Hyunmin Kim | 18 Apr 06:53 2014
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gbrowse DNA track no visible (tutorial)

Dear All,

Hi, 

I leaning the gbrowse with tutorial.

I success all tutorial except for DNA track.

What problem?

(This situation occur in example data too) (like : Yeast chromosomes 1+2 (advanced) )

Thanks,
Hyunmin
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John Portwood | 17 Apr 19:47 2014
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Configuring Genes to show exons and UTRs

Hello,

I'm having an issue trying to render exons and UTRs together. Here is a
sample of the GFF3 I'm working with:

/Chr10   Ensembl_AGPv3   gene    1720611 1722779 .       +       .      
Name=GRMZM2G129907;biotype=protein_coding;description=Uncharacterized%20protein%20%20[Source:UniProtKB/TrEMBL%3BAcc:B4FHQ6];logic_name=genebuilder;ID=GRMZM2G129907
Chr10   Ensembl_AGPv3   mRNA    1720611 1722779 .       +       .      
Name=GRMZM2G129907_T02;Parent=GRMZM2G129907;biotype=protein_coding;description=cdna|est|omrna;logic_name=genebuilder;ID=GRMZM2G129907_T02
Chr10   Ensembl_AGPv3   mRNA    1720611 1722779 .       +       .      
Name=GRMZM2G129907_T01;Parent=GRMZM2G129907;biotype=protein_coding;description=est|omrna|protein;logic_name=genebuilder;ID=GRMZM2G129907_T01
Chr10   Ensembl_AGPv3   mRNA    1721887 1722779 .       +       .      
Name=GRMZM2G129907_T03;Parent=GRMZM2G129907;biotype=protein_coding;description=est|omrna|protein;logic_name=genebuilder;ID=GRMZM2G129907_T03
Chr10   Ensembl_AGPv3   exon    1720611 1720931 .       +       .      
Name=GRMZM2G129907_E02;Parent=GRMZM2G129907_T01;ensembl_end_phase=2;ensembl_phase=-1;rank=1;ID=GRMZM2G129907_E02
Chr10   Ensembl_AGPv3   five_prime_UTR  1720611 1720713 .       +       .      
Parent=GRMZM2G129907_T01;
Chr10   Ensembl_AGPv3   CDS     1720714 1720931 .       +       0      
Name=GRMZM2G129907_P01;Parent=GRMZM2G129907_T01;rank=1;ID=GRMZM2G129907_P01
Chr10   Ensembl_AGPv3   CDS     1721395 1721501 .       +       0      
Name=GRMZM2G129907_P01;Parent=GRMZM2G129907_T01;rank=2;ID=GRMZM2G129907_P01
Chr10   Ensembl_AGPv3   exon    1721395 1721501 .       +       .      
Name=GRMZM2G129907_E04;Parent=GRMZM2G129907_T01;ensembl_end_phase=1;ensembl_phase=2;rank=2;ID=GRMZM2G129907_E04
Chr10   Ensembl_AGPv3   CDS     1722296 1722459 .       +       0      
Name=GRMZM2G129907_P01;Parent=GRMZM2G129907_T01;rank=3;ID=GRMZM2G129907_P01
Chr10   Ensembl_AGPv3   exon    1722296 1722779 .       +       .      
Name=GRMZM2G129907_E03;Parent=GRMZM2G129907_T01;ensembl_end_phase=-1;ensembl_phase=1;rank=3;ID=GRMZM2G129907_E03
Chr10   Ensembl_AGPv3   three_prime_UTR 1722460 1722779 .       +       .      
Parent=GRMZM2G129907_T01;
Chr10   Ensembl_AGPv3   exon    1720611 1721501 .       +       .      
Name=GRMZM2G129907_E06;Parent=GRMZM2G129907_T02;ensembl_end_phase=-1;ensembl_phase=-1;rank=1;ID=GRMZM2G129907_E06
Chr10   Ensembl_AGPv3   five_prime_UTR  1720611 1720713 .       +       .      
Parent=GRMZM2G129907_T02;
Chr10   Ensembl_AGPv3   CDS     1720714 1720935 .       +       0      
Name=GRMZM2G129907_P02;Parent=GRMZM2G129907_T02;rank=1;ID=GRMZM2G129907_P02
Chr10   Ensembl_AGPv3   three_prime_UTR 1720936 1722779 .       +       .      
Parent=GRMZM2G129907_T02;
Chr10   Ensembl_AGPv3   exon    1721994 1722055 .       +       .      
Name=GRMZM2G129907_E05;Parent=GRMZM2G129907_T02;ensembl_end_phase=-1;ensembl_phase=-1;rank=2;ID=GRMZM2G129907_E05
Chr10   Ensembl_AGPv3   exon    1722296 1722779 .       +       .      
Name=GRMZM2G129907_E01;Parent=GRMZM2G129907_T02;ensembl_end_phase=-1;ensembl_phase=-1;rank=3;ID=GRMZM2G129907_E01
Chr10   Ensembl_AGPv3   exon    1721887 1722055 .       +       .      
Name=GRMZM2G129907_E07;Parent=GRMZM2G129907_T03;ensembl_end_phase=-1;ensembl_phase=-1;rank=1;ID=GRMZM2G129907_E07
Chr10   Ensembl_AGPv3   five_prime_UTR  1721887 1722363 .       +       .      
Parent=GRMZM2G129907_T03;
Chr10   Ensembl_AGPv3   exon    1722296 1722779 .       +       .      
Name=GRMZM2G129907_E01;Parent=GRMZM2G129907_T03;ensembl_end_phase=-1;ensembl_phase=-1;rank=2;ID=GRMZM2G129907_E01
Chr10   Ensembl_AGPv3   CDS     1722364 1722459 .       +       0      
Name=GRMZM2G129907_P03;Parent=GRMZM2G129907_T03;rank=1;ID=GRMZM2G129907_P03
Chr10   Ensembl_AGPv3   three_prime_UTR 1722460 1722779 .       +       .      
Parent=GRMZM2G129907_T03;/

