[med-svn] r21705 - in trunk/packages/gmod/chado/tags: . 1.31-1/debian 1.31-1/debian/patches
Olivier Sallou
osallou at moszumanska.debian.org
Tue Apr 12 15:58:27 UTC 2016
Author: osallou
Date: 2016-04-12 15:58:25 +0000 (Tue, 12 Apr 2016)
New Revision: 21705
Added:
trunk/packages/gmod/chado/tags/1.31-1/
trunk/packages/gmod/chado/tags/1.31-1/debian/changelog
trunk/packages/gmod/chado/tags/1.31-1/debian/patches/fix_spelling_manpage
trunk/packages/gmod/chado/tags/1.31-1/debian/patches/remove_pl_extension.patch
trunk/packages/gmod/chado/tags/1.31-1/debian/patches/setBinPathForBuilder
Removed:
trunk/packages/gmod/chado/tags/1.31-1/debian/changelog
trunk/packages/gmod/chado/tags/1.31-1/debian/patches/fix_spelling_manpage
trunk/packages/gmod/chado/tags/1.31-1/debian/patches/remove_pl_extension.patch
trunk/packages/gmod/chado/tags/1.31-1/debian/patches/setBinPathForBuilder
Log:
[svn-buildpackage] Tagging libchado-perl 1.31-1
Deleted: trunk/packages/gmod/chado/tags/1.31-1/debian/changelog
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/changelog 2016-04-12 15:38:21 UTC (rev 21703)
+++ trunk/packages/gmod/chado/tags/1.31-1/debian/changelog 2016-04-12 15:58:25 UTC (rev 21705)
@@ -1,68 +0,0 @@
-libchado-perl (1.23-5) unstable; urgency=medium
-
- * Enhanced patch from Niko Tyni really
- Closes: #802042
-
- -- Andreas Tille <tille at debian.org> Sat, 12 Dec 2015 20:35:21 +0100
-
-libchado-perl (1.23-4) unstable; urgency=medium
-
- * Enable reproducible builds (Thanks for the patch to Niko Tyni
- <ntyni at debian.org>)
- Closes: #802042
- * cme fix dpkg-control
-
- -- Andreas Tille <tille at debian.org> Sat, 17 Oct 2015 13:21:08 +0200
-
-libchado-perl (1.23-3) unstable; urgency=medium
-
- * Add libmodule-build-perl dependency (Closes: #789114).
-
- -- Olivier Sallou <osallou at debian.org> Fri, 19 Jun 2015 11:08:05 +0200
-
-libchado-perl (1.23-2) unstable; urgency=medium
-
- * cme fix dpkg-control
- * debhelper 9
- * debian/rules: Fix location of manpages
- Closes: #747569
-
- -- Andreas Tille <tille at debian.org> Sun, 11 May 2014 00:14:09 +0200
-
-libchado-perl (1.23-1) unstable; urgency=low
-
- * New upstream release
-
- -- Olivier Sallou <osallou at debian.org> 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 <osallou at debian.org> 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 <osallou at debian.org> 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 <olivier.sallou at irisa.fr> Wed, 22 Feb 2012 16:22:19 +0100
-
-libchado-perl (1.22-1) unstable; urgency=low
-
- * Initial Release (Closes: #639868).
-
- -- Olivier Sallou <olivier.sallou at irisa.fr> Thu, 14 Jul 2011 12:44:56 +0200
Copied: trunk/packages/gmod/chado/tags/1.31-1/debian/changelog (from rev 21704, trunk/packages/gmod/chado/trunk/debian/changelog)
===================================================================
--- trunk/packages/gmod/chado/tags/1.31-1/debian/changelog (rev 0)
+++ trunk/packages/gmod/chado/tags/1.31-1/debian/changelog 2016-04-12 15:58:25 UTC (rev 21705)
@@ -0,0 +1,74 @@
+libchado-perl (1.31-1) unstable; urgency=medium
+
+ * New upstream release
+
+ -- Olivier Sallou <osallou at debian.org> Tue, 12 Apr 2016 17:45:45 +0200
+
+libchado-perl (1.23-5) unstable; urgency=medium
+
+ * Enhanced patch from Niko Tyni really
+ Closes: #802042
+
+ -- Andreas Tille <tille at debian.org> Sat, 12 Dec 2015 20:35:21 +0100
+
+libchado-perl (1.23-4) unstable; urgency=medium
+
+ * Enable reproducible builds (Thanks for the patch to Niko Tyni
+ <ntyni at debian.org>)
+ Closes: #802042
+ * cme fix dpkg-control
+
+ -- Andreas Tille <tille at debian.org> Sat, 17 Oct 2015 13:21:08 +0200
+
+libchado-perl (1.23-3) unstable; urgency=medium
+
+ * Add libmodule-build-perl dependency (Closes: #789114).
