debian/0000755000000000000000000000000012215236230007162 5ustar debian/README.source0000644000000000000000000000026011671035370011346 0ustar This package uses patches to manage all modifications to the upstream source. Changes are stored in the source package as diffs in debian/patches and applied during the build. debian/rules0000755000000000000000000000154112215236075010252 0ustar #!/usr/bin/make -f export DH_VERBOSE=1 %: dh $@ --with apache2 override_dh_auto_test: # disabled because of http://sourceforge.net/tracker/index.php?func=detail&aid=1994385&group_id=124389&atid=699414 override_dh_install: dh_install $(MAKE) install DESTDIR=$(CURDIR)/debian/emboss-explorer PREFIX=/usr # Move ACD.pm to a separate package, that is useful for making # manpages from EMBOSS ACD files without being bothered by the # dependancy on web servers. mv $(CURDIR)/debian/emboss-explorer/usr/share/perl5/EMBOSS/ACD.pm $(CURDIR)/debian/libemboss-acd-perl/usr/share/perl5/EMBOSS/ mv $(CURDIR)/debian/emboss-explorer/usr/share/man/man3/EMBOSS::ACD.3pm $(CURDIR)/debian/libemboss-acd-perl/usr/share/man/man3/ override_dh_fixperms: dh_fixperms install -m 755 -o www-data -g www-data -d $(CURDIR)/debian/emboss-explorer/var/lib/emboss-explorer/output debian/patches/0000755000000000000000000000000012215236230010611 5ustar debian/patches/05-build-manpages.diff0000644000000000000000000000133012215225100014544 0ustar Author: Charles Plessy Description: Automatically build and install the POD manpages of acdcheckd and mkstatic. Forwarded: http://sourceforge.net/tracker/index.php?func=detail&aid=1994395&group_id=124389&atid=699414 diff -urNad emboss-explorer~/t/ACD.t emboss-explorer/t/ACD.t --- emboss-explorer-2.2.0/Makefile.PL.old 2008-06-16 07:53:53.000000000 +0900 +++ emboss-explorer-2.2.0/Makefile.PL 2008-06-16 07:55:33.000000000 +0900 @@ -10,5 +10,6 @@ }, PREREQ_FATAL => 1, ABSTRACT_FROM => 'lib/EMBOSS/GUI.pm', - AUTHOR => 'Luke McCarthy ' + AUTHOR => 'Luke McCarthy ', + EXE_FILES => => [ qw( bin/acdcheck bin/mkstatic ) ] ); debian/patches/series0000644000000000000000000000013412215226457012036 0ustar 01-fix_examples.diff 02-fix_Conf.pm.diff 05-build-manpages.diff emboss-6.4-group-list.patch debian/patches/emboss-6.4-group-list.patch0000644000000000000000000000132412215226457015544 0ustar Description: correct menu when using EMBOSS >= 6.4. Origin: http://sourceforge.net/p/embossgui/bugs/_discuss/thread/b0c058e8/fc9b/attachment/emboss-6.4-group-list.patch Bug: http://sourceforge.net/p/embossgui/bugs/21/ Bug-Debian: http://bugs.debian.org/722982 --- emboss-explorer/lib/EMBOSS/GUI/XHTML.pm.orig 2012-11-15 09:35:20.390050595 -0700 +++ emboss-explorer/lib/EMBOSS/GUI/XHTML.pm 2012-11-15 09:35:58.083051229 -0700 @@ -314,7 +314,7 @@ my $html = < EOF - if (@{$entries[0]} > 2) { # entries are groups... + if (ref($entries[0][1]) eq "ARRAY") { # entries are groups... my $menu_url = $self->{static} ? "alphamenu.html" : "$self->{script_url}/menu?sort=alpha"; $html .= < Description: The Debian package for EMBOSS installs its files in /usr/share/EMBOSS. This patch is necessary for the test of the ACD module to function. Forwarded: no As it is Debian-specific, it has not been forwarded upstream. diff -urNad emboss-explorer~/t/ACD.t emboss-explorer/t/ACD.t --- emboss-explorer~/t/ACD.t 2006-11-13 00:38:39.000000000 +0100 +++ emboss-explorer/t/ACD.t 2007-05-20 15:33:09.000000000 +0200 @@ -15,7 +15,7 @@ BEGIN { # locate the EMBOSS ACD files in order to validate against them... # - @ACDFILES = glob "/usr/local/share/EMBOSS/acd/*.acd"; + @ACDFILES = glob "/usr/share/EMBOSS/acd/*.acd"; $XHTML = EMBOSS::GUI::XHTML->new( script_url => 