[med-svn] r6658 - in trunk/packages/gbrowse/tags: . 2.26~dfsg-2/debian
Aaron M. Ucko
ucko at alioth.debian.org
Wed Apr 27 01:49:34 UTC 2011
Author: ucko
Date: 2011-04-27 01:49:33 +0000 (Wed, 27 Apr 2011)
New Revision: 6658
Added:
trunk/packages/gbrowse/tags/2.26~dfsg-2/
trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/changelog
trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/control
trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/gbrowse.dirs
trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/rules
Removed:
trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/changelog
trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/control
trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/gbrowse.dirs
trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/rules
Log:
[svn-buildpackage] Tagging gbrowse 2.26~dfsg-2
Deleted: trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/changelog
===================================================================
--- trunk/packages/gbrowse/trunk/debian/changelog 2011-04-26 15:49:20 UTC (rev 6648)
+++ trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/changelog 2011-04-27 01:49:33 UTC (rev 6658)
@@ -1,6 +0,0 @@
-gbrowse (2.26~dfsg-1) experimental; urgency=low
-
- [ Olivier Sallou ]
- * Initial Release (Closes: #429610).
-
- -- Charles Plessy <plessy at debian.org> Wed, 13 Apr 2011 14:45:45 +0900
Copied: trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/changelog (from rev 6656, trunk/packages/gbrowse/trunk/debian/changelog)
===================================================================
--- trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/changelog (rev 0)
+++ trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/changelog 2011-04-27 01:49:33 UTC (rev 6658)
@@ -0,0 +1,16 @@
+gbrowse (2.26~dfsg-2) unstable; urgency=low
+
+ * Team upload.
+ * Upload to unstable, where -1 accidentally landed.
+ * debian/{gbrowse.dirs,rules}: Tweak to avoid errors when building just
+ the architecture-dependent gbrowse-calign package. (Closes: #624130.)
+ * debian/control: Temporarily add myself to uploaders to placate dak.
+
+ -- Aaron M. Ucko <ucko at debian.org> Tue, 26 Apr 2011 21:46:23 -0400
+
+gbrowse (2.26~dfsg-1) experimental; urgency=low
+
+ [ Olivier Sallou ]
+ * Initial Release (Closes: #429610).
+
+ -- Charles Plessy <plessy at debian.org> Wed, 13 Apr 2011 14:45:45 +0900
Deleted: trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/control
===================================================================
--- trunk/packages/gbrowse/trunk/debian/control 2011-04-26 15:49:20 UTC (rev 6648)
+++ trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/control 2011-04-27 01:49:33 UTC (rev 6658)
@@ -1,62 +0,0 @@
-Source: gbrowse
-Section: science
-Priority: optional
-Build-Depends: bioperl (>= 1.5.9), debhelper (>= 8),
- libbio-graphics-perl (>= 2.09), libcapture-tiny-perl,
- libcgi-session-perl (>= 4.02),
- libgd-gd2-perl (>= 2.07) | libgd-gd2-noxpm-perl (>= 2.07), libio-string-perl,
- libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, perl,
- perl (>= 5.10.0) | libextutils-cbuilder-perl, sqlite3,libdbd-sqlite3-perl, libterm-readkey-perl, libjs-prototype (>=1.7), libjs-scriptaculous (>= 1.9)
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Olivier Sallou <olivier.sallou at irisa.fr>,
- Charles Plessy <plessy at debian.org>
-DM-Upload-Allowed: yes
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/gbrowse/trunk/
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/gbrowse/?rev=0&sc=0
-Standards-Version: 3.9.1
-Homepage: http://www.gbrowse.org/
-
-Package: gbrowse
-Architecture: all
-Depends: ${misc:Depends}, ${perl:Depends},
- bioperl (>= 1.5.9), libbio-graphics-perl (>= 2.09),
- libcgi-session-perl (>= 4.02),
- libgd-gd2-noxpm-perl (>= 2.07) | libgd-gd2-perl (>= 2.07), libio-string-perl,
- libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, perl,
- perl (>= 5.10.0) | libextutils-cbuilder-perl, libterm-readkey-perl, sqlite3, libdbd-sqlite3-perl, libjs-prototype (>=1.7), libjs-scriptaculous (>=1.9)
-Suggests: gbrowse-data, gbrowse-calign
-Description: The GMOD Generic Genome Browser
- The Generic Genome Browser is a simple but highly
- configurable web-based genome browser. It is a component of the
- Generic Model Organism Systems Database project (GMOD).
