debian/0000755000000000000000000000000012071257637007200 5ustar debian/postrm0000644000000000000000000000015711731565764010457 0ustar #!/bin/bash set -e case "$1" in purge) rm -rf /usr/share/gmod/chado ;; esac #DEBHELPER# debian/copyright0000644000000000000000000003002712071256113011121 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://gmod.org/wiki/Chado_-_Getting_Started Upstream-Name: chado Files: * Copyright: 2004, Indiana University 2003-2011, Scott Cain Cold Spring Harbor Laboratory License: Artistic-2.0 Files: doc/* Copyright: 2004, Indiana University License: BSD-3 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of Indiana University, Bloomington nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. . 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On Debian systems, the complete text of version 1 of the GNU General Public License can be found in `/usr/share/common-licenses/GPL-1'. debian/libchado-perl.install0000644000000000000000000000042311731565764013301 0ustar Makefile.PL usr/share/gmod/chado/ chado-module-metadata.xml usr/share/gmod/chado/ load usr/share/gmod/chado/ stag-templates usr/share/gmod/chado/ soi usr/share/gmod/chado/ schemas usr/share/gmod/chado/ modules usr/share/gmod/chado/ debian/testdb.pl usr/share/gmod/chado/bin/ debian/patches/0000755000000000000000000000000012071257637010627 5ustar debian/patches/fix_manpages0000644000000000000000000000157011731565764013223 0ustar Subject: add missing what-is Author: Olivier Sallou Description: Add missing what-is description in man pages of binaries Last-Updated: 09/11/11 --- a/bin/gmod_bulk_load_pubmed.pl +++ b/bin/gmod_bulk_load_pubmed.pl @@ -1,7 +1,7 @@ #!/usr/bin/perl =head1 NAME -gmod_bulk_load_pubmed.pl +gmod_bulk_load_pubmed.pl - stores pubmed entries in the database =head1 DESCRIPTION --- a/bin/gmod_load_cvterms.pl +++ b/bin/gmod_load_cvterms.pl @@ -2,7 +2,7 @@ =head1 NAME -load_cvterms.pl +load_cvterms.pl - compares which terms are new in the file compared to the database and inserts them =head1 SYNOPSIS --- a/bin/gmod_make_cvtermpath.pl +++ b/bin/gmod_make_cvtermpath.pl @@ -4,7 +4,7 @@ =head1 NAME -gmod_make_cvtermpath.pl +gmod_make_cvtermpath.pl - calculates the transitive closure on the ontology terms in the cvterm table =head1 USAGE debian/patches/series0000644000000000000000000000015711731567060012043 0ustar fix_perl_headers force_SIMPLE fix_spelling_manpage fix_manpages setBinPathForBuilder remove_pl_extension.patch debian/patches/fix_perl_headers0000644000000000000000000000163512071257265014057 0ustar Subject: fix interpreter path Description: default perl interpreter path is wrong Author: Olivier Sallou Last-Updated: 02/11/2011 --- a/bin/gmod_bulk_load_pubmed.pl +++ b/bin/gmod_bulk_load_pubmed.pl @@ -1,4 +1,4 @@ - +#!/usr/bin/perl =head1 NAME gmod_bulk_load_pubmed.pl --- a/bin/load_ncbi_taxonomy.pl +++ b/bin/load_ncbi_taxonomy.pl @@ -1,4 +1,4 @@ - +#!/usr/bin/perl =head1 NAME load_ncbi_taxonomy.pl --- a/bin/load_taxonomy_cvterms.pl +++ b/bin/load_taxonomy_cvterms.pl @@ -1,4 +1,4 @@ - +#!/usr/bin/perl =head1 NAME load_taxonomy_cvterms.pl --- a/load/bin/bulk_load_gff3.PLS +++ b/load/bin/bulk_load_gff3.PLS @@ -1,4 +1,4 @@ -#!perl -w +#!/usr/bin/perl -w use Config; use File::Basename qw(&basename &dirname); --- a/load/bin/load_gff3.PLS +++ b/load/bin/load_gff3.PLS @@ -1,4 +1,4 @@ -#!perl -w +#!