Samy Jeevan Karloss Antony | 18 Dec 13:33 2014
Picon

Host IP in bp_seqfeature_load.pl

I have to load GFF3 files into MySQL server using host ip address. How to mention the IP address in
bp_seqfeature_load.pl? 

Jeevan
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
Samy Jeevan Karloss Antony | 16 Dec 12:37 2014
Picon

Loading GFF3 to remote MySQL server

Hello, 

I am using MySQL for our GBrowse installation. I use bp_seqfeature_load.pl to load GFF3 files to MySQL.

Our MySQL server is moved to remote server. I can’t login directly to load the files there. I have to load
remotely. 

My question is, how to mention the MySQL Host IP address when using bp_seqfeature_load.pl? 

The tried the below command is not working. 

bp_seqfeature_load.pl -d ‘Database_Test;host=192.168.168.110 -f -c Test_Genome.gff3
Test_Genome.fasta -u <username> -p xxxx 

Thanks,
Jeevan
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
Haiming Wang | 15 Dec 21:14 2014
Picon

"hide empty subtracks" not working - bigwig metadata file

Hi,


It appears that GBrowse does not even display subtrack headers when there is no data  to display, as shown by the blank spaces in the image attached, which should display eight subtracks instead of six. "hide empty subtracks" is set to false. The following is the related config. I wonder if anyone has any idea about this issue? Thanks!


[tgonME49_DBP_Hehl-Grigg_rnaSeq_RSRC:database]
db_adaptor    = Bio::DB::BigWigSetEuPath
db_args       = sub { { -index => '/path/tgonME49_DBP_Hehl-Grigg_rnaSeq_RSRC/metadata' } }

[tgonME49_DBP_Hehl-Grigg_rnaSeq_RSRCCoverage]
feature = Coverage
database = tgonME49_DBP_Hehl-Grigg_rnaSeq_RSRC
glyph    = wiggle_xyplot
no_grid  = 1  
height   = 40
key          = Transcriptomes of Cat Enteroepithelial Stages (CZ-H3) ...
bgcolor      = sub { GBrowse::Display::rnaseqColorFromBigWig(shift) }
scale        = both
autoscale    = local
link         = javascript:void(0)
category     = Transcript Expression Evidence: B. RNA-seq: T gondii ME49 mRNA-seq: Logged
group_label  = 0  
group_label_position = top

hide empty subtracks = 0


-Haiming

------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
John Portwood | 6 Dec 00:26 2014
Picon

Problems with Net::SMTP::SSL

Hello,

I've recently installed a new instance of GBrowse v2.55 on a machine with CentOS 6.5 x86_64, with everything going smoothly except user account registration. When using the create account or forgotten password links, this error is returned:

Can't locate object method "auth" via package "Net::SMTP::SSL" at /usr/local/lib64/perl5/Bio/Graphics/Browser2/SendMail.pm line 58

Net::SMTP::SSL fails an installation test, but force installing it does not resolve the issue.

Here's the make test error:
Running make test
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/test.t .. 1/1
#   Failed test 'use Net::SMTP::SSL;'
#   at t/test.t line 2.
#     Tried to use 'Net::SMTP::SSL'.
#     Error:  Not a GLOB reference at /home/john/.cpan/build/Net-SMTP-SSL-1.01-gm5tOZ/blib/lib/Net/SMTP/SSL.pm line 16.
# Compilation failed in require at t/test.t line 2.
# BEGIN failed--compilation aborted at t/test.t line 2.
# Looks like you failed 1 test of 1.
t/test.t .. Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/1 subtests

Test Summary Report
-------------------
t/test.t (Wstat: 256 Tests: 1 Failed: 1)
  Failed test:  1
  Non-zero exit status: 1
Files=1, Tests=1,  0 wallclock secs ( 0.04 usr  0.00 sys +  0.15 cusr  0.01 csys =  0.20 CPU)
Result: FAIL
Failed 1/1 test programs. 1/1 subtests failed.

If anyone has any recommendations please let me know.

Thanks!

--
John Portwood
1032 Crop Genome Informatics Labaoratory 
Iowa State University - USDA - ARS
Ames, IA 50010
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Iram sharif | 4 Dec 14:37 2014
Picon

(no subject)

Hi there,


I I want to explore the wheat A genome for which I explored  http://www.wheatgenome.info/wheat_genome_databases.php
 link  but it shows the assmbly of 7A chromosome only from where I can find out the rest of 6 chromosomal assemblies ,kindly tell me.
best regards 
Iram

------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Monica Munoz-Torres | 26 Nov 20:47 2014

New Web Apollo release WA1.0.2(JB1.11.5)

Hello Everyone,

We would like to announce a new Web Apollo release.

This is our first official mavenized release, and it includes a number of changes. If you currently have Web Apollo instances running, please be sure to read carefully through the updated documentation. Specially note: no more symlinking; please use property files instead.

This latest release can be downloaded from GitHub:
https://github.com/GMOD/Apollo/releases/latest

The Readme contains steps for a Quick Update to version 1.0.x (note changes):
https://github.com/GMOD/Apollo/blob/master/README.md

Complete WebApollo installation and configuration instructions for 1.x are available at:
http://webapollo.readthedocs.org

For a detailed account of all changes, please visit:
https://github.com/GMOD/Apollo/blob/master/ChangeLog.md

These are a few highlighted changes:

Features:
+ Added functionality for extending to downstream/upstream acceptor/donor splice sites
+ Added "revert" buttons on rows in history to allow one click change of state
+ Added "{" and "}" for navigating between top level features
+ Added feature coordinates to the "Get Sequence" (get_sequence) output
+ Added tool to split all isoforms into individual genes (RemoveIsoforms.java)
+ Added ability to hide track labels under "view".
+ Added ability to switch between light / dark background color schemes.
+ Added tool for fixing gene boundaries based on children transcripts (FixGeneBoundaries.java)
+ Added option to allow use of encrypted database but does not require it, and
+ Added ability to encrypt an unencrypted  database via encrypt_passwords.pl
+ Using javascript minimization for JBrowse+WebApollo to allow faster initial load time
+ Using Maven build system for deployment (See new installation guide listed above)
+ Integrate with TravisCI: https://travis-ci.org/GMOD/Apollo
+ Added ability to visualize latest changes, and menu items to changes and sequence-selection pages to the annotation screen, fixing memory issues from selectTrack.jsp and recentChanges.jsp pages.
+ alt/Option+click brings up Information Editor on annotated track.
+ Added webservices doc links to interface.
+ Added command line exporters for GFF3 files.
+ Using JBrowse 1.11.5

Bugfixes:
+ Fixed phase in GFF3 output
+ Disabled scrollToPreviousEdge/scrollToNextEdge if the feature is fully visible at the current zoom level
+ Included Chado libraries that were missing in 2014-04-03 release
+ Removed 'null' tracks from changes.
+ Menus use proper CSS pointer.

If you are new to Apollo, we suggest that you learn more about our software and its functionality by taking a tour of the Web Apollo Demo (http://genomearchitect.org/WebApolloDemo) and exploring the User Guide (http://genomearchitect.org/web_apollo_user_guide)

We look forward to receiving your questions and suggestions.


Sincerely,
The Web Apollo Development Team



-----------------------
Please receive our apologies in advance if you have received this message more than once. In an attempt to spread the word, we may have inadvertently reached to you through two or more mailing lists. - BBOP.

--
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory

Mailing Address:
Joint Genome Institute (400-0415)
for the US Department of Energy
2800 Mitchell Dr. Ste 100
Walnut Creek, CA 94598-1631
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Rayapadi Swetha | 26 Nov 16:13 2014
Picon

Need a help

Respected Sir,

We have developed a database for Haemophilus influenzae and we used Gbrowse to visualize their annotation. Now, we are developing the database for other organism and we need to use the Gbrowse. We are going to host the second database in the same server where GBrowse is already installed. But, I have a doubt. The dropdown menu for the second database should be changed in GBrowse. How is it possible?

For example:

In Haemophilus influenzae database, we have included 10 different strains of H. influenzae. I have attached the screenshot for your reference.

In second database, I need to include 25 strains of other organism.

Query: these 25 strains should be in dropdown menu instead of those 10 strains. And, When the user access H. influenzae database, 10 strains should be there and when the user access second database, 25 strains should be there. How is it possible?

Waiting for your reply.

Yours sincerely,
Swetha R G.
Attachment (Haemophilus influenzae): application/octet-stream, 138 KiB
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Ryan Thomas | 20 Nov 16:36 2014
Picon

Quick question regarding the content on fungalgenomes.org

Hey,

I hope you don't mind me contacting you today but I just have a few quick questions,

Would you be interested in sparking up a mutually beneficial relationship with me over some content submissions for your site?

We are basically looking to place a short and sweet 500 word article on your website with a link pointing to a page on my clients website with payment for your effort.

Let me know if it's of interest and we can get it moving.

Thanks!

Ryan Thomas - DMA
slap up media
ryan-nvjVByHBJPzd97z9P8fs216hYfS7NtTn@public.gmane.org

This message is private and confidential. If you have received this message in error, please notify us and remove it from your system.


If you no longer wish to receive emails from us, please click here.
IDENT: 7a2eaf105c8f44eb0eb7baeaf9e777ea2b5ee7584b89c2db4783c625f5a9d786-79b124fbb699c51d6de98b2a6b190aa08737324e20ba7e6a72d95a8b50881668

------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Asma Riyaz | 24 Nov 20:36 2014
Picon

gff3 file loading

Hi,

I am trying to load a gff3 file into chado, but it fails with the error below:

Sorting the contents of /etc/BioDIG/biodig/web/static/genomicFiles/new/Tribolium_casteneum/ChLG10_official_gene.gff3 ...

DBD::Pg::st execute failed: ERROR:  null value in column "parent" violates not-null constraint

DETAIL:  Failing row contains (ChLG10, TCOGS2:TC004355, null, ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Na..., null). at /usr/local/share/perl/5.18.2/Bio/GMOD/DB/Adapter.pm line 4722, <IN> line 3.

Inserting into the sort table failed:,

Probably due to this line: ChLG10 TCOGS2 gene 11381335 11383395 . - . ID=TCOGS2:TC004355;Name=TC004355;Alias=GLEAN_04355

I have checked to see if there are extra tab spaces but I couldn't find any.

How do I re-format these gff3 files so as to overcome this?

Thanks,

Asma




------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Asma Riyaz | 24 Nov 18:48 2014
Picon

Re-load gene ontologies into Chado

Hi,

I need to re-load the ontologies into Chado as I don't think the 1st installed all of it. According https://github.com/scottcain/chado_test/blob/master/chado/INSTALL.Chado, I will need to delete the temporary files but I don't know where to locate these. Could someone point me in the right direction for this?

Thank you 
Asma
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-gbrowse mailing list
Gmod-gbrowse@...
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Samy Jeevan Karloss Antony | 18 Nov 09:09 2014
Picon

Displaying Duplicated Regions

Hello,

Is there a “”built-in” way to display Duplicated regions within a genome as track in GBrowse? 

E.g. Parts of Chromosome 2 is a duplicated copy of Chromosome 1.  When some one looks at Chromosome 1 in
Gbrowse, I want to show the genes in the duplicated (Chromosome 2) region (and vice-versa) as a separate track.

Thanks,
Jeevan  
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk

Gmane