- Some of its features:
- * Simultaneous bird's eye and detailed views of the genome;
- * Scroll, zoom, center;
- * Attach arbitrary URLs to any annotation;
- * Order and appearance of tracks are customizable by administrator and
- end-user;
- * Search by annotation ID, name, or comment;
- * Supports third party annotation using GFF formats;
- * Settings persist across sessions;
- * DNA and GFF dumps;
- * Connectivity to different databases, including BioSQL and Chado;
- * Multi-language support;
- * Third-party feature loading;
- * Customizable plug-in architecture (e.g. run BLAST, dump & import many
- formats, find oligonucleotides, design primers, create restriction maps,
- edit features).
-
-Package: gbrowse-data
-Architecture: all
-Depends: ${misc:Depends}
-Recommends: gbrowse
-Description: Sample data to use GBrowse
- This package contains sample data to test the gbrowse tool
- with the Yeast genome.
-
-Package: gbrowse-calign
-Architecture: any
-Depends: ${perl:Depends},${shlibs:Depends},${misc:Depends}, perl (>= 5.10.0), gbrowse
-Description: CAlign helper
- This package provides the CAlign helper
- for use with Realign. It speeds up Smith-Waterman alignment.
Copied: trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/control (from rev 6656, trunk/packages/gbrowse/trunk/debian/control)
===================================================================
--- trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/control (rev 0)
+++ trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/control 2011-04-27 01:49:33 UTC (rev 6658)
@@ -0,0 +1,62 @@
+Source: gbrowse
+Section: science
+Priority: optional
+Build-Depends: bioperl (>= 1.5.9), debhelper (>= 8),
+ libbio-graphics-perl (>= 2.09), libcapture-tiny-perl,
+ libcgi-session-perl (>= 4.02),
+ libgd-gd2-perl (>= 2.07) | libgd-gd2-noxpm-perl (>= 2.07), libio-string-perl,
+ libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, perl,
+ perl (>= 5.10.0) | libextutils-cbuilder-perl, sqlite3,libdbd-sqlite3-perl, libterm-readkey-perl, libjs-prototype (>=1.7), libjs-scriptaculous (>= 1.9)
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <olivier.sallou at irisa.fr>,
+ Charles Plessy <plessy at debian.org>, Aaron M. Ucko <ucko at debian.org>
+DM-Upload-Allowed: yes
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/gbrowse/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/gbrowse/?rev=0&sc=0
+Standards-Version: 3.9.1
+Homepage: http://www.gbrowse.org/
+
+Package: gbrowse
+Architecture: all
+Depends: ${misc:Depends}, ${perl:Depends},
+ bioperl (>= 1.5.9), libbio-graphics-perl (>= 2.09),
+ libcgi-session-perl (>= 4.02),
+ libgd-gd2-noxpm-perl (>= 2.07) | libgd-gd2-perl (>= 2.07), libio-string-perl,
+ libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, perl,
+ perl (>= 5.10.0) | libextutils-cbuilder-perl, libterm-readkey-perl, sqlite3, libdbd-sqlite3-perl, libjs-prototype (>=1.7), libjs-scriptaculous (>=1.9)
+Suggests: gbrowse-data, gbrowse-calign
+Description: The GMOD Generic Genome Browser
+ The Generic Genome Browser is a simple but highly
+ configurable web-based genome browser. It is a component of the
+ Generic Model Organism Systems Database project (GMOD).
+ Some of its features:
+ * Simultaneous bird's eye and detailed views of the genome;
+ * Scroll, zoom, center;
+ * Attach arbitrary URLs to any annotation;
+ * Order and appearance of tracks are customizable by administrator and
+ end-user;
+ * Search by annotation ID, name, or comment;
+ * Supports third party annotation using GFF formats;
+ * Settings persist across sessions;
+ * DNA and GFF dumps;
+ * Connectivity to different databases, including BioSQL and Chado;
+ * Multi-language support;
+ * Third-party feature loading;
+ * Customizable plug-in architecture (e.g. run BLAST, dump & import many
+ formats, find oligonucleotides, design primers, create restriction maps,
+ edit features).
+
+Package: gbrowse-data
+Architecture: all
+Depends: ${misc:Depends}
+Recommends: gbrowse
+Description: Sample data to use GBrowse
+ This package contains sample data to test the gbrowse tool
+ with the Yeast genome.