/usr/bin/perl -w use Config; use File::Basename qw(&basename &dirname); debian/patches/force_SIMPLE0000644000000000000000000000161211731565764012726 0ustar Subject: remove questions at setup Description: Remove "simple install" question from setup Author: Olivier Sallou Last-Updated: 02/11/2011 --- a/Makefile.PL +++ b/Makefile.PL @@ -243,9 +243,10 @@ my ( $DBDRIVER, $DBNAME, $DBUSER, $DBPASS, $DBHOST, $DBPORT,$SCHEMA, $SQLFILES, $EXTERNAL_DDL, $LOCAL_TMP, $DBORGANISM, $APOLLO, $DEFAULT); -$O{'SIMPLE'} = prompt( - "Use the simple install (uses default database schema, which contains\nall of the modules and extensions to the schema and all of the non-trigger functions.\nThis is probably what you want)", 'Y' - ); +#$O{'SIMPLE'} = prompt( +# "Use the simple install (uses default database schema, which contains\nall of the modules and extensions to the schema and all of the non-trigger functions.\nThis is probably what you want)", 'Y' +# ); +$O{'SIMPLE'} = "Y"; if ( ! @argv && %conf ) { my $answer = prompt( debian/patches/remove_pl_extension.patch0000644000000000000000000000370412071257334015732 0ustar Subject: remove extension to call libdbix-dbstag-perl binaries Description: libdbix-dbstag-perl binaries have perl extension removed, current scripts must call those binaries without extension too Author: Olivier Sallou Last-Updated: 19/03/2012 --- a/INSTALL.Chado +++ b/INSTALL.Chado @@ -360,17 +360,17 @@ the Sequence Ontology (SO) is absolutely required for proper functioning of the database. The commands to load an ontology are: - $ go2fmt.pl -p obo_text -w xml /path/to/obofile | \ + $ go2fmt -p obo_text -w xml /path/to/obofile | \ go-apply-xslt oboxml_to_chadoxml - > obo_text.xml This creates a chadoxml file of the obo file - then execute: - $ stag-storenode.pl \ + $ stag-storenode \ -d 'dbi:Pg:dbname=$CHADO_DB_NAME;host=$CHADO_DB_HOST;port=$CHADO_DB_PORT' \ --user $CHADO_DB_USERNAME --password $CHADO_DB_PASSWORD obo_text.xml If you have other ontology format files, the commands are similar; -consult the documentation for go2fmt.pl and go-apply-xslt for your +consult the documentation for go2fmt and go-apply-xslt for your file format. It is a good idea at this point to make a back up of the database, --- a/lib/Bio/Chado/Builder.pm +++ b/lib/Bio/Chado/Builder.pm @@ -350,7 +350,7 @@ } # loading chadoxml - my $stag_string = "stag-storenode.pl -d 'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'"; + my $stag_string = "stag-storenode -d 'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'"; $stag_string .= " --user $db_user " if $db_user; $stag_string .= " --password '$db_pass' " if $db_pass; $sys_call = join( ' ', @@ -387,7 +387,7 @@ $sys_call = join( ' ', - "stag-storenode.pl -d 'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'", + "stag-storenode -d 'dbi:Pg:dbname=$db_name;host=$db_host;port=$db_port'", catfile( $conf->{'path'}{'data'}, $deffile->{'local'}.'xml') ); debian/patches/setBinPathForBuilder0000644000000000000000000000235411731565764014602 0ustar Author: Olivier Sallou Subject: set binary path Last-Updated: 06/12/11 Description: update path for binaries to match gmod chado installation --- a/lib/Bio/Chado/Builder.pm +++ b/lib/Bio/Chado/Builder.pm @@ -96,12 +96,12 @@ my $result = `bin/gmod_add_organism.pl --name_only --common_name $db_org`; unless ($result) { print "Adding $db_org to the database...\n"; - system('bin/gmod_add_organism.pl','--common_name',$db_org); + system('/usr/share/gmod/chado/bin/gmod_add_organism.pl','--common_name',$db_org); } } #set the chado schema version in the database - system("gmod_chado_properties.pl --dbprofile $db_name --force --version $schema_version"); + system("/usr/share/gmod/chado/bin/gmod_chado_properties.pl --dbprofile $db_name --force --version $schema_version"); } @@ -133,7 +133,7 @@ if (looks_like_number($version) and $version < $schema_version) { print "Attempting schema update.