Using the gene glyph produces this
rendering:
<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712467/geneModelsv3_UTRs.png> 

This is close to what I want, but the inner exons aren't showing. When I use
"sub_part=exon" in this track's stanza, the exons show but the gray
UTRs
disappear:
<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5712467/genModelsv3_Exons.png> 

I want to render a display that looks exactly like the image above, but with
the grayed UTR regions showing in the exons. Any help on accomplishing this
would be greatly appreciated.

Thanks,
John

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Qisen Zhang | 13 Apr 09:14 2014
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features are not displayed

Hi

I am new on using Gbrowse2. I have installed it on ubuntu and following the tutorial till view example data set (volvox). I am able to open the volvox page, but all displayed details are different from the figure showing on Toturial. There is no marked ruler nor features. Features are not displyed.

Why is that? where is the problem?
Best Regard
Qisen

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John Portwood | 7 Apr 23:15 2014
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Searching names loading incorrect section in gbrowse

Hello,

I'm having a problem with GBrowse2 (v 2.43) and the link to the archive mailing list wasn't working so I'm not able to see if this has been reported before. 

For only one track, when the name is searched in GBrowse the browser will navigate to a section that is slightly off from where the name is located. For example take this section from my GFF3 (rendered from grepping "GRMZM2G124745"):