+
+ -- Olivier Sallou <osallou at debian.org> Fri, 19 Jun 2015 11:08:05 +0200
+
+libchado-perl (1.23-2) unstable; urgency=medium
+
+ * cme fix dpkg-control
+ * debhelper 9
+ * debian/rules: Fix location of manpages
+ Closes: #747569
+
+ -- Andreas Tille <tille at debian.org> Sun, 11 May 2014 00:14:09 +0200
+
+libchado-perl (1.23-1) unstable; urgency=low
+
+ * New upstream release
+
+ -- Olivier Sallou <osallou at debian.org> 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 <osallou at debian.org> 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 <osallou at debian.org> 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 <olivier.sallou at irisa.fr> Wed, 22 Feb 2012 16:22:19 +0100
+
+libchado-perl (1.22-1) unstable; urgency=low
+
+ * Initial Release (Closes: #639868).
+
+ -- Olivier Sallou <olivier.sallou at irisa.fr> Thu, 14 Jul 2011 12:44:56 +0200
Deleted: trunk/packages/gmod/chado/tags/1.31-1/debian/patches/fix_spelling_manpage
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/fix_spelling_manpage 2016-04-12 15:38:21 UTC (rev 21703)
+++ trunk/packages/gmod/chado/tags/1.31-1/debian/patches/fix_spelling_manpage 2016-04-12 15:58:25 UTC (rev 21705)
@@ -1,213 +0,0 @@
-Subject: Fix spelling errors
-Author: Olivier Salllou <olivier.sallou at irisa.fr>
-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.
-
Copied: trunk/packages/gmod/chado/tags/1.31-1/debian/patches/fix_spelling_manpage (from rev 21704, trunk/packages/gmod/chado/trunk/debian/patches/fix_spelling_manpage)
===================================================================
--- trunk/packages/gmod/chado/tags/1.31-1/debian/patches/fix_spelling_manpage (rev 0)
+++ trunk/packages/gmod/chado/tags/1.31-1/debian/patches/fix_spelling_manpage 2016-04-12 15:58:25 UTC (rev 21705)
@@ -0,0 +1,213 @@
+Subject: Fix spelling errors
+Author: Olivier Salllou <olivier.sallou at irisa.fr>
+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
+
+@@ -3476,7 +3476,7 @@
+ -- 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.
+
Deleted: trunk/packages/gmod/chado/tags/1.31-1/debian/patches/remove_pl_extension.patch
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/remove_pl_extension.patch 2016-04-12 15:38:21 UTC (rev 21703)
+++ trunk/packages/gmod/chado/tags/1.31-1/debian/patches/remove_pl_extension.patch 2016-04-12 15:58:25 UTC (rev 21705)
@@ -1,48 +0,0 @@
-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 <osallou at debian.org>
-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')
- );
-
Copied: trunk/packages/gmod/chado/tags/1.31-1/debian/patches/remove_pl_extension.patch (from rev 21704, trunk/packages/gmod/chado/trunk/debian/patches/remove_pl_extension.patch)
===================================================================
--- trunk/packages/gmod/chado/tags/1.31-1/debian/patches/remove_pl_extension.patch (rev 0)
+++ trunk/packages/gmod/chado/tags/1.31-1/debian/patches/remove_pl_extension.patch 2016-04-12 15:58:25 UTC (rev 21705)
@@ -0,0 +1,28 @@
+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 <osallou at debian.org>
+Last-Updated: 19/03/2012
+--- a/INSTALL.Chado
++++ b/INSTALL.Chado
+@@ -367,17 +367,17 @@
+ 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,
Deleted: trunk/packages/gmod/chado/tags/1.31-1/debian/patches/setBinPathForBuilder
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/patches/setBinPathForBuilder 2016-04-12 15:38:21 UTC (rev 21703)
+++ trunk/packages/gmod/chado/tags/1.31-1/debian/patches/setBinPathForBuilder 2016-04-12 15:58:25 UTC (rev 21705)
@@ -1,31 +0,0 @@
-Author: Olivier Sallou <olivier.sallou at irisa.fr>
-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";
Copied: trunk/packages/gmod/chado/tags/1.31-1/debian/patches/setBinPathForBuilder (from rev 21704, trunk/packages/gmod/chado/trunk/debian/patches/setBinPathForBuilder)
===================================================================
--- trunk/packages/gmod/chado/tags/1.31-1/debian/patches/setBinPathForBuilder (rev 0)
+++ trunk/packages/gmod/chado/tags/1.31-1/debian/patches/setBinPathForBuilder 2016-04-12 15:58:25 UTC (rev 21705)
@@ -0,0 +1,31 @@
+Author: Olivier Sallou <olivier.sallou at irisa.fr>
+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
+@@ -97,12 +97,12 @@
+ 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 $schema_version");
+
+ }
+
+@@ -134,7 +134,7 @@
+
+ if (looks_like_number($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";
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