\n"; - system("gmod_update_chado.pl --dbprofile $db_name"); + system("/usr/share/gmod/chado/bin/gmod_update_chado.pl --dbprofile $db_name"); } elsif (looks_like_number($version) and $version >= $schema_version) { print "No update necessary.\n"; debian/patches/fix_spelling_manpage0000644000000000000000000002111712071257316014721 0ustar Subject: Fix spelling errors Author: Olivier Salllou Description: fix spelling errors in man pages Last-Updated: 09/11/11 --- a/lib/Bio/GMOD/DB/Adapter.pm +++ b/lib/Bio/GMOD/DB/Adapter.pm @@ -868,7 +868,7 @@ =item Returns -On create, void. With an arguement, returns the requested file handle +On create, void. With an argument, returns the requested file handle =item Arguments @@ -968,7 +968,7 @@ =item Returns -See Arguements. +See Arguments. =item Arguments @@ -3470,7 +3470,7 @@ -- short identifier that can help people find an analysis they -- want. for instance "tRNAscan", "cDNA", "FlyPep", "SwissProt" -- it should not be assumed to be unique. for instance, there may --- be lots of seperate analyses done against a cDNA database. +-- be lots of separate analyses done against a cDNA database. -- -- program: not NULL (and programversion is NOT NULL...) -- e.g. blastx, blastp, sim4, genscan --- a/lib/Bio/GMOD/Config2.pm +++ b/lib/Bio/GMOD/Config2.pm @@ -81,7 +81,7 @@ Takes one optional argument that is the path to the root of the GMOD installation. If that argument is not provided, Bio::GMOD::Config will -fall back to the enviroment variable GMOD_ROOT, which should be defined +fall back to the environment variable GMOD_ROOT, which should be defined for any GMOD installation. =cut @@ -267,7 +267,7 @@ =head2 appendHash($tohash, $addhash, $replace) -add keys to hash without replacing existing .. prefered behavior ? +add keys to hash without replacing existing .. preferred behavior ? unless $replace is flagged =cut --- a/lib/Bio/GMOD/Config.pm +++ b/lib/Bio/GMOD/Config.pm @@ -41,7 +41,7 @@ Takes one optional argument that is the path to the root of the GMOD installation. If that argument is not provided, Bio::GMOD::Config will -fall back to the enviroment variable GMOD_ROOT, which should be defined +fall back to the environment variable GMOD_ROOT, which should be defined for any GMOD installation. =cut --- a/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm +++ b/lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm @@ -640,7 +640,7 @@ full of match: analysis types (messy names, types, etc.) -- no feats written to fff in many hours !? - due to holding BAC and cytoband features -- try dropping gffForwards; maybe better (gff written) but still memuse balloons - -- added clearFinishedObs() - no apparent help; dont see what else is holding objects here + -- added clearFinishedObs() - no apparent help; don't see what else is holding objects here -- ok now, added min base loc to keep in oidobs, delete all before runs fast - chr 3L in 10 min. instead of >2hr. @@ -775,8 +775,8 @@ if (!$type && $DEBUG && !/NULL|repeatmask/) { print STDERR "missing type: $_\n"; } ##<< repeatmasker kid objs if ($type eq 'skip' || !