debian/0000755000000000000000000000000012233741521007166 5ustar debian/control0000644000000000000000000000242012233704744010575 0ustar Source: libace-perl Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Section: perl Priority: optional Build-Depends: debhelper (>= 9) Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libace-perl/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/libace-perl/trunk/ Homepage: http://search.cpan.org/dist/AcePerl/ Package: libace-perl Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}, libcache-cache-perl Description: Object-Oriented Access to ACEDB Databases AcePerl is an object-oriented Perl interface for the AceDB database. It provides functionality for connecting to remote AceDB databases, performing queries, fetching ACE objects, and updating databases. The programmer's API is compatible with the JADE Java API, and interoperable with the API used by BoulderIO. . AceDB is a genome database system developed since 1989 primarily by Jean Thierry-Mieg (CNRS, Montpellier) and Richard Durbin (Sanger Institute). It was originally developed for the C.elegans genome project , from which its name was derived (A C. elegans DataBase). debian/ace.10000644000000000000000000000712112233724411010000 0ustar .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.3. .TH NAME "1" "October 2013" "Name "readline::rl_completion_function" used only once: possible typo at ./ace line 162." "User Commands" .SH NAME ace \- Interactive Perl client for ACEDB .SH SYNOPSIS .B ace [\fIoptions\fR] [\fIURL\fR] .SH DESCRIPTION .PP AcePerl is an object-oriented Perl interface for the AceDB database. It provides functionality for connecting to remote AceDB databases, performing queries, fetching ACE objects, and updating databases. The programmer's API is compatible with the JADE Java API, and interoperable with the API used by BoulderIO. .SH OPTIONS .TP \fB\-host\fR Server host (localhost) .TP \fB\-port\fR Server port (200005) .TP \fB\-path\fR Local database path (no default) .TP \fB\-url\fR Server URL (see below .TP \fB\-login\fR Username .TP \fB\-pass\fR Password .TP \fB\-tcsh\fR Use T\-shell completion mode .TP \fB\-save\fR Save database updates automatically .TP \fB\-exec\fR Run a command and quit .PP Respects the environment variables $ACEDB_HOST and $ACEDB_PORT, if present. You can edit the command line using the cursor keys and emacs style key bindings. Use up and down arrows (or ^P, ^N) to access the history. The tab key completes partial commands. In tcsh mode, the tab key cycles among the completions, otherwise pressing the tab key a second time lists all the possibilities. .PP You may use multiple \fB\-exec\fR switches to run a sequence of commands, or separate multiple commands in a single string by semicolons: .IP ace.pl \fB\-e\fR 'find Author Thierry\-Mieg*' \fB\-e\fR 'show' ace.pl \fB\-e\fR 'find Author Thierry\-Mieg*; show' .SS "Server URLs:" .TP rpcace://hostname:port RPC server .TP sace://hostname:port Socket server .TP tace:/path/to/database Local database .TP \fI/path/to/database\fP Local database .IP Usernames can be provided as sace://user@hostname:port .PP Name "readline::rl_special_prefixes" used only once: possible typo at ./ace line 161. Unknown option: version Usage: ./ace [options] [URL] Interactive Perl client for ACEDB .SS "Options (can be abbreviated):" .TP \fB\-host\fR Server host (localhost) .TP \fB\-port\fR Server port (200005) .TP \fB\-path\fR Local database path (no default) .TP \fB\-url\fR Server URL (see below .TP \fB\-login\fR Username .TP \fB\-pass\fR Password .TP \fB\-tcsh\fR Use T\-shell completion mode .TP \fB\-save\fR Save database updates automatically .TP \fB\-exec\fR Run a command and quit .PP Respects the environment variables $ACEDB_HOST and $ACEDB_PORT, if present. You can edit the command line using the cursor keys and emacs style key bindings. Use up and down arrows (or ^P, ^N) to access the history. The tab key completes partial commands. In tcsh mode, the tab key cycles among the completions, otherwise pressing the tab key a second time lists all the possibilities. .PP You may use multiple \fB\-exec\fR switches to run a sequence of commands, or separate multiple commands in a single string by semicolons: .IP ace.pl \fB\-e\fR 'find Author Thierry\-Mieg*' \fB\-e\fR 'show' ace.pl \fB\-e\fR 'find Author Thierry\-Mieg*; show' .SS "Server URLs:" .TP rpcace://hostname:port RPC server .TP sace://hostname:port Socket server .TP tace:/path/to/database Local database .TP \fI/path/to/database\fP Local database .IP Usernames can be provided as sace://user@hostname:port .SH AUTHOR This manual page was created using help2man for the Debian distribution by Andreas Tille . It can be used freely for any other distribution. debian/rules0000755000000000000000000000422212233741333010247 0ustar #!