, 02 Aug 2010)
New Revision: 5095
Added:
trunk/packages/bagphenotype/
trunk/packages/bagphenotype/README
trunk/packages/bagphenotype/r-other-valdar-bagphenotype
trunk/packages/bagphenotype/trunk/
trunk/packages/bagphenotype/trunk/debian/
trunk/packages/bagphenotype/trunk/debian/README.source
trunk/packages/bagphenotype/trunk/debian/bagphenotype.debhelper.log
trunk/packages/bagphenotype/trunk/debian/bagphenotype.dirs
trunk/packages/bagphenotype/trunk/debian/bagphenotype.install
trunk/packages/bagphenotype/trunk/debian/bagphenotype.substvars
trunk/packages/bagphenotype/trunk/debian/changelog
trunk/packages/bagphenotype/trunk/debian/compat
trunk/packages/bagphenotype/trunk/debian/control
trunk/packages/bagphenotype/trunk/debian/debhelper.log
trunk/packages/bagphenotype/trunk/debian/patches/
trunk/packages/bagphenotype/trunk/debian/patches/bagphenotype_default_path.patch
trunk/packages/bagphenotype/trunk/debian/patches/series
trunk/packages/bagphenotype/trunk/debian/rules
trunk/packages/bagphenotype/trunk/debian/source/
trunk/packages/bagphenotype/trunk/debian/source/format
trunk/packages/bagphenotype/trunk/debian/watch
Log:
Adding the Perl/R interface to the more core-level
bagphenotype library.
Added: trunk/packages/bagphenotype/README
===================================================================
--- trunk/packages/bagphenotype/README (rev 0)
+++ trunk/packages/bagphenotype/README 2010-08-02 12:38:13 UTC (rev 5095)
@@ -0,0 +1,2 @@
+bagphenotype - the perl code primarily used
+r-other-valdar-bagphenotype - the R code that the perl code uses
Added: trunk/packages/bagphenotype/r-other-valdar-bagphenotype
===================================================================
--- trunk/packages/bagphenotype/r-other-valdar-bagphenotype
(rev 0)
+++ trunk/packages/bagphenotype/r-other-valdar-bagphenotype 2010-08-02
12:38:13 UTC (rev 5095)
@@ -0,0 +1 @@
+link ../R/r-other-valdar-bagphenotype/
\ No newline at end of file
Property changes on: trunk/packages/bagphenotype/r-other-valdar-bagphenotype
___________________________________________________________________
Added: svn:special
+ *
Added: trunk/packages/bagphenotype/trunk/debian/README.source
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/README.source
(rev 0)
+++ trunk/packages/bagphenotype/trunk/debian/README.source 2010-08-02
12:38:13 UTC (rev 5095)
@@ -0,0 +1 @@
+Moved the license file into the root directory.
Added: trunk/packages/bagphenotype/trunk/debian/bagphenotype.debhelper.log
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/bagphenotype.debhelper.log
(rev 0)
+++ trunk/packages/bagphenotype/trunk/debian/bagphenotype.debhelper.log
2010-08-02 12:38:13 UTC (rev 5095)
@@ -0,0 +1,32 @@
+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.dirs
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/bagphenotype.dirs
(rev 0)
+++ trunk/packages/bagphenotype/trunk/debian/bagphenotype.dirs 2010-08-02
12:38:13 UTC (rev 5095)
@@ -0,0 +1,2 @@
+usr/bin
+usr/share/
Added: trunk/packages/bagphenotype/trunk/debian/bagphenotype.install
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/bagphenotype.install
(rev 0)
+++ trunk/packages/bagphenotype/trunk/debian/bagphenotype.install
2010-08-02 12:38:13 UTC (rev 5095)
@@ -0,0 +1,2 @@
+lib/* usr/share/bagphenotype
+bagphenotype.pl usr/bin
Added: trunk/packages/bagphenotype/trunk/debian/bagphenotype.substvars
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/bagphenotype.substvars
(rev 0)
+++ trunk/packages/bagphenotype/trunk/debian/bagphenotype.substvars
2010-08-02 12:38:13 UTC (rev 5095)
@@ -0,0 +1,2 @@
+perl:Depends=perl
+misc:Depends=
Added: trunk/packages/bagphenotype/trunk/debian/changelog
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/changelog
(rev 0)
+++ trunk/packages/bagphenotype/trunk/debian/changelog 2010-08-02 12:38:13 UTC
(rev 5095)
@@ -0,0 +1,5 @@
+bagphenotype (0.20100316-1) UNRELEASED; urgency=low
+
+ * Initial release.