'dummy' debian/patches/02-fix_Conf.pm.diff0000644000000000000000000000453412215225100014030 0ustar Author: David Paleino Description: Moving configuration to /etc/emboss-explorer.conf Forwarded: http://sourceforge.net/tracker/index.php?func=detail&aid=1992075&group_id=124389&atid=699414 diff -urNad emboss-explorer~/lib/EMBOSS/GUI/Conf.pm emboss-explorer/lib/EMBOSS/GUI/Conf.pm --- emboss-explorer~/lib/EMBOSS/GUI/Conf.pm 2007-05-25 09:13:23.000000000 +0200 +++ emboss-explorer/lib/EMBOSS/GUI/Conf.pm 2007-05-25 09:13:57.000000000 +0200 @@ -43,79 +43,16 @@ package EMBOSS::GUI::Conf; -use strict; use warnings; use Carp; our $VERSION = 1.10; -# path to the EMBOSS::GUI HTML files -our $HTML_PATH = "/var/www/emboss/html"; - -# URL corresponding to $HTML_PATH above -our $HTML_URL = "/emboss"; - -# URL specifying the style sheet to use -our $STYLE_URL = "$HTML_URL/style/emboss.css"; - -# URL prefix to place before image links -our $IMAGE_URL = "$HTML_URL/images"; - -# URL prefix to place before manual links (only used in static pages) -our $MANUAL_URL = "$HTML_URL/manual"; - -# path to the EMBOSS::GUI temporary output directory -our $OUTPUT_PATH = "$HTML_PATH/output"; - -# URL corresponding to $OUTPUT_PATH above -our $OUTPUT_URL = "$HTML_URL/output"; - -# prefix under which EMBOSS was installed -our $EMBOSS_PREFIX = "/usr/local"; - -# path to EMBOSS binaries -our $EMBOSS_BIN = "$EMBOSS_PREFIX/bin"; - -# path to EMBOSS installation -our $EMBOSS_HOME = "$EMBOSS_PREFIX/share/EMBOSS"; - -# path to EMBOSS ACD files -our $EMBOSS_ACDROOT = "$EMBOSS_HOME/acd"; - -# path to EMBOSS data -our $EMBOSS_DATA = "$EMBOSS_HOME/data"; - -# path to EMBOSS application manuals -our $EMBOSS_MANUAL = "$EMBOSS_HOME/doc/html"; - -# list of groups and applications to exclude from the main menu -our @EXCLUDED = ( - "ACD", - "acdc", - "acdpretty", - "acdtable", - "acdtrace", - "acdvalid", - "UTILS DATABASE CREATION", - "aaindexextract", - "cutgextract", - "printsextract", - "prosextract", - "rebaseextract", - "tfextract", - "UTILS DATABASE INDEXING", - "dbiblast", - "dbifasta", - "dbiflat", - "dbigcg", -); - -# number of seconds to delay between placeholder page refreshes -our $REFRESH_DELAY = 1; - -# whether or not to display using frames -our $FRAMES = 1; +open (config_file, "; +eval join("\n", @conf); +die $@ if $@; =item new() debian/source/0000755000000000000000000000000012215236230010462 5ustar debian/source/format0000644000000000000000000000001411671034100011665 0ustar 3.0 (quilt) debian/copyright0000644000000000000000000000222411671035211011116 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://downloads.sourceforge.net/embossgui/emboss-explorer-2.2.0.tar.gz Files: * Copyright: © 2004-2006 Luke McCarthy License: GPL-1+ or Artistic-1 Emboss Explorer is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.8.3 or, at your option, any later version of Perl 5 you may have available. . On Debian GNU/Linux systems, the complete text of the GNU General Public License version 1 can be found in `/usr/share/common-licenses/GPL-1' and the Artistic Licence in `/usr/share/common-licenses/Artistic'. Comment: Perl license: This program is free software; you can redistribute it and/or modify it under the terms of either: . a) the GNU General Public License as published by the Free Software Foundation; either version 1, or (at your option) any later version, or . b) the "Artistic License" which comes with Perl. Files: debian/* Copyright: © 2007-2008 David Paleino © 2007-2008 Charles Plessy License: same Same as EMBOSS explorer itself debian/docs0000644000000000000000000000000711671046434010044 0ustar README debian/watch0000644000000000000000000000010011024233226010201 0ustar version=3 http://sf.net/embossgui/emboss-explorer-(.