Chr7    AGPv3   protein_coding_gene     176806695       176810119       .       +       .       Name=GRMZM2G124745;biotype=protein_coding;logic_name=genebuilder;ID=GRMZM2G124745
Chr7    AGPv3   transcript      176806695       176810119       .       +       .       Name=GRMZM2G124745_T01;Parent=GRMZM2G124745;biotype=protein_coding;description=est;logic_name=genebuilder;ID=GRMZM2G124745_T01
Chr7    AGPv3   exon    176806695       176806968       .       +       .       Name=GRMZM2G124745_E04;Parent=GRMZM2G124745_T01;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;rank=1;ID=GRMZM2G124745_E04
Chr7    AGPv3   five_prime_UTR  176806695       176806706       .       +       .       Parent=GRMZM2G124745_T01;
Chr7    AGPv3   CDS     176806707       176806968       .       +       0       Name=GRMZM2G124745_P01;Parent=GRMZM2G124745_T01;rank=1;ID=GRMZM2G124745_P01
Chr7    AGPv3   CDS     176808089       176808340       .       +       0       Name=GRMZM2G124745_P01;Parent=GRMZM2G124745_T01;rank=2;ID=GRMZM2G124745_P01
Chr7    AGPv3   exon    176808089       176808340       .       +       .       Name=GRMZM2G124745_E03;Parent=GRMZM2G124745_T01;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;rank=2;ID=GRMZM2G124745_E03
Chr7    AGPv3   CDS     176808921       176809060       .       +       0       Name=GRMZM2G124745_P01;Parent=GRMZM2G124745_T01;rank=3;ID=GRMZM2G124745_P01
Chr7    AGPv3   exon    176808921       176809060       .       +       .       Name=GRMZM2G124745_E01;Parent=GRMZM2G124745_T01;constitutive=1;ensembl_phase=1;rank=3;ID=GRMZM2G124745_E01
Chr7    AGPv3   CDS     176810033       176810119       .       +       0       Name=GRMZM2G124745_P01;Parent=GRMZM2G124745_T01;rank=4;ID=GRMZM2G124745_P01
Chr7    AGPv3   exon    176810033       176810119       .       +       .       Name=GRMZM2G124745_E02;Parent=GRMZM2G124745_T01;constitutive=1;ensembl_end_phase=-1;rank=4;ID=GRMZM2G124745_E02

Searching for "GRMZM2G124745" in GBrowse will bring me to this region:
Chr7:176,822,753..176,826,177

However, on the first line in the above snippet you can see this element is actually located between 176,806,695 and 176,810,119 on Chr7. All of the elements are being rendered at their correct positions specified in the gff -- It's only when you search for them by name the browser takes you to a region ahead of them. 

This problem is not occurring with other tracks that I have loaded, so I'm guessing there's a problem either with the gff or the config file but after much research I'm still unable to find the cause of this issue.

Any help is greatly appreciated. Thanks!

-John 

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Brad Covey | 10 Apr 16:44 2014
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Problem With Custom Track Entries in the Uploads Table of the Users.SQLite Database

Hi Guys,

I'm uploading large files to GBrowse manually as custom tracks. I've written scripts to create the sqlite database for the upload, the proper folder structure under "userdata", and the entry in the users.sqlite database.

The directory structure that is created looks like this:
userdata/
    datasource_name/
        user_uploadsid/
            feature_name/
                index.SQLite  
                STATUS     
                feature_name.conf  
                SOURCES/
                    feature_name


The upload seems to work fine and the new track appears under "Custom Tracks" as shown in the following screenshot:


here "might-have-fixed-the-featurefile" is the new upload.

But the upload is not shown under "Select Tracks":


I've done a bit of troubleshooting to try to figure out why this is happening. I've narrowed the problem down to the entry in the "uploads" table of the "users.sqlite" database.
These are the current entries in the database:

"2","private","trying-again",                            "","yoxphwmgxhjlzf3ngjk3ew5xbuwnoytl","Toceanica2","2014-04-08 16:24:11","2014-04-08 16:24:11","","trying-again",                            "0"
"2","private","might-have-fixed-the-featurefile","","6c0yilb5r2yirwffht32ixg1tusdsjpk",      "Toceanica2","2014-04-10 10:42:03","2014-04-10 10:42:03","","might-have-fixed-the-featurefile","0"

I included the "trying-again" entry as a working example for reference.
note: the trackid is 32 characters long for both