/usr/bin/make -f PERL ?= /usr/bin/perl PACKAGE = $(shell dh_listpackages) TMP = $(CURDIR)/debian/$(PACKAGE) %: dh $@ override_dh_auto_build: # The following is pasted from an interactive session, to better understand what is echoed to Makefile.PL. # Add commands to compile the package here # # Following echo answers the questions below. # What do you want to build? # 1) Interface to Ace socket server and local databases (pure Perl) # 2) The above plus XS optimizations (requires C compiler) # 3) The above plus RPC server interface (requires C compiler) # # Enter your choice: [1] # Do you want to install Ace::Browser? [n] # Directory for the site-specific configuration files (~username ok): [/usr/local/apache/conf/ace] # Directory does not exist. Shall I create it for you? [y] # Directory for the acebrowser CGI scripts (~username ok): [/usr/local/apache/cgi-bin/ace] # Directory does not exist. Shall I create it for you? [y] # Directory for the acebrowser HTML files and images (~username ok): [/usr/local/apache/htdocs/ace] perl -e "print qq(3\ny\n$(CURDIR)/debian/$(PACKAGE)/etc/libace-perl\ny\n$(CURDIR)/debian/$(PACKAGE)/usr/lib/cgi-bin\ny\n$(CURDIR)/debian/$(PACKAGE)/usr/share/$(PACKAGE))" | $(PERL) Makefile.PL INSTALLDIRS=vendor dh_auto_build -- OPTIMIZE="$(CFLAGS)" LD_RUN_PATH="" OTHERLDFLAGS="$(LDFLAGS)" override_dh_auto_test: # Disabled as they need internet access. override_dh_clean: [ ! -f Makefile ] || $(MAKE) realclean $(RM) --recursive docs/Ace dh_clean .docs Ace/Browser/LocalSiteDefs.pm docs/Ace.html pod2htmd.tmp pod2htmi.tmp util/ace.pl util/install.pl override_dh_auto_install: # Add commands to install the package into $(TMP) $(MAKE) install DESTDIR=$(TMP) PREFIX=/usr mv $(TMP)/usr/bin/ace.pl $(TMP)/usr/bin/ace # Manpage is somehow empty and will be replaced by the manually edited debian/ace.1 rm -f $(TMP)/usr/share/man/man1/ace.pl.1p [ ! -d $(TMP)/usr/share/perl5 ] || \ rmdir --ignore-fail-on-non-empty --parents --verbose \ $(TMP)/usr/share/perl5 override_dh_installexamples: dh_installexamples sed -i 's?#!/usr/local/bin/perl?#!/usr/bin/perl?' $(TMP)/usr/share/doc/$(PACKAGE)/examples/*.pl debian/manpages0000644000000000000000000000001312233724451010701 0ustar debian/*.1 debian/examples0000644000000000000000000000001312214301201010703 0ustar examples/* debian/watch0000644000000000000000000000034312214301201010201 0ustar # format version number, currently 3; this line is compulsory! version=3 # URL to the package page followed by a regex to search http://search.cpan.org/dist/AcePerl/ .*/AcePerl-v?(\d[\d_.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$ debian/upstream0000644000000000000000000000057712233712363010764 0ustar Reference: Author: Lincoln D. Stein and Jean Thierry-Mieg Title: Scriptable Access to the Caenorhabditis elegans Genome Sequence and Other ACEDB Databases Journal: Genome Research Year: 1998 Volume: 8 Number: 12 Pages: 1308-1315 PMID: 9872985 URL: http://genome.cshlp.org/content/8/12/1308.abstract eprint: http://genome.cshlp.org/content/8/12/1308.full.pdf+html debian/copyright0000644000000000000000000000446512233726600011133 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: AcePerl Upstream-Contact: Lincoln Stein Source: http://search.cpan.org/CPAN/authors/id/L/LD/LDS/AcePerl-1.92.tar.gz Files: * Copyright: © 1998 Cold Spring Harbor Laboratory License: Perl License: Perl This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See the Artistic License file in the main Perl distribution for specific terms and conditions of use. In addition, the following disclaimers apply: . CSHL makes no representations whatsoever as to the SOFTWARE contained herein. It is experimental in nature and is provided WITHOUT WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR IMPLIED. CSHL MAKES NO REPRESENTATION OR WARRANTY THAT THE USE OF THIS SOFTWARE WILL NOT INFRINGE ANY PATENT OR OTHER PROPRIETARY RIGHT. . By