*)\.tar\.gz debian/menu0000644000000000000000000000025511205116722010054 0ustar ?package(emboss-explorer):needs="X11" section="Applications/Science/Biology"\ title="EMBOSS Explorer" command="/usr/bin/sensible-browser http://localhost/emboss-explorer" debian/changelog0000644000000000000000000001613712215236220011043 0ustar emboss-explorer (2.2.0-8) unstable; urgency=low [ David Paleino ] * Removed myself from Uploaders [ Charles Plessy ] * Converted patches from dpatch to quilt format. * Converted the source package to dpkg source format 3.0 (quilt). * Added a DEP 3 header to the patches. * Removed debian/emboss-explorer.preinst, useless after Lenny. * Conforms with Policy 3.9.4 (debian/control, no other changes needed). * Use canonical VCS URLs in debian/control. * Updated debian/copyright to latest machine-readable format. * Switch to Debhelpers compatibility level 9 (debian/compat, debian/control). * Convert to Debhelper's tiny mode (debian/rules, debian/docs). * Removed obsolete DM-Upload-Allowed field. * Normalised debian/control with config-model-edit. * Removed restriction on EMBOSS version, satisified even in oldstable. * Verbose build logs (debian/rules). * Added Debhelper’s misc:Depends substitution variable. * Use dh_apache2 (Closes: #669738). - Build-depend on apache2-dev for dh_apache2. - Invoke dh_apache2 through dh. - Updated Apache configuration file for 2.4. - Updated debian/emboss-explorer.links for new name of configuration file. - Override ‘apache2-deprecated-auth-config’ warning (would conflict with another file). - Delete obsolete postinst and postrm files. - Recommend apache2 or httpd through misc:Recommends. * Added keywords to the desktop entry. * Correct path for moving ACD.pm and its manual page. * Apply patch from upstream tracker to use emboss-explorer with EMBOSS 6.4 (Closes: #722982 LP:#1083426). * Correct the alias to the EMBOSS documentation. Closes: #485735. -- Charles Plessy Sun, 15 Sep 2013 13:50:12 +0900 emboss-explorer (2.2.0-7) unstable; urgency=low * debian/emboss-explorer.postinst: reloads apache. * debian/menu, debian/emboss-explorer.desktop, debian/rules, debian/emboss-explorer.install: adding menu entries starting a browser on http://localhost/emboss-explorer. * debian/README.source, debian/control: added instructions for patching and updated Standards-Version. * debian/compat, debian/control: using Debhelper 7. -- Charles Plessy Sun, 07 Dec 2008 20:21:35 +0900 emboss-explorer (2.2.0-6) unstable; urgency=low [ Charles Plessy ] * Relicensed the packaging work to "Same as EMBOSS explorer". * debian/patches: - Documented 01-fix_examples.dpatch. - Documented and forwarded 02-fix_Conf.pm.dpatch and 05-build-manpages.dpatch. - Suppressed 04-fix_install.dpatch. Its role is taken by debian/rules and debian/index.html. * debian/rules: - refreshed using dh-make-perl version 0.45; - tests disable because of upstream bug 1994385; - sets the owner of the emboss output directory as `www-data'; - touches the makefile to avoid timestamp artefacts due to the patching of Makefile.PL (Thanks to Damyan and Gregor for the hint!). * Package made compatible with FHS by not using /var/www. - HTML files moved to `/usr/emboss-explorer/html'. - Cascade stylesheets moved to `/etc/emboss-explorer/style' (they are intended to be modifiable). - Temporary files moved to `/var/lib/emboss-explorer' - /etc/emboss-explorer/apache.conf allows apache2 to access the files in the /user/share/emboss-explorer directory, as well as the EMBOSS documentation in /usr/share/doc/emboss-explorer/ (Closes: #485735). * debian/emboss-explorer.manpages, debian/acdcheck.1*, debian/mkstatic.1* suppressed to use Upstream's manpages. * debian/emboss-explorer.postrm removes the temporary files when the package is purged. * debian/emboss-explorer.preinst moves the emboss-explorer.conf in its new place. [ David Paleino ] * debian/control: - dropped dependency on libcgi-perl (Closes: #485009) - updated Charles' email :) * debian/copyright updated -- Charles Plessy Sat, 05 Jul 2008 16:29:07 +0900 emboss-explorer (2.2.0-5) unstable; urgency=low * debian/control: - Allowed upload by Debian maintainers. - Changed Maintainer to Debian-Med Packaging Team. - Changed VCS to Debian-Med's subversion repository. - Checked conformance with Policy 3.7.3 (no changes needed). * debian/copyright: converted to machine-readable format. -- Charles Plessy Wed, 05 Mar 2008 20:14:55 +0900 emboss-explorer (2.2.0-4) unstable; urgency=low [ David Paleino ] * debian/do_cleanup.sh removed -- its contents are now directly put in the crontab file. (Closes: #435991) [ Charles Plessy ] * Gave ownersip of /var/www/emboss-explorer/output to www-data in debian/rules, removed the postinst script which was doing this before. * Added a reference to the stylesheets in the xml sources of the manpages, to simplify their use with xsltproc. * Generated the manpages offline, and dropped the build-dependency on xsltproc, docbook-xml and docbook-xsl. * Using debian/emboss-explorer instead of debian/tmp as build directory. * Removed the XS- prefix in front of the Vcs-* fields on debian/control. * Removed instructions to handle a deleted script, do_cleanup.sh -- Charles Plessy Mon, 05 Nov 2007 10:38:07 +0900 emboss-explorer (2.2.0-3) unstable; urgency=low [ David Paleino ] * debian/do_cleanup.sh added to handle crontab (Closes: #435991) * debian/emboss-explorer.cron.d and debian/emboss-explorer.install edited to reflect the changes * debian/emboss-explorer.dirs edited to add /usr/share/emboss-explorer/ * debian/control - removing unused ${misc:Depends} [ Charles Plessy ] * Changed section of libemboss-acd-perl from science to perl. -- David Paleino Sun, 07 Oct 2007 13:08:54 +0200 emboss-explorer (2.2.0-2) unstable; urgency=low * Migration from /var/www/emboss to /var/www/emboss-explorer was incomplete. Correcting this. * Fixed double-building of the manpages. * Added myself to the uploaders. * Swiched to apache2 as the default webserver. * emboss-explorer.conf now defaults to /usr/lib/emboss, which is the only place where the emboss binaries are guaranteed to keep their original name (therefore depending on emboss >= 5.0.0). * Provides emboss-explorer.conf through a file, not a patch. Modifying ./install so that it does not manipulate emboss-explorer.conf anymore so that there is a single entry point to change the default configuration. * Added a configure rule so that the clean rule can always run make clean. * Using include /usr/share/dpatch/dpatch.make. * Added libcgi-perl in the Depends: field of emboss-explorer. * Added libparse-recdescent-perl in the Depends: field of libemboss-acd-perl (Thanks to Anthony Boureux). * Moved dpatch from Build-depends-indep to Build-depends, because it is needed for debian/rules clean. -- Charles Plessy Sun, 15 Jul 2007 16:08:24 +0900 emboss-explorer (2.2.0-1) experimental; urgency=low * Initial release (Closes: #423548) -- David Paleino Sat, 12 May 2007 17:52:59 +0200 debian/emboss-explorer.install0000644000000000000000000000042312215222532013677 0ustar /cgi/emboss usr/lib/cgi-bin/ html/style/* etc/emboss-explorer/style/ debian/emboss-explorer.conf etc/emboss-explorer/ debian/index.html usr/share/emboss-explorer/html html/images/* usr/share/emboss-explorer/images