As far as I can tell there is no difference between the two entries, but if I point the working "trying-again" entry at the non-working "might-have-fixed-the-featurefile" path like so:

"2","private","might-have-fixed-the-featurefile","","yoxphwmgxhjlzf3ngjk3ew5xbuwnoytl","Toceanica2","2014-04-08 16:24:11","2014-04-08 16:24:11","","trying-again showing might-have-fixed-the-featurefile","0"
"2","private","might-have-fixed-the-featurefile","","6c0yilb5r2yirwffht32ixg1tusdsjpk",      "Toceanica2","2014-04-10 10:42:03","2014-04-10 10:42:03","","might-have-fixed-the-featurefile",                               "0"

My initially non-working track is displayed properly:


Which tells me that the folder structure, sqlite sqlite database, and configuration for my new custom track are being created properly but there is some problem with the entry in the "uploads" table of the users.sqlite database preventing the track from being displayed properly.


Does anyone have any idea what may be wrong with the "uploads" entries that my script is creating?


Thanks,
Brad

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Scott Cain | 7 Apr 15:12 2014
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Re: missing CGI-BIN folder

Hi Gonzalo,

Please keep the gbrowse mailing list cc'ed. 

What is in your apache error log that mentions gbrowse (if there is a 404 message, there should be something in the error log).

Scott


Sent from my iPad

On Apr 7, 2014, at 8:32 AM, Gonzalo Sepulveda <gosepulvedah-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:

Thanks Scott!
when i go to localhost/gbrowse2 i got the html about the "Generic Genome Browser, v2", the tutorials, and everything else.
the problem comes in http://localhost/cgi-bin/gb2/gbrowse/yeast/, there i got 404 =/

i also checked /usr/lib/cgi-bin/gb2 and all seems to be fine there.

Still nothing, any ideas?
Regards.


2014-04-04 17:24 GMT-03:00 Scott Cain <scott-XkniDE3L5z0cWVvVuXF20w@public.gmane.org>:
Hi Gonzalo,

The snippet of error log that you sent doesn't have anything to do with GBrowse; it's just the normal messages one sees when apache is stopped and started.  What happens when you go to http://localhost/gbrowse2?  What about http://localhost/cgi-bin/gb2/gbrowse/yeast/?  What do you see in the browser, and what do you see in the error log?

By the way, changing the installed path of the cgi files to somewhere in /var/www won't work unless you also modify the apache config, which would be a pain to do.  Instead, just make sure the scripts go into /usr/lib/cgi-bin/gb2.

Scott




On Fri, Apr 4, 2014 at 3:49 PM, Gonzalo Sepulveda <gosepulvedah-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
Hi! i'm writting for some help about how to proper launch GBrowse2, locally.
I followed the tutorial  for installing and everything went ok, i got every pre-requisite.
Then, i followed /var/www/gbrowse2/tutorial/tutorial.html to try one of the example databases but couldn't get to that...

i got stucked where it says to point the browser to localhost/cgi-bin/gb2/gbrowse/volvox 

Apache2 is running Ok, i think. Here's tails of error.log

AH00558: apache2: Could not reliably determine the server's fully qualified domain name, using 127.0.1.1. Set the 'ServerName' directive globally to suppress this message
[Fri Apr 04 15:21:00.840630 2014] [mpm_prefork:notice] [pid 7004] AH00163: Apache/2.4.6 (Ubuntu) PHP/5.5.3-1ubuntu2.2 configured -- resuming normal operations
[Fri Apr 04 15:21:00.840641 2014] [core:notice] [pid 7004] AH00094: Command line: '/usr/sbin/apache2'
[Fri Apr 04 15:30:40.723617 2014] [mpm_prefork:notice] [pid 7004] AH00171: Graceful restart requested, doing restart
AH00558: apache2: Could not reliably determine the server's fully qualified domain name, using 127.0.1.1. Set the 'ServerName' directive globally to suppress this message
[Fri Apr 04 15:30:40.745626 2014] [mpm_prefork:notice] [pid 7004] AH00163: Apache/2.4.6 (Ubuntu) PHP/5.5.3-1ubuntu2.2 configured -- resuming normal operations
[Fri Apr 04 15:30:40.745637 2014] [core:notice] [pid 7004] AH00094: Command line: '/usr/sbin/apache2'
[Fri Apr 04 15:52:59.138698 2014] [mpm_prefork:notice] [pid 7004] AH00169: caught SIGTERM, shutting down
[Fri Apr 04 15:53:00.207955 2014] [mpm_prefork:notice] [pid 24416] AH00163: Apache/2.4.6 (Ubuntu) PHP/5.5.3-1ubuntu2.2 configured -- resuming normal operations
[Fri Apr 04 15:53:00.207992 2014] [core:notice] [pid 24416] AH00094: Command line: '/usr/sbin/apache2'