+
+Package: gbrowse-calign
+Architecture: any
+Depends: ${perl:Depends},${shlibs:Depends},${misc:Depends}, perl (>= 5.10.0), gbrowse
+Description: CAlign helper
+ This package provides the CAlign helper
+ for use with Realign. It speeds up Smith-Waterman alignment.
Deleted: trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/gbrowse.dirs
===================================================================
--- trunk/packages/gbrowse/trunk/debian/gbrowse.dirs 2011-04-26 15:49:20 UTC (rev 6648)
+++ trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/gbrowse.dirs 2011-04-27 01:49:33 UTC (rev 6658)
@@ -1,4 +0,0 @@
-etc/gbrowse
-usr/share/perl5
-var/cache/gbrowse/sessions
-var/lib/gbrowse/databases
Copied: trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/gbrowse.dirs (from rev 6653, trunk/packages/gbrowse/trunk/debian/gbrowse.dirs)
===================================================================
--- trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/gbrowse.dirs (rev 0)
+++ trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/gbrowse.dirs 2011-04-27 01:49:33 UTC (rev 6658)
@@ -0,0 +1,3 @@
+etc/gbrowse
+var/cache/gbrowse/sessions
+var/lib/gbrowse/databases
Deleted: trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/rules
===================================================================
--- trunk/packages/gbrowse/trunk/debian/rules 2011-04-26 15:49:20 UTC (rev 6648)
+++ trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/rules 2011-04-27 01:49:33 UTC (rev 6658)
@@ -1,50 +0,0 @@
-#!/usr/bin/make -f
-
-GBROWSE_BUILD_OPTIONS = --conf=/etc/gbrowse --htdocs=/usr/share/gbrowse/htdocs --tmp=/var/cache/gbrowse --databases=/var/lib/gbrowse/databases --cgibin=/usr/lib/cgi-bin/gbrowse --www-user=www-data --registration_done=1
-
-%:
- dh $@
-
-override_dh_auto_configure:
- dh_auto_configure -- $(GBROWSE_BUILD_OPTIONS)
-
-override_dh_auto_install:
- ./Build --install_base=debian/gbrowse debianinstall
- ./Build apache_conf > debian/gbrowse/etc/gbrowse/apache2.conf
- perl Build.PL $(GBROWSE_BUILD_OPTIONS) --installetc=y
- ./Build --install_base=debian/gbrowse install_slave
- mv debian/gbrowse/lib/perl5/*/* debian/gbrowse/usr/share/perl5/
- # Remove arch dependant data
- mv debian/gbrowse/usr/share/perl5/auto/Bio/Graphics/Browser2/CAlign/* debian/gbrowse-calign/usr/lib/perl5/auto/Bio/Graphics/Browser2/CAlign/
- #rm -rf debian/gbrowse/usr/lib/perl5/auto/Bio/Graphics/Browser2/CAlign
- mv debian/gbrowse/usr/share/perl5/Bio/Graphics/Browser2/CAlign.pm debian/gbrowse-calign/usr/lib/perl5/Bio/Graphics/Browser2/CAlign.pm
- #rm -f debian/gbrowse/usr/lib/perl5/Bio/Graphics/Browser2/CAlign.pm
- rm -rf debian/gbrowse/lib
- rm -f debian/gbrowse/usr/share/doc/gbrowse/INSTALL
- rm -f debian/gbrowse/usr/share/perl5/auto/GBrowse/.packlist
- rm -f debian/gbrowse/usr/share/gbrowse/htdocs/js/prototype.js
- rm -f debian/gbrowse/usr/share/gbrowse/htdocs/js/scriptaculous.js
- chmod 644 debian/gbrowse/etc/gbrowse/MobyServices/text_xml_renderer.pm
- chmod 644 debian/gbrowse/etc/gbrowse/synteny/oryza.synconf.disabled
- #Remove database (kept as separate package)
- rm -rf debian/gbrowse/var/lib/gbrowse/databases/*
- #Rename pl scripts in bin
- rename 's/\.pl//' debian/gbrowse/bin/*.pl
- mv debian/gbrowse/bin debian/gbrowse/usr/bin
- # Activate configuration files.