$type) { # or what? undef? got some bad feats w/ no type?? - ## dont keep old oid: ($l_arm,$l_oid,$l_fmin)= ($arm,$oid,$fmin); - ##dont save arm for skip !? if changed here, cant miss below openout.. + ## don't keep old oid: ($l_arm,$l_oid,$l_fmin)= ($arm,$oid,$fmin); + ##don't save arm for skip !? if changed here, cant miss below openout.. ($l_oid,$l_fmin)= (-1,$fmin); next; } @@ -827,7 +827,7 @@ else { ## FIXME - bad if fob not in @fobs ## .. e.g. repeat region - many locs over arm, few oid's - ## most of these we dont want to join - too far apart; need max_max setting below to keep small ranges together? + ## most of these we don't want to join - too far apart; need max_max setting below to keep small ranges together? # print STDERR "missed join to last $type,$name,$oid\n" if $DEBUG; } } @@ -875,7 +875,7 @@ if ($flushok) { if ($self->hasObForwards(\@fobs, \%oidobs)) { $flushok = 0; - $min_max= $fmin + 2000; ##smaller step so we dont miss chance to flush + $min_max= $fmin + 2000; ##smaller step so we don't miss chance to flush } warn "hasObForwards no=$flushok at $fmin $type:$name $oid\n" if ($DEBUG>1); } @@ -908,7 +908,7 @@ $fob= $newob; foreach my $fk (keys %addfob) { $fob->{$fk}= $addfob{$fk}; } %addfob=(); - #?? dont add here if it is simple feature; wait till know if it is parent or kid? + #?? don't add here if it is simple feature; wait till know if it is parent or kid? # this is bad for 'gene' NOT? simple feat unless( $simplefeat{$type} ) { $oidobs{$oid}->{fob}= $newob; @@ -1157,7 +1157,7 @@ } } } - ## else { } # $iskid only - dont save + ## else { } # $iskid only - don't save } return \@cobs; @@ -1256,7 +1256,7 @@ looks like chado pg reporting instance with CDS_exons is bad for transspliced mod(mdg4) 08may: change behavior for GenbankSubmit to offsetLocation: - dont return Genbank style string location, but + don't return Genbank style string location, but adjust @loc to CDS_exons by CDS span offset; See also getCDSexons and makeCompound @@ -1573,7 +1573,7 @@ ## for each gene model part; should add locus_tag == gene ID # if ($gff_keepoids) { $at{$k} .= ATTR_LISTCHAR if $at{$k}; $at{$k} .= $v; } - next if $segmentfeats{$type}; # dont do parent for these ... ? + next if $segmentfeats{$type}; # don't do parent for these ... ? $v =~ s/:.*$//; $k= 'Parent'; --- a/lib/Bio/GMOD/Bulkfiles/SWISS_CRC64.pm +++ b/lib/Bio/GMOD/Bulkfiles/SWISS_CRC64.pm @@ -7,7 +7,7 @@ =head2 SYNOPSIS -** dgg: rewrite for line-add so dont need to suck all into mem ** +** dgg: rewrite for line-add so don't need to suck all into mem ** use SWISS::CRC64; --- a/bin/gmod_gff3_preprocessor.pl +++ b/bin/gmod_gff3_preprocessor.pl @@ -24,7 +24,7 @@ --gfffile The file containing GFF3 (optional, can read from stdin) --outfile The name kernel that will be used for naming result files - --splitfile Split the files into more managable chunks, providing + --splitfile Split the files into more manageable chunks, providing an argument to control splitting --onlysplit Split the files and then quit (ie, don't sort) --nosplit Don't split the files (ie, only sort) @@ -61,7 +61,7 @@ =head2 FASTA sequence If the GFF3 file contains FASTA sequence at the end, the sequence -will be placed in a separate file with the extention '.fasta'. This +will be placed in a separate file with the extension '.fasta'. This fasta file can be loaded separately after the split and/or sorted GFF3 files are loaded, using the command: --- a/bin/gmod_make_gff_from_dbxref.pl +++ b/bin/gmod_make_gff_from_dbxref.pl @@ -21,7 +21,7 @@ =head1 DESCRIPTION -This tool takes a list of tab seperated db identifiers and accessions on +This tool takes a list of tab separated db identifiers and accessions on the command line (like gmod_extract_dbxref_from_gff.pl would produce) along with a directory containing fasta files and creates a GFF file. The script tries several options for identifying the accession in the --- a/bin/gmod_materialized_view_tool.pl +++ b/bin/gmod_materialized_view_tool.pl @@ -59,7 +59,7 @@ =item 1 Data syncronisity When normal tables are updated with values that are reflected in a MV, -there will be a delay (usually a