i also tried re-installing Gbrowse2 and changing the route for CGI-BIN scripts to /var/www, still nothing.

any help will be very appreciated
Regards


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Gonzalo Sepulveda | 4 Apr 21:49 2014
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missing CGI-BIN folder

Hi! i'm writting for some help about how to proper launch GBrowse2, locally.
I followed the tutorial  for installing and everything went ok, i got every pre-requisite.
Then, i followed /var/www/gbrowse2/tutorial/tutorial.html to try one of the example databases but couldn't get to that...

i got stucked where it says to point the browser to localhost/cgi-bin/gb2/gbrowse/volvox 

Apache2 is running Ok, i think. Here's tails of error.log

AH00558: apache2: Could not reliably determine the server's fully qualified domain name, using 127.0.1.1. Set the 'ServerName' directive globally to suppress this message
[Fri Apr 04 15:21:00.840630 2014] [mpm_prefork:notice] [pid 7004] AH00163: Apache/2.4.6 (Ubuntu) PHP/5.5.3-1ubuntu2.2 configured -- resuming normal operations
[Fri Apr 04 15:21:00.840641 2014] [core:notice] [pid 7004] AH00094: Command line: '/usr/sbin/apache2'
[Fri Apr 04 15:30:40.723617 2014] [mpm_prefork:notice] [pid 7004] AH00171: Graceful restart requested, doing restart
AH00558: apache2: Could not reliably determine the server's fully qualified domain name, using 127.0.1.1. Set the 'ServerName' directive globally to suppress this message
[Fri Apr 04 15:30:40.745626 2014] [mpm_prefork:notice] [pid 7004] AH00163: Apache/2.4.6 (Ubuntu) PHP/5.5.3-1ubuntu2.2 configured -- resuming normal operations
[Fri Apr 04 15:30:40.745637 2014] [core:notice] [pid 7004] AH00094: Command line: '/usr/sbin/apache2'
[Fri Apr 04 15:52:59.138698 2014] [mpm_prefork:notice] [pid 7004] AH00169: caught SIGTERM, shutting down
[Fri Apr 04 15:53:00.207955 2014] [mpm_prefork:notice] [pid 24416] AH00163: Apache/2.4.6 (Ubuntu) PHP/5.5.3-1ubuntu2.2 configured -- resuming normal operations
[Fri Apr 04 15:53:00.207992 2014] [core:notice] [pid 24416] AH00094: Command line: '/usr/sbin/apache2'

i also tried re-installing Gbrowse2 and changing the route for CGI-BIN scripts to /var/www, still nothing.

any help will be very appreciated
Regards

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Scott Cain | 4 Apr 18:11 2014
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Re: Displaying problem of tophat alignment in Gbrowse

Hi Jairui and Jack,

It's best to ask a question like this on the mailing list, since there are lots of people who work with this everyday and can usually answer faster than I can.  I've cc'ed the list here.

My initial guess is a configuration problem: for example, not getting bases would lead me to believe it's not looking in the right place for the fasta file.  Can you send the section of your configuration file dealing with setting up this bam file as a database and the track stanza, and while you're at it, verify that the path specified in the fasta section points at the appropriate fasta file for your reference sequence.

