scottcain

{
  "description": "Pythium",
  "db_adaptor": "Bio::DB::Das::Chado",
  "db_args": { "-dsn": "dbi:Pg:dbname=chado",
               "-user": "gmod",
               "-pass": ""},

  "TRACK DEFAULTS": {
    "class": "feature"
  },

scottcain

unpacking...
BioPerl-1.6.901/t/Variation/SNP.t
BioPerl-1.6.901/t/Variation/Variation_IO.t
Use of uninitialized value $_[0] in join or string at /usr/lib/perl5/File/Spec/Unix.pm line 86.
Use of uninitialized value $path in pattern match (m//) at /usr/lib/perl5/File/Spec/Unix.pm line 267

...repeats many times (100s)....

CPAN: Time::HiRes loaded ok (v1.9719)

scottcain

Use of uninitialized value $path in pattern match (m//) at /usr/local/lib/perl/5.10.1/File/Spec/Unix.pm line 267
	File::Spec::Unix::splitpath('File::Spec', undef) called at /usr/share/perl/5.10/Archive/Tar.pm line 706
	Archive::Tar::_extract_file('Archive::Tar=HASH(0xdd6a498)', 'Archive::Tar::File=HASH(0xdea0b28)') called at /usr/share/perl/5.10/Archive/Tar.pm line 571
	Archive::Tar::extract('Archive::Tar=HASH(0xdd6a498)', 'BioPerl-1.6.901', 'BioPerl-1.6.901/AUTHORS', 'BioPerl-1.6.901/BioPerl.pm', 'BioPerl-1.6.901/BUGS', 'BioPerl-1.6.901/Build.PL', 'BioPerl-1.6.901/Changes', 'BioPerl-1.6.901/DEPENDENCIES', 'BioPerl-1.6.901/DEPRECATED', ...) called at /usr/share/perl/5.10/CPAN/Tarzip.pm line 351
	CPAN::Tarzip::untar('CPAN::Tarzip=HASH(0xdae3e48)') called at /usr/share/perl/5.10/CPAN/Distribution.pm line 1095
	eval {...} called at /usr/share/perl/5.10/CPAN/Distribution.pm line 1095
	CPAN::Distribution::untar_me('CPAN::Distribution=HASH(0xda0dc90)', 'CPAN::Tarzip=HASH(0xdae3e48)') called at /usr/share/perl/5.10/

scottcain

[main:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
                -dir '/Library/WebServer/Documents/gbrowse2/databases/volvox'


[samdb:database]
db_adaptor     = Bio::DB::Sam
db_args        = -fasta /Library/WebServer/Documents/gbrowse2/databases/volvox/volvox.fa
                 -bam  /Library/WebServer/Documents/gbrowse2/databases/volvox/volvox.sort.bam

scottcain

M	bin/gbrowse_attach_slaves.pl
U	cgi-bin/admin
M	cgi-bin/attach.pl
U	cgi-bin/slaveStatus.pl
M	cgi-bin/slaves.pl
M	cgi-bin/volumeStatus.pl
A	lib/Bio/Graphics/Browser2/Cloud/Userdata.pm
Pull is not possible because you have unmerged files.
Please, fix them up in the work tree, and then use 'git add/rm <file>'
as appropriate to mark resolution, or use 'git commit -a'.

scottcain

This is the mail system at host leela.spi-inc.org.

I'm sorry to have to inform you that your message could not
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For further assistance, please send mail to postmaster.

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scottcain

diff config.xml /data/var/lib/tomcat7/webapps/WebApollo/config/config.xml 
25,28d24
< 	<!-- set to false to use hybrid disk/memory store which provides a little slower performance
< 	but uses a lot less memory - great for annotation rich genomes -->
< 	<use_pure_memory_store>true</use_pure_memory_store>
< 
98,123c94,108
< 		<!-- grouping for the configuration.  The "feature_types" attribute takes a list of
< 		SO terms (comma separated) to apply this configuration to
< 		(e.g., feature_types="sequence:transcript,sequence:mRNA" will make it so the group

scottcain

format-version: 1.2
saved-by: cjm
auto-generated-by: cjm
default-namespace: relationship
remark: <p>This ontology contains logical relations to be shared across the different OBO ontologies. Each OBO ontology is free to extend this set with relations specific to the biology within that ontology</p><div class="notes"><p>In the definitions, variables c, d, ..., p, q, ... range over instances of continuants and processes respectively. C, D, ..., P, Q, ... range over the corresponding classes</p><p> For a discussion of instance-level relations and also of additional axioms needed to infer transitivity and other properties of the relations listed above see <a href="http://genomebiology.com/2005/6/5/R46">http://genomebiology.com/2005/6/5/R46</a> or the OBO relations page hosted at <a href="http://obo.sourceforge.net/relationship">http://obo.sourceforge.net/relationship</a></div>
idspace: OBO_REL http://www.obofoundry.org/ro/ro.owl# "OBO Relation ontology official home on OBO Foundry"
remark: cvs version $Revision: 

scottcain

'RestrictionSearch/View/SearchSeqDialog':function(){
define([
        'dojo/_base/declare',
        'dojo/dom-construct',
        'dojo/aspect',
        'dijit/focus',
        'dijit/form/Button',
        'dijit/form/CheckBox',
        'dijit/form/FilteringSelect',
        'dojo/store/Memory',

scottcain

I	landmark	gene	146486	154850	.	-	.	ID=landmark:bli-3;locus=bli-3
I	landmark	gene	1176471	1190829	.	+	.	ID=landmark:smg-2;locus=smg-2
I	landmark	gene	2706883	2717549	.	+	.	ID=landmark:lin-17;locus=lin-17
I	landmark	gene	3798566	3805737	.	-	.	ID=landmark:unc-11;locus=unc-11
I	landmark	gene	4675135	4679409	.	+	.	ID=landmark:unc-57;locus=unc-57
I	landmark	gene	5432158	5433054	.	-	.	ID=landmark:dpy-5;locus=dpy-5
I	landmark	gene	6342231	6356678	.	+	.	ID=landmark:bli-4;locus=bli-4
I	landmark	gene	7422785	7454088	.	+	.	ID=landmark:unc-13;locus=unc-13
I	landmark	gene	8897613	8901435	.	-	.	ID=landmark:unc-29;locus=unc-29
I	landmark	gene	8928748	8931089	.	+	.	ID=landmark:tsp-15;locus=tsp-15