very noticable one) between when +there will be a delay (usually a very noticeable one) between when the normal table is updated and when the MV is updated. This tool provides the means of updating the MVs; see --automatic below. --- a/load/bin/bulk_load_gff3.PLS +++ b/load/bin/bulk_load_gff3.PLS @@ -90,7 +90,7 @@ to use the current directory) --no_target_syn By default, the loader adds the targetId in the synonyms list of the feature. This flag - desactivate this. + deactivate this. --unique_target Trust the unicity of the target IDs. IDs are case sensitive. By default, the uniquename of a new target will be 'TargetId_PrimaryKey'. With this flag, @@ -256,7 +256,7 @@ db_name must have an entry in the db table, with a value of db.name equal to 'DB:db_name'; several database names were preinstalled with the database when 'make prepdb' was run. Execute 'SELECT name -FROM db' to find out what databases are already availble. New dbxref +FROM db' to find out what databases are already available. New dbxref entries are created in the dbxref table, and dbxrefs are linked to features via the feature_dbxref table. debian/rules0000755000000000000000000000533312036224053010247 0ustar #!/usr/bin/make -f pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') #export GMOD_ROOT=/usr/share/gmod/chado export GMOD_ROOT=$(CURDIR)/debian/$(pkg)/usr/share/gmod/chado export CHAOS_HOME=$(CURDIR)/debian/$(pkg)/usr/share/gmod/chaos export CHADO_DB_NAME=gmod-chado export PREFIX=/usr %: dh $@ --buildsystem=perl_makemaker override_dh_auto_configure: perl Makefile.PL INSTALL_BASE=/usr DBNAME=$(CHADO_DB_NAME) DBUSER=chado DBPASS=chado DBHOST=localhost DBPORT=5432 GMOD_ROOT=$(GMOD_ROOT) DBDRIVER=PostgreSQL RECONFIGURE=1 SIMPLE=Y LOCAL_TMP=$(CURDIR)/debian/$(pkg)/tmp override_dh_install: dh_install -O--buildsystem=perl_makemaker rm -f debian/$(pkg)/usr/share/gmod/chado/load/etc/load.conf sed -i 's/SQLFILE=\/.*\/$(pkg)/SQLFILE=/' debian/$(pkg)/usr/share/gmod/chado/conf/gmod-chado.conf sed -i 's/TMP=\/.*\/tmp/CONF=\/tmp/' debian/$(pkg)/usr/share/gmod/chado/conf/gmod.conf sed -i 's/CONF=.*\/conf/CONF=\/etc\/gmod/' debian/$(pkg)/usr/share/gmod/chado/conf/gmod.conf mv $(GMOD_ROOT)/conf/* debian/$(pkg)/etc/gmod/ # Give exexution rights to perl scripts find debian/$(pkg)/ -name *.pl | xargs chmod 755 find debian/$(pkg)/ -name *.tmpl | xargs chmod 644 find debian/$(pkg)/ -name *.pm | xargs chmod 644 find debian/$(pkg)/ -name *.pod | xargs rm -f find debian/$(pkg)/ -name .packlist | xargs rm -f find debian/$(pkg)/ -name "*.sql" | xargs chmod a-x chmod 755 debian/$(pkg)/usr/share/gmod/chado/soi/t/t_soi_parse_intersect chmod 755 debian/$(pkg)/usr/share/gmod/chado/src/chado/modules/audit/make_audit_ddl mv debian/tmp/usr/bin/test* debian/$(pkg)/usr/share/gmod/chado/bin/ mv debian/tmp/usr/bin/gmod_chado* debian/$(pkg)/usr/share/gmod/chado/bin/ mv debian/tmp/usr/bin/config* debian/$(pkg)/usr/share/gmod/chado/bin/ mv debian/tmp/usr/bin/Auto* debian/$(pkg)/usr/share/gmod/chado/bin/ mv debian/tmp/usr/bin/* debian/chado-utils/usr/share/gmod/chado/bin/ mv debian/tmp/usr/lib/perl5/* debian/$(pkg)/usr/share/perl5/ rm -rf debian/$(pkg)/usr/lib/perl5 mv debian/tmp/usr/man/man3 debian/$(pkg)/usr/share/man/man3 mv debian/tmp/usr/man/man1 debian/chado-utils/usr/share/man/man1 cp debian/testdb.pl debian/$(pkg)/usr/share/gmod/chado/bin/ rm -rf debian/$(pkg)/usr/share/perl5/x86_64-linux-gnu-thread-multi # Needed for runtime configure rm -rf debian/$(pkg)/usr/share/gmod/chado/lib rm -rf debian/$(pkg)/usr/bin rm -rf debian/$(pkg)/usr/lib rm -rf debian/$(pkg)/usr/share/gmod/chado/load/logs rm -rf debian/$(pkg)/usr/share/gmod/chado/tmp # Remove not required man pages for user (also contains pod2man errors and missing what-is) rm -rf debian/$(pkg)/usr/share/man override_dh_auto_test: echo "Skipping tests to avoid db access" override_dh_fixperms: dh_fixperms chmod 600 debian/$(pkg)/etc/gmod/gmod-chado.conf debian/testdb.pl0000644000000000000000000000141111731565764011024 0ustar #!