+
+ -- Steffen Moeller <[email protected]> Mon, 02 Aug 2010 12:06:32 +0200
Added: trunk/packages/bagphenotype/trunk/debian/compat
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/compat
(rev 0)
+++ trunk/packages/bagphenotype/trunk/debian/compat 2010-08-02 12:38:13 UTC
(rev 5095)
@@ -0,0 +1 @@
+5
Added: trunk/packages/bagphenotype/trunk/debian/control
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/control
(rev 0)
+++ trunk/packages/bagphenotype/trunk/debian/control 2010-08-02 12:38:13 UTC
(rev 5095)
@@ -0,0 +1,16 @@
+Source: bagphenotype
+Section: perl
+Priority: optional
+Maintainer: Debian Med Packaging Team
<[email protected]>
+Uploaders: Steffen Moeller <[email protected]>
+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/
+
+Package: bagphenotype
+Architecture: all
+Depends: ${shlibs:Depends}, r-other-valdar-bagphenotype.library,
libcarp-assert-perl, r-base-core, libgetopt-long-descriptive-perl, perl
+Description: CLI for the bagphenotype R package
+ mapping QTLs in populations descended from known founders
Added: trunk/packages/bagphenotype/trunk/debian/debhelper.log
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/debhelper.log
(rev 0)
+++ trunk/packages/bagphenotype/trunk/debian/debhelper.log 2010-08-02
12:38:13 UTC (rev 5095)
@@ -0,0 +1 @@
+dh_installdirs
Added:
trunk/packages/bagphenotype/trunk/debian/patches/bagphenotype_default_path.patch
===================================================================
---
trunk/packages/bagphenotype/trunk/debian/patches/bagphenotype_default_path.patch
(rev 0)
+++
trunk/packages/bagphenotype/trunk/debian/patches/bagphenotype_default_path.patch
2010-08-02 12:38:13 UTC (rev 5095)
@@ -0,0 +1,20 @@
+Index: bagphenotype-0.20100316/bagphenotype.pl
+===================================================================
+--- bagphenotype-0.20100316.orig/bagphenotype.pl 2010-08-02
14:31:44.511364778 +0200
++++ bagphenotype-0.20100316/bagphenotype.pl 2010-08-02 14:36:01.613238056
+0200
+@@ -21,7 +21,14 @@
+ {
+ unless ($ENV{'BAGPHENOTYPE_LIBS'})
+ {
+- die "Error: shell variable \$BAGPHENOTYPE_LIBS must be
defined.\n";
++ my $d = "/usr/share/bagphenotype";
++ if ( -d "$d" ) {
++ $ENV{'BAGPHENOTYPE_LIBS'} = $d;
++ }
++ else {
++ die "Error: shell variable \$BAGPHENOTYPE_LIBS must be
defined. "
++ ."Would have set it myself, but default directory
expected at '$d' was not found.\n";
++ }
+ }
+ }
+ # General packages
Added: trunk/packages/bagphenotype/trunk/debian/patches/series
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/patches/series
(rev 0)
+++ trunk/packages/bagphenotype/trunk/debian/patches/series 2010-08-02
12:38:13 UTC (rev 5095)
@@ -0,0 +1 @@
+bagphenotype_default_path.patch
Added: trunk/packages/bagphenotype/trunk/debian/rules
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/rules
(rev 0)
+++ trunk/packages/bagphenotype/trunk/debian/rules 2010-08-02 12:38:13 UTC
(rev 5095)
@@ -0,0 +1,7 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/debhelper.mk
+
+clean::
+ $(RM) -r debian/stamp-*
+
Property changes on: trunk/packages/bagphenotype/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/bagphenotype/trunk/debian/source/format
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/source/format
(rev 0)
+++ trunk/packages/bagphenotype/trunk/debian/source/format 2010-08-02
12:38:13 UTC (rev 5095)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/bagphenotype/trunk/debian/watch
===================================================================
--- trunk/packages/bagphenotype/trunk/debian/watch
(rev 0)
+++ trunk/packages/bagphenotype/trunk/debian/watch 2010-08-02 12:38:13 UTC
(rev 5095)
@@ -0,0 +1,3 @@
+version=3
+opts="uversionmangle=s/^/0./;s/_//g" \
+http://www.unc.edu/~wvaldar/software/bagphenotype/distrib/bagphenotype_([0-9_]+)\.tgz
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