Author: fourmond Date: 2011-09-29 23:07:55 +0000 (Thu, 29 Sep 2011) New Revision: 15138
Added: trunk/jalview/debian/jalview.manpages trunk/jalview/debian/jalview.menu trunk/jalview/debian/manpages/ trunk/jalview/debian/manpages/jalview.1 Removed: trunk/jalview/debian/README.Debian trunk/jalview/debian/menu.ex Modified: trunk/jalview/debian/changelog trunk/jalview/debian/control trunk/jalview/debian/copyright trunk/jalview/debian/rules trunk/jalview/debian/wrappers/jalview Log: [jalview] Make the package presentable -- and almost ready for upload ! Deleted: trunk/jalview/debian/README.Debian =================================================================== --- trunk/jalview/debian/README.Debian 2011-09-29 21:31:49 UTC (rev 15137) +++ trunk/jalview/debian/README.Debian 2011-09-29 23:07:55 UTC (rev 15138) @@ -1,6 +0,0 @@ -jalview for Debian ------------------- - -<possible notes regarding this package - if none, delete this file> - - -- Vincent Fourmond <[email protected]> Thu, 15 Jan 2009 23:12:16 +0100 Modified: trunk/jalview/debian/changelog =================================================================== --- trunk/jalview/debian/changelog 2011-09-29 21:31:49 UTC (rev 15137) +++ trunk/jalview/debian/changelog 2011-09-29 23:07:55 UTC (rev 15138) @@ -1,8 +1,9 @@ -jalview (2.6.1.dfsg-1) unstable; urgency=low +jalview (2.6.1.dfsg~almost-1) unstable; urgency=low * Initial release (Closes: #507436) * Adding a debian/new-upstream script to repackage the original tarball, getting rid of the bundled JAR file (I love JAR files) + (well, almost, which is why this goes in non-free for now) * Using dh 7 and javahelper * Using jh_build for building Modified: trunk/jalview/debian/control =================================================================== --- trunk/jalview/debian/control 2011-09-29 21:31:49 UTC (rev 15137) +++ trunk/jalview/debian/control 2011-09-29 23:07:55 UTC (rev 15138) @@ -1,5 +1,5 @@ Source: jalview -Section: science +Section: non-free/science Priority: optional Maintainer: Vincent Fourmond <[email protected]> Build-Depends: cdbs, debhelper (>= 7), default-jdk, @@ -27,5 +27,5 @@ alignement produced by programs implementing alignment algorithms such as clustalw, kalign and t-coffee. . - It has lots of features, and can be considered a decent BioEdit - replacement for Debian systems. + It has lots of features, and will compare advantageously to BioEdit, + while being free as in free speech ! Modified: trunk/jalview/debian/copyright =================================================================== --- trunk/jalview/debian/copyright 2011-09-29 21:31:49 UTC (rev 15137) +++ trunk/jalview/debian/copyright 2011-09-29 23:07:55 UTC (rev 15138) @@ -1,52 +1,66 @@ -This package was debianized by: +Format: http://anonscm.debian.org/viewvc/dep/web/deps/dep5.mdwn?revision=174 +Upstream-Name: freecol +Upstream-Contact: [email protected] +Source: + The original tarball was made downloading the jalview-*.tar.gz + tarball on http://www.jalview.org/versions.html, and stripping most + of the binary-only jars excepted lib/vamsas-client.jar. + . + For more details, see the debian/new-upstream script that does precisely + this. +Disclaimer: + The tarball contains a sourceless binary jar, + lib/vamsas-client.jar. Though the distribution and use of this file + is allowed by its copyright holders, the absence of source prevents + it from being integrated into Debian main. - Vincent Fourmond <[email protected]> on Thu, 15 Jan 2009 23:12:16 +0100 +Files: * +Copyright: Copyright 2007-2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle +License: GPL-3+ + This package 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 2 of the License, or + (at your option) any later version. + . + This package 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 this package; if not, write to the Free Software + Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + . + On Debian systems, the complete text of the GNU General Public + License version 3 can be found in `/usr/share/common-licenses/GPL-3'. -It was downloaded from: - <url://example.com> +Files: debian/* +Copyright: Copyright (C) 2009-2011 Vincent Fourmond <[email protected]> +License: GPL-3+ + (see above) -Upstream Author(s): +Files: lib/vamsas-client.jar +Copyright: +License: ... - <put author's name and email here> - <likewise for another author> - -Copyright: - - <Copyright (C) YYYY Firtname Lastname> - <likewise for another author> - -License: - -### SELECT: ### - This package 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 2 of the License, or - (at your option) any later version. -### OR ### - This package is free software; you can redistribute it and/or modify - it under the terms of the GNU General Public License version 2 as - published by the Free Software Foundation. -########## - - This package 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 this package; if not, write to the Free Software - Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA - -On Debian systems, the complete text of the GNU General -Public License can be found in `/usr/share/common-licenses/GPL'. - -The Debian packaging is: - - Copyright C) 2009, Vincent Fourmond <[email protected]> - -and is licensed under the GPL, see above. - - -# Please also look if there are files or directories which have a -# different copyright/license attached and list them here. +Files: src/com/stevesoft/pat/* +Copyright: Copyright 2001, Steven R. Brandt +License: LGPL3+ + This package is free software; you can redistribute it and/or + modify it under the terms of the GNU Lesser General Public License + as published by the Free Software Foundation; either version 3 of + the License, or (at your option) any later version. + . + This package 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 + Lesser General Public License for more details. + . + You should have received a copy of the GNU Lesser General Public + License along with this package; if not, write to the Free + Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA + 02110-1301 USA + . + On Debian systems, the complete text of the GNU Lesser Public + License version 3 can be found in `/usr/share/common-licenses/LGPL-3'. Added: trunk/jalview/debian/jalview.manpages =================================================================== --- trunk/jalview/debian/jalview.manpages (rev 0) +++ trunk/jalview/debian/jalview.manpages 2011-09-29 23:07:55 UTC (rev 15138) @@ -0,0 +1 @@ +debian/manpages/jalview.1 \ No newline at end of file Added: trunk/jalview/debian/jalview.menu =================================================================== --- trunk/jalview/debian/jalview.menu (rev 0) +++ trunk/jalview/debian/jalview.menu 2011-09-29 23:07:55 UTC (rev 15138) @@ -0,0 +1,2 @@ +?package(jalview):needs="X11" section="Applications/Science/Biology"\ + title="Jalview" command="/usr/bin/jalview" Added: trunk/jalview/debian/manpages/jalview.1 =================================================================== --- trunk/jalview/debian/manpages/jalview.1 (rev 0) +++ trunk/jalview/debian/manpages/jalview.1 2011-09-29 23:07:55 UTC (rev 15138) @@ -0,0 +1,34 @@ +.\" Hey, EMACS: -*- nroff -*- +.\" First parameter, NAME, should be all caps +.\" Copyright 2011 by Vincent Fourmond +.\" Can be modified and distributed under the terms of the GNU General +.\" public license, version 3 or any later version at your option. +.TH JALVIEW 1 "26-01-2009" +.SH NAME +jalview \- Sequence alignement viewer +.SH SYNOPSIS +.B jalview + +.SH DESCRIPTION + +.B jalview +provides facilities for viewing/editing and otherwise manipulating +sequence alignments (DNA, amino acids). + + +.SH JAVA-WRAPPERS NOTE + +This program is a shell script wrapper based on +.BR java-wrappers (7). +You therefore benefit from several features; please see the +.BR java-wrappers (7) +manual page for more information about them. + + +.SH SEE ALSO + +.B http://www.jalview.org + +.SH AUTHOR +This manual page was written by Vincent Fourmond <[email protected]> +from the Debian project, but may be used by others. Deleted: trunk/jalview/debian/menu.ex =================================================================== --- trunk/jalview/debian/menu.ex 2011-09-29 21:31:49 UTC (rev 15137) +++ trunk/jalview/debian/menu.ex 2011-09-29 23:07:55 UTC (rev 15138) @@ -1,2 +0,0 @@ -?package(jalview):needs="X11|text|vc|wm" section="Applications/see-menu-manual"\ - title="jalview" command="/usr/bin/jalview" Modified: trunk/jalview/debian/rules =================================================================== --- trunk/jalview/debian/rules 2011-09-29 21:31:49 UTC (rev 15137) +++ trunk/jalview/debian/rules 2011-09-29 23:07:55 UTC (rev 15138) @@ -22,5 +22,9 @@ axis jh lib/vamsas-client.jar /usr/share/jmol-applet/JmolApplet.jar -ANT_OPTS := -Dbuild.sysclasspath=last -DPACKAGE_VERSION=$(VERSION) +ANT_OPTS := -Dbuild.sysclasspath=last \ + -DJALVIW_VERSION=$(VERSION) +FINAL_CLASSPATH = $(subst lib/vamsas-client.jar, /usr/share/jalview/vamsas-client.jar, $(DEB_CLASSPATH)) + +JH_CLASSPATH_ARGS := -c"$(shell echo $(FINAL_CLASSPATH) | sed 's/:/ /g')" debian/jalview/usr/share/java/jalview.jar Modified: trunk/jalview/debian/wrappers/jalview =================================================================== --- trunk/jalview/debian/wrappers/jalview 2011-09-29 21:31:49 UTC (rev 15137) +++ trunk/jalview/debian/wrappers/jalview 2011-09-29 23:07:55 UTC (rev 15138) @@ -6,10 +6,6 @@ # We need openjdk or sun6 find_java_runtime openjdk sun6 -find_jars castor-xml commons-logging log4j-1.2 \ - castor-core Jmol min-jaba-client axis-jaxrpc \ - axis jh /usr/share/jalview/vamsas-client.jar \ - /usr/share/jmol-applet/JmolApplet.jar \ - jalview +find_jar_classpath jalview run_java jalview.bin.Jalview "$@" _______________________________________________ pkg-java-commits mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-java-commits