Scott



On Thu, Apr 3, 2014 at 6:23 PM, Jiarui Li <jla337-z1KUqvL5UUQ@public.gmane.org> wrote:
Hi Scott,

I am Jiarui Li, a post-doc of Dr.Jack Chen. I have a problem about displaying tophat alignment on Gbrowse.

I used TopHat to align RNA-seq reads to reference and got a bam file named "accepted_hits.bam", in which there are reads supporting introns. Those reads are splitted and aligned to reference, so in the bam file they have CIGAR string like "30M40N70M" and MD:Z as "MD:Z:100", which should show 30bps perfect matches, then skip 40 bps in reference sequences, and finally 70 bps perfect matches. However, on Gbrowse, I saw a problem in those 70bps part:

First, there are no bases displaying;
Second, there are lots of red color marked bases within those 70bps, indicating mismatches
Third, when I click on that read, I saw the 40bps part is missing in reference sequence.

Could you help me with that please?
Many thanks!

Cheers,
Jiarui



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empyrean999 | 3 Apr 21:30 2014
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GBrowse rendering track error

Hello All,

GBrowse was working perfectly fine and since 2 days the tracks are not loading and i am getting the following error. Any suggestions on what is going on?

Use of uninitialized value in exists at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2.pm line 395., referer:.....

[error] [client 1.1.1.2] [50778] rendering error track:  Can't connect to 1.2.1.11:85 (Connection refused) at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 3531.

Thanks

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Sanjeev Sariya | 29 Mar 06:12 2014

Errors after installing JBrowse

Dear developers,

We are still facing issues in installing jbrowse (JBrowse version: JBrowse-1.11.3-devon our server. we have followed all the posts related to jbrowse installation errors and tried using the below mentioned commands:

1) nohup ./setup.sh &

2)bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa

3) bin/prepare-refseqs.pl --conf docs/tutorial/conf_files/volvox.json
I got warnings after running the above command:
WARNING: multiple reference sequences found named 'ctgB', using only the first one.
WARNING: multiple reference sequences found named 'ctgA', using only the first one.

However, we didn't get any library ( <at> INC...., etc) or installation related errors.

when we try to view volvox sample data on our server, it didn't display any track(s). Also, reference sequence is not being displayed. http://gbrowse2014.biology.gatech.edu/

We tried to hard code the url (below URL) where sample volvox data is provided by jbrowse.org to check if we are missing something related to path and we are able to view the sample volvox data.

http://jbrowse.org/code/JBrowse-1.11.3/index.html?data=sample_data%2Fjson%2Fvolvox&loc=ctgA%3A20003..30108&tracks=DNA%2Cvolvox-paired_bam&highlight=

our server url: 
http://gbrowse2014.biology.gatech.edu/index.html?data=sample_data%2Fjson%2Fvolvox%2F&loc=ctgB%3A1806..1849&tracks=DNA%2Cvolvox_microarray.wig%2Cvolvox-sorted_bam_coverage%2CEST%2Cmalformed_alignments&highlight=

We are still confused where are we missing the actual path so that we can view the volvox data without any hard coding.
I am attaching 2 jpeg files:
1) default:default server URL 
2) error_install: hard coded URL


Let me know if any further details are required on files, installation or server from my side.
Looking forward for help from you. 

Attachment (nohup.out): application/octet-stream, 720 bytes
Attachment (setup.log): application/octet-stream, 512 KiB
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方健飞 | 31 Mar 15:34 2014
Picon

GBrowse

Dear Proessor:
      Recently, I adopt the GBrowse software to construct own genome.
I folow the hg19 genome to config my data. But in the chromosomes
directory ,It doesn't auto create the directory.index. Can you tell me
how to auto create the directory.index file? The process is stored in
the accessory.
Attachment (process.doc): application/msword, 35 KiB
Attachment (armiger.conf): application/octet-stream, 4648 bytes
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Gmane