/usr/bin/perl -w use strict; use DBI; use Bio::GMOD::Config; use Bio::GMOD::DB::Config; use Getopt::Long; use URI::Escape; my $gmod_conf = $ENV{'GMOD_ROOT'} ? Bio::GMOD::Config->new($ENV{'GMOD_ROOT'}) : Bio::GMOD::Config->new(); my $db_conf = Bio::GMOD::DB::Config->new($gmod_conf,'gmod-chado'); my $dbh = eval {$db_conf->dbh}; if( $@ =~ m/couldn't create db connection/i ) { exit 102; } my $nbtables = $dbh->prepare("select count(*) as nbtables from pg_tables"); $nbtables->execute() or exit 102; my $arrayref = $nbtables->fetchrow_arrayref(); $nbtables = $$arrayref[0]; $dbh->disconnect; if($nbtables>0) { print "Database already exists, update it\n"; exit 101; } else { print "Empty database, create it\n"; exit 100; } debian/source/0000755000000000000000000000000012071257637010500 5ustar debian/source/format0000644000000000000000000000001411731565764011713 0ustar 3.0 (quilt) debian/libchado-perl.lintian-overrides0000644000000000000000000000015411731565764015272 0ustar libchado-perl: package-contains-upstream-install-documentation usr/share/doc/libchado-perl/INSTALL.Chado.gz debian/libchado-perl.dirs0000644000000000000000000000016611731565764012600 0ustar usr/share/gmod/chado/bin usr/share/man/man3 etc/gmod usr/share/perl5 usr/share/gmod/chado/lib/Bio/Chado var/log/chado debian/control0000644000000000000000000000540111731570126010574 0ustar Source: libchado-perl Section: perl Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Scott Cain , Steffen Moeller , Olivier Sallou DM-Upload-Allowed: yes Build-Depends: debhelper (>= 8) Build-Depends-Indep: perl, libclass-dbi-pg-perl, libxml-libxslt-perl, liblog-log4perl-perl, bioperl, libgo-perl, libdbd-pg-perl, libdbi-perl, libgd-gd2-perl,libdigest-md5-file-perl, libgraph-perl, libdata-stag-perl, libxml-perl, libmodule-build-perl, libclass-dbi-perl, libclass-dbi-pager-perl, libxml-simple-perl, libwww-perl, libtemplate-perl, libcgi-session-perl, libsql-translator-perl, libdbix-dbstag-perl Standards-Version: 3.9.3 Homepage: http://gmod.org/wiki/Chado Vcs-Browser: http://svn.debian.org/viewvc/debian-med/trunk/packages/gmod/chado/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/gmod/chado/trunk/ Package: libchado-perl Architecture: all Depends: ${misc:Depends}, ${perl:Depends}, postgresql-client, libbio-chado-schema-perl, libclass-dbi-pg-perl, libxml-libxslt-perl, liblog-log4perl-perl, bioperl, libgo-perl, libdbd-pg-perl, libdbi-perl, libgd-gd2-perl, libdigest-md5-file-perl, libgraph-perl, libdata-stag-perl, libxml-perl, libmodule-build-perl, libclass-dbi-perl, libclass-dbi-pager-perl, libxml-simple-perl,libwww-perl, libtemplate-perl, libcgi-session-perl, libsql-translator-perl, libdbix-dbstag-perl, make Recommends: xsltproc, chado-utils Description: database schema and tools for genomic data Chado is a relational database schema that underlies many GMOD installations. It is capable of representing many of the general classes of data frequently encountered in modern biology such as sequence, sequence comparisons, phenotypes, genotypes, ontologies, publications, and phylogeny. It has been designed to handle complex representations of biological knowledge and should be considered one of the most sophisticated relational schemas currently available in molecular