- find $(CURDIR)/debian/gbrowse/etc -name '*.new' | xargs rename 's/.new//'
-
-override_dh_installman:
- #Rename due to perl extension seen as polish
- rename 's/\.pl\.1p/\.1p/' debian/gbrowse/man/man1/*.pl.1p
- mkdir -p debian/gbrowse-calign/man/man3/
- mv debian/gbrowse/man/man3/Bio::Graphics::Browser2::CAlign.3pm debian/gbrowse-calign/man/man3/Bio::Graphics::Browser2::CAlign.3pm
- dh_installman
- rm -rf debian/gbrowse/man
- rm -rf debian/gbrowse-calign/man
-
-override_dh_builddeb:
- dh_builddeb -- -Zbzip2
-
-get-orig-source:
- . debian/get-orig-source
Copied: trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/rules (from rev 6653, trunk/packages/gbrowse/trunk/debian/rules)
===================================================================
--- trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/rules (rev 0)
+++ trunk/packages/gbrowse/tags/2.26~dfsg-2/debian/rules 2011-04-27 01:49:33 UTC (rev 6658)
@@ -0,0 +1,50 @@
+#!/usr/bin/make -f
+
+GBROWSE_BUILD_OPTIONS = --conf=/etc/gbrowse --htdocs=/usr/share/gbrowse/htdocs --tmp=/var/cache/gbrowse --databases=/var/lib/gbrowse/databases --cgibin=/usr/lib/cgi-bin/gbrowse --www-user=www-data --registration_done=1
+
+%:
+ dh $@
+
+override_dh_auto_configure:
+ dh_auto_configure -- $(GBROWSE_BUILD_OPTIONS)
+
+override_dh_auto_install:
+ ./Build --install_base=debian/gbrowse debianinstall
+ ./Build apache_conf > debian/gbrowse/etc/gbrowse/apache2.conf
+ perl Build.PL $(GBROWSE_BUILD_OPTIONS) --installetc=y
+ ./Build --install_base=debian/gbrowse install_slave
+ mv debian/gbrowse/lib/perl5/* debian/gbrowse/usr/share/perl5
+ # Remove arch dependant data
+ mv debian/gbrowse/usr/share/perl5/auto/Bio/Graphics/Browser2/CAlign/* debian/gbrowse-calign/usr/lib/perl5/auto/Bio/Graphics/Browser2/CAlign/
+ #rm -rf debian/gbrowse/usr/lib/perl5/auto/Bio/Graphics/Browser2/CAlign
+ mv debian/gbrowse/usr/share/perl5/Bio/Graphics/Browser2/CAlign.pm debian/gbrowse-calign/usr/lib/perl5/Bio/Graphics/Browser2/CAlign.pm
+ #rm -f debian/gbrowse/usr/lib/perl5/Bio/Graphics/Browser2/CAlign.pm
+ rm -rf debian/gbrowse/lib
+ rm -f debian/gbrowse/usr/share/doc/gbrowse/INSTALL
+ rm -f debian/gbrowse/usr/share/perl5/auto/GBrowse/.packlist
+ rm -f debian/gbrowse/usr/share/gbrowse/htdocs/js/prototype.js
+ rm -f debian/gbrowse/usr/share/gbrowse/htdocs/js/scriptaculous.js
+ chmod 644 debian/gbrowse/etc/gbrowse/MobyServices/text_xml_renderer.pm
+ chmod 644 debian/gbrowse/etc/gbrowse/synteny/oryza.synconf.disabled
+ #Remove database (kept as separate package)
+ rm -rf debian/gbrowse/var/lib/gbrowse/databases/*
+ #Rename pl scripts in bin
+ rename 's/\.pl//' debian/gbrowse/bin/*.pl
+ mv debian/gbrowse/bin debian/gbrowse/usr/bin
+ # Activate configuration files.
+ find $(CURDIR)/debian/gbrowse/etc -name '*.new' | xargs rename 's/.new//'
+
+override_dh_installman:
+ #Rename due to perl extension seen as polish
+ rename 's/\.pl\.1p/\.1p/' debian/gbrowse/man/man1/*.pl.1p
+ mkdir -p debian/gbrowse-calign/man/man3/
+ mv debian/gbrowse/man/man3/Bio::Graphics::Browser2::CAlign.3pm debian/gbrowse-calign/man/man3/Bio::Graphics::Browser2::CAlign.3pm
+ dh_installman
+ rm -rf debian/gbrowse/man
+ rm -rf debian/gbrowse-calign/man
+
+override_dh_builddeb:
+ dh_builddeb -- -Zbzip2
+
+get-orig-source:
+ . debian/get-orig-source
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