debian/emboss-explorer.desktop usr/share/applications debian/emboss-explorer.links0000644000000000000000000000045212215222342013352 0ustar usr/share/EMBOSS/doc/html/emboss/apps/ usr/share/doc/emboss-explorer/html etc/apache2/conf-available/emboss-explorer.apache2.conf etc/emboss-explorer/apache2.conf etc/emboss-explorer/style/ usr/share/emboss-explorer/html/style var/lib/emboss-explorer/output usr/share/emboss-explorer/html/output debian/emboss-explorer.examples0000644000000000000000000000001011023677256014054 0ustar t/ACD.t debian/emboss-explorer.desktop0000644000000000000000000000130612214765266013722 0ustar # This file was orignially written for Debian, and can be copied, used, # modified and redistributed under the same licence as EMBOSS Explorer itself. [Desktop Entry] Version=1.0 Terminal=false Icon=emboss-explorer Exec=sensible-browser http://localhost/emboss-explorer Name=EMBOSS Explorer GenericName=EMBOSS frontend GenericName[en]=EMBOSS frontend GenericName[fr]=Interface graphique pour EMBOSS Keywords=GUI;web; Comment=Starts the default web browser on the local EMBOSS Explorer website. Comment[en]=Starts the default web browser on the local EMBOSS Explorer website. Comment[fr]=Lance le navigateur par défaut sur le site local EMBOSS Explorer. Type=Application Categories=Biology;Science;Education; debian/emboss-explorer.apache2.conf0000644000000000000000000000121312215234163014461 0ustar # I used /etc/gallery2/apache.conf as a template. -- Charles Plessy Alias /emboss-explorer /usr/share/emboss-explorer/html Options FollowSymLinks # AllowOverride Limit Options FileInfo Alias /doc/emboss-explorer "/usr/share/EMBOSS/doc/programs" Options Indexes MultiViews FollowSymLinks AllowOverride None Require all granted # some people prefer a simple URL like http://emboss-explorer.example # # DocumentRoot /usr/share/emboss-explorer # ServerName emboss-explorer.example # debian/emboss-explorer.apache20000644000000000000000000000005112215222532013531 0ustar conf debian/emboss-explorer.apache2.conf debian/emboss-explorer.conf0000644000000000000000000000334211033626705013170 0ustar # Starting from emboss-explorer 2.2.0-6, files in /var/www were moved to more # appropriate locations in /usr/share/emboss-explorer and # /var/lib/emboss-explorer. # path to the EMBOSS::GUI HTML files our $HTML_PATH = "/usr/share/emboss-explorer/html"; # URL corresponding to $HTML_PATH above our $HTML_URL = "/emboss-explorer"; # URL specifying the style sheet to use our $STYLE_URL = "$HTML_URL/style/emboss.css"; # URL prefix to place before image links our $IMAGE_URL = "$EMBOSS_HOME/doc/html/"; # URL prefix to place before manual links (only used in static pages) our $MANUAL_URL = "/doc/emboss-explorer/html"; # path to the EMBOSS::GUI temporary output directory our $OUTPUT_PATH = "/var/lib/emboss-explorer/output"; # URL corresponding to $OUTPUT_PATH above our $OUTPUT_URL = "/emboss-explorer/output"; # prefix under which EMBOSS was installed our $EMBOSS_PREFIX = "/usr"; # path to EMBOSS binaries our $EMBOSS_BIN = "/usr/lib/emboss"; # path to EMBOSS installation our $EMBOSS_HOME = "$EMBOSS_PREFIX/share/EMBOSS"; # path to EMBOSS ACD files our $EMBOSS_ACDROOT = "$EMBOSS_HOME/acd"; # path to EMBOSS data our $EMBOSS_DATA = "$EMBOSS_HOME/data"; # path to EMBOSS application manuals our $EMBOSS_MANUAL = "$EMBOSS_HOME/doc/html"; # list of groups and applications to exclude from the main menu our @EXCLUDED = ( "ACD", "acdc", "acdpretty", "acdtable", "acdtrace", "acdvalid", "UTILS DATABASE CREATION", "aaindexextract", "cutgextract", "printsextract", "prosextract", "rebaseextract", "tfextract", "UTILS DATABASE