biology. The price of this capability is that the new user must spend some time becoming familiar with its fundamentals. Package: chado-utils Architecture: all Depends: ${misc:Depends}, ${perl:Depends}, libchado-perl Recommends: xsltproc Description: tools to add/extract data from Chado This package contains several tools that can be used to extract data from Chado database or prepare data before upload. It is a subset above the Chado database schema and libraries. . Chado is a relational database schema that underlies many GMOD installations. It is capable of representing many of the general classes of data frequently encountered in modern biology such as sequence, sequence comparisons, phenotypes, genotypes, ontologies, publications, and phylogeny. debian/README.Debian0000644000000000000000000000254512036226704011237 0ustar Chado needs to connect to a database to load or upgrade its schema. It loads its configuration from /etc/gmod/gmod-chado.conf. This file is protected as it contains db password. If file is not present, or configuration is not correct (db user not created ...), package will continue its install, with a warning message containing instructions for a manual schema installation. Instructions to create user and database: ********************** Connect with user postgres postgres@debiansid:~$ createuser --createdb -P chado Enter password for new role: Enter it again: Shall the new role be a superuser? (y/n) n Shall the new role be allowed to create more new roles? (y/n) n root@debiansid:/usr/share/gmod/chado# psql -U chado -W -h localhost template1 Password for user chado: psql (9.1.1) SSL connection (cipher: DHE-RSA-AES256-SHA, bits: 256) Type "help" for help. template1=> CREATE DATABASE "gmod-chado" *********************** Additional instructions for database tuning are available in /usr/share/doc/chado/INSTALL.Chado In case of db access failure during installation, after setting the configuration one should execute: cd /usr/share/gmod/chado/ export GMOD_ROOT=/usr/share/gmod/chado export PGPASSFILE=/usr/share/gmod/chado/pgpass For a new installation: make load_schema make prepdb OR make update to upgrade the schema from a previous install debian/changelog0000644000000000000000000000224212071257614011045 0ustar libchado-perl (1.23-1) unstable; urgency=low * New upstream release -- Olivier Sallou Thu, 03 Jan 2013 11:24:54 +0100 libchado-perl (1.22-4) unstable; urgency=low * debian/rules: fix permissions on gmod-chado file and remove unneeded file load.conf (Closes: #689111). * debian/postinst: fix permissions on pgpass file (Closes: #689111). -- Olivier Sallou Tue, 09 Oct 2012 14:27:37 +0200 libchado-perl (1.22-3) unstable; urgency=low * debian/patches/remove_pl_extension.patch: - add patch to use libdbix-dbstag-perl binary without extension -- Olivier Sallou Mon, 19 Mar 2012 09:26:00 +0100 libchado-perl (1.22-2) unstable; urgency=low [Olivier Sallou] * Fix perl Depends not set by perl:Depends (Closes: #659295) * debian/postrm: in case of purge, remove generated files [Charles Plessy] * Corrected Vcs fields (debian/control). -- Olivier Sallou Wed, 22 Feb 2012 16:22:19 +0100 libchado-perl (1.22-1) unstable; urgency=low * Initial Release (Closes: #639868). -- Olivier Sallou Thu, 14 Jul 2011 12:44:56 +0200 debian/README.source0000644000000000000000000000153211731565764011365 0ustar Chado is patched to adapt to Debian file system hierarchy, using quilt. For more info on quilt, see /usr/share/doc/quilt/README.source. Regarding lintian warnings: W: libchado-perl: maintainer-script-ignores-errors postinst Errors are not ignored, errors are catched in