downloading this SOFTWARE, your Institution hereby indemnifies CSHL against any loss, claim, damage or liability, of whatsoever kind or nature, which may arise from your Institution's respective use, handling or storage of the SOFTWARE. . If publications result from research using this SOFTWARE, we ask that CSHL be acknowledged and/or credit be given to CSHL scientists, as scientifically appropriate. Comment: On Debian systems, the complete text of the latest version of the GNU General Public License can be found in ‘/usr/share/common-licenses/GPL’, and the complete text of the Artistic license can be found in ‘/usr/share/common-licenses/Artistic’. Files: Ace/Model.pm Ace/Object.pm Ace/Local.pm Ace/Sequence/Multi.pm Ace/Sequence/Homol.pm Ace/Sequence/GappedAlignment.pm Ace/Sequence/FeatureList.pm Ace/Sequence/Feature.pm Ace/Sequence/Gene.pm Ace/Sequence/Transcript.pm Ace/Sequence.pm Copyright: © 1997-1999 Lincoln D. Stein License: Perl Files: acelib/* Copyright: © 1991-1998 J Thierry-Mieg and R Durbin License: LGPL-2+ This file is part of the ACEDB genome database package, written by Richard Durbin (Sanger Centre, UK) rd@sanger.ac.uk, and Jean Thierry-Mieg (CRBM du CNRS, France) mieg@kaa.crbm.cnrs-mop.fr Comment: These files can be found licensed either as GPL-2+ or LGPL-2+ in ftp://ftp.sanger.ac.uk/pub/acedb/SUPPORTED/ACEDB-source.4.9.39.tar.gz debian/source/0000755000000000000000000000000012214301046010457 5ustar debian/source/format0000644000000000000000000000001412214301046011665 0ustar 3.0 (quilt) debian/README.Debian0000644000000000000000000000177012233726522011240 0ustar libace-perl for Debian ---------------------- When rebuilding the package with latest packaging standards and comparing with previous content it was noticed that some settings definitely are not sanely chosen. Since this was also not done before this fact is not changed but mentioned here to enable tracking down potential problems quickly. Se questionable settings are in the file /usr/lib/perl5/Ace/Browser/LocalSiteDefs.pm where the build directory remains hardcoded: $SITE_DEFS = '/tmp/buildd/libace-perl-1.92/debian/libace-perl/etc/libace-perl'; $CGI_PATH = '/tmp/buildd/libace-perl-1.92/debian/libace-perl/usr/lib/cgi-bin'; $HTML_PATH = '/tmp/buildd/libace-perl-1.92/debian/libace-perl/usr/share/libace-perl'; Since the relevant directories are not existent inside the package this is most probably harmless but in case a user might happen to try the server features via CGI this should be reported in a potential bug report. -- Andreas Tille Tue, 29 Oct 2013 11:08:14 +0100 debian/changelog0000644000000000000000000000325412233741521011044 0ustar libace-perl (1.92-3) unstable; urgency=low * debian/source/format: 3.0 (quilt) * debian/control: - added myself to Uploaders - cme fix dpkg-control - debhelper 9 - canonical Vcs fields * debian/README.Debian: Remark about hard coding of build directory in probably unused file. * debian/rules: - use short dh - enable propagation of hardening options * debian/upstream: Take over content of reference (DOI was wrongly specified at URL so I decided to remove) * debian/ace.1: automatically created manpage was broken - use help2man to create some valid ace.1 * debian/copyright: DEP5 -- Andreas Tille Tue, 29 Oct 2013 11:08:14 +0100 libace-perl (1.92-2) unstable; urgency=low * debian/rules - Replaced an echo command by the Perl equivalent in debian/rules (Closes: #535390). - Use dh clean and binary-arch, and created debian/docs and debian/examples. - Override dh_auto_install, that created duplicates. * debian/control: - Added links to the Subversion repository where libace-perl is. - Incremented Standards-Version to reflect conformance with Policy 3.8.2 (no changes needed). - Made the Debian Med packaging team the maintainer. - Dropped the build dependency on Perl. * Updated debian/copyright to my latest exploration of a possible machine-readable format. * Added bibliographic information in BibTeX format in debian/reference. -- Charles Plessy Sun, 02 Aug 2009 23:15:09 +0900 libace-perl (1.92-1) unstable; urgency=low * Initial Release (Closes: #468760). -- Charles Plessy Mon, 10 Nov 2008 14:18:23 +0900 debian/compat0000644000000000000000000000000212233704636010372 0ustar 9 debian/docs0000644000000000000000000000006512214301201010024 0ustar README README.ACEBROWSER docs/README examples/README