INDEXING", "dbiblast", "dbifasta", "dbiflat", "dbigcg", ); # number of seconds to delay between placeholder page refreshes our $REFRESH_DELAY = 1; # whether or not to display using frames our $FRAMES = 1; debian/emboss-explorer.lintian-overrides0000644000000000000000000000025212214761347015702 0ustar # We already have another file called emboss-explorer.conf. emboss-explorer: non-standard-apache2-configuration-name emboss-explorer.apache2.conf != emboss-explorer.conf debian/control0000644000000000000000000000304612215235106010571 0ustar Source: emboss-explorer Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy Section: science Priority: optional Build-Depends: debhelper (>= 9), apache2-dev Build-Depends-Indep: libparse-recdescent-perl, libmailtools-perl Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/emboss-explorer/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/emboss-explorer/trunk/ Homepage: http://embossgui.sourceforge.net/ Package: emboss-explorer Architecture: all Depends: ${perl:Depends}, libmailtools-perl, libemboss-acd-perl, emboss, emboss-data, ${misc:Depends} Recommends: emboss-doc, ${misc:Recommends} Description: web-based GUI to EMBOSS EMBOSS explorer is a web-based graphical user interface to the EMBOSS suite of bioinformatics tools. It is written in Perl. . If you use the Apache HTTP server, you will at most have to restart it before using EMBOSS explorer. For other web servers, you will have to do the configuration by yourself. Package: libemboss-acd-perl Architecture: all Section: perl Depends: ${perl:Depends}, libparse-recdescent-perl, ${misc:Depends} Description: perl module to parse EMBOSS ACD files EMBOSS::ACD parses EMBOSS Ajax Command Definition files and provides object-oriented access to the data contained therein. . For a complete specification of the ACD format, see http://emboss.sourceforge.net/developers/acd debian/README.Debian0000644000000000000000000000230611033620174011225 0ustar EMBOSS Explorer for Debian -------------------------- If you are using Apache, you may have to restart it before being able to use EMBOSS explorer. For other http servers, you will have to do the configuration by yourself. Visit http://localhost/emboss-explorer to test EMBOSS explorer. Site configuration (including a list of applications to be excluded from public access) is stored in /etc/emboss-explorer/emboss-explorer.conf). The main style sheet, which can be edited to customize the appearance of EMBOSS Explorer is `/etc/emboss-explorer/style/emboss.css'. If you prefer the look and feel of the old EMBOSS GUI, you can use `classic.css' instead (the style sheet is specified in /etc/emboss-explorer/emboss-explorer.conf). EMBOSS Explorer generates temporary output files every time an application is used. Depending on the tasks being performed, these output files can consume space fairly quickly. The old output is cleaned up everyday at midnight by a task to the root user's crontab. By default, all output files that have not been accessed in the last 24 hours are removed. You can modify this in /etc/cron.d/emboss-explorer. -- Charles Plessy Mon, 23 Jun 2008 22:43:36 +0900 debian/emboss-explorer.cron.d0000644000000000000000000000022411033620174013414 0ustar 0 0 * * * root [ -d "/var/lib/emboss-explorer/output" ] && find /var/lib/emboss-explorer/output -mindepth 1 -maxdepth 1 -atime 1 -exec rm -rf {} \; debian/compat0000644000000000000000000000000212214752441010366 0ustar 9 debian/libemboss-acd-perl.dirs0000644000000000000000000000005311023700520013501 0ustar usr/share/perl5/EMBOSS/ usr/share/man/man3 debian/index.html0000644000000000000000000000061112215235453011163 0ustar EMBOSS Explorer