the script as some error codes are a correct behaviour in scripts. Other error codes are thrown as usual W: libchado-perl: package-contains-upstream-install-documentation usr/share/doc/libchado-perl/INSTALL.Chado.gz Lintian override: INSTALL doc is required for database optimization setup and manual schema installation if automatic setup was not used. Binaries tools are not set in /usr/bin but under /usr/share/gmod/chado/bin because part of those scripts are used by other gmod tools, not necessarly with same version and not necessarly all same tools, leading to conflicts. debian/watch0000644000000000000000000000006611731565764010240 0ustar version=3 http://sf.net/gmod/chado-([0-9.]+)\.tar\.gz debian/libchado-perl.docs0000644000000000000000000000030311731565764012560 0ustar README.Apollo README modules/phylogeny/examples/README modules/sequence/bdgp/README modules/sequence/apollo-bridge/sample_db/README load/etc/README stag-templates/README soi/README INSTALL.Chado debian/compat0000644000000000000000000000000211731565764010403 0ustar 8 debian/postinst0000644000000000000000000000444112035011116010765 0ustar #!/bin/bash set -E trap onexit ERR function onexit() { EXITCODE=$? if [ $EXITCODE -eq 102 ]; then echo "Database access not correctly configured" echo "Check your configuration and run manually the database update:" echo "cd /usr/share/gmod/chado/" echo "export GMOD_ROOT=/usr/share/gmod/chado" echo "export PGPASSFILE=/usr/share/gmod/chado/pgpass" echo "For a new installation:" echo "make load_schema" echo "make prepdb" echo "OR" echo "make update to upgrade the schema from a previous install" exit 0 fi if [ $EXITCODE -eq 100 ]; then make load_schema make prepdb make clean &> /dev/null rm -f /usr/share/gmod/chado/pgpass exit 0 fi if [ $EXITCODE -eq 101 ]; then make update make clean &> /dev/null rm -f /usr/share/gmod/chado/pgpass exit 0 fi exit $EXITCODE } case "$1" in configure) mkdir -p /usr/share/gmod/chado/lib/Bio/Chado/ if [ -e /etc/gmod/gmod-chado.conf ]; then export GMOD_ROOT=/usr/share/gmod/chado . /etc/gmod/gmod-chado.conf cd /usr/share/gmod/chado export CHADO_DB_NAME=gmod-chado CHADOTMP=`mktemp -d` perl Makefile.PL update GMOD_ROOT=/usr/share/gmod/chado DBNAME=$CHADO_DB_NAME DBUSER=$DBUSER DBPASS=$DBPASS DBHOST=$DBHOST DBPORT=$DBPORT DBDRIVER=PostgreSQL SIMPLE=Y RECONFIGURE=1 LOCAL_TMP=$CHADOTMP &> /dev/null rm -rf $CHADOTMP export PATH=$PATH:/usr/share/gmod/chado/bin touch /usr/share/gmod/chado/pgpass chmod 0600 /usr/share/gmod/chado/pgpass echo "*:*:*:$DBUSER:$DBPASS" > /usr/share/gmod/chado/pgpass export PGPASSFILE=/usr/share/gmod/chado/pgpass # Need to detect with testdb if access to db is ok or need to be configured perl /usr/share/gmod/chado/bin/testdb.pl else echo "Application is not yet configured." echo "To install or upgrade the database:" echo " - create a user in the database" echo " - configure the application" echo " - perl /usr/share/gmod/chado/Makefile.PL update" fi ;; abort-upgrade|abort-remove|abort-deconfigure) ;; *) echo "postinst called with unknown argument \`$1'" >&2 exit 1 ;; esac #DEBHELPER# debian/libchado-perl.links0000644000000000000000000000030611731565764012753 0ustar etc/gmod/gmod.conf usr/share/gmod/chado/conf/gmod.conf etc/gmod/gmod-chado.conf usr/share/gmod/chado/conf/gmod-chado.conf var/log/chado /usr/share/gmod/chado/load/logs tmp /usr/share/gmod/chado/tmp debian/chado-utils.dirs0000644000000000000000000000005411731565764012303 0ustar usr/share/gmod/chado/bin usr/share/man/man1 debian/libchado-perl.examples0000644000000000000000000000006111731565764013447 0ustar modules/phylogeny modules/organism chado-xml doc