Sofia Robb | 19 Apr 16:06 2016
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require valid-user

Hello,

I would like to require that a specific track is only viewable from a specific IP range or from a valid user. The IP range works great. When I am not in the IP range, i would like the apache login box to pop up and ask for the user and pasword. I set up my .httpd.conf and passwords file, but i am not getting the box asking me to log in when i have a link that contains a region with this track to be displayed, and the snp track is not being displayed.

[snps]
restrict = Order deny,allow
                  deny from all
                  Allow from 172.16.[9-63]
                  require valid-user

How do I properly set up "require valid-user" ?

Thanks,
Sofia
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Tevfik Hamdi Kitapci | 1 Apr 01:17 2016
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gbrowse problem

Hi,
I installed gbrowse following this:


I can see the main page when I point my browser to


I am trying to visualize the volvox data set as described here


I followed all the steps and double checked to make sure I did everything and set all the permissions when I point my browser to http://localhost/cgi-bin/gb2/gbrowse/volvox I got the following message:

I am running Ubuntu 14.04.4 LTS so I set the my_user_name to www-data 

Not Found

The requested URL /cgi-bin/gb2/gbrowse/volvox was not found on this server.

Apache/2.4.7 (Ubuntu) Server at localhost Port 80
I checked the error.log located at /var/log/apache2/error.log there is no message.
Then I tried to point my browser to: http://localhost/gb2/gbrowse/volvox this time I am getting the following:

Forbidden

You don't have permission to access /gb2/gbrowse/volvox on this server.

Apache/2.4.7 (Ubuntu) Server at localhost Port 80
this time I have this message added to the /var/log/apache2/error.log file
[Thu Mar 31 16:14:44.349626 2016] [authz_core:error] [pid 12936:tid 140590595376896] [client 127.0.0.1:58597] AH01630: client denied by server configuration: /usr/lib/cgi-bin/gbrowse/gbrowse

I will appreciate if you can help me with this problem
Thanks a lotBest RegardsT. Hamdi Kitapci
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Thomas LETELLIER | 23 Mar 14:16 2016
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SVG & PNG export failed

Hello,

I have a trouble with images export with my GBrowse, I saw in the 
documentation that it was a known bug, but I did not find any solution 
to this problem...

When I click on the export I get an "Internal server error" with this 
stack :

> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] Can't locate
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] 
> \t/home/gbrowse/webapps/GBrowse-2.33/etc/gbrowse2/plugins/GFFDumper.pm 
> in  <at> INC ( <at> INC contains: 
> /home/gbrowse/webapps/GBrowse-2.33/etc/gbrowse2/plugins 
> /usr/local/lib64/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 
> /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl 
> /usr/lib64/perl5 /usr/share/perl5 .) at 
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/PluginSet.pm line 31 (#1)
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] (F) You 
> said to do (or require, or use) a file that couldn't be
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] found. 
> Perl looks for the file in all the locations mentioned in  <at> INC,
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] unless the 
> file name included the full path to the file.  Perhaps you
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] need to 
> set the PERL5LIB or PERL5OPT environment variable to say where
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] the extra 
> library is, or maybe the script needs to add the library name
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]     to 
>  <at> INC.  Or maybe you just misspelled the name of the file.  See
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] 
> perlfunc/require and lib.
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] Can't call 
> method "seq_id" on an undefined value at
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] 
> \t/usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 
> 1971 (#2)
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] (F) You 
> used the syntax of a method call, but the slot filled by the
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] object 
> reference or package name contains an undefined value. Something
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] like this 
> will reproduce the error:
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]         
> $BADREF = undef;
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]         
> process $BADREF 1,2,3;
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]         
> $BADREF->process(1,2,3);
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] Uncaught 
> exception from user code:
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] \tCan't 
> call method "seq_id" on an undefined value at 
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 1971.
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243]  at 
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 1971.
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] 
>
\tBio::Graphics::Browser2::RenderPanels::create_panel_args(Bio::Graphics::Browser2::RenderPanels=HASH(0x4da35d0), 
> HASH(0x56fb120)) called at 
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 259
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] 
>
\tBio::Graphics::Browser2::RenderPanels::make_requests(Bio::Graphics::Browser2::RenderPanels=HASH(0x4da35d0), 
> HASH(0x56fb120)) called at 
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 130
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] 
>
\tBio::Graphics::Browser2::RenderPanels::request_panels(Bio::Graphics::Browser2::RenderPanels=HASH(0x4da35d0), 
> HASH(0x56fb120)) called at 
> /usr/local/lib64/perl5/Bio/Graphics/Browser2/RenderPanels.pm line 219
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] 
>
\tBio::Graphics::Browser2::RenderPanels::render_track_images(Bio::Graphics::Browser2::RenderPanels=HASH(0x4da35d0), 
> HASH(0x56fb120)) called at 
> /home/gbrowse/webapps/GBrowse-2.33/var/www/cgi-bin/gb2/gbrowse_img 
> line 311
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] 
> \tGBrowse_img::render_tracks(GBrowse_img=HASH(0x4e32de0), 
> Bio::Graphics::Browser2::RenderPanels=HASH(0x4da35d0), "GD", 0, undef) 
> called at 
> /home/gbrowse/webapps/GBrowse-2.33/var/www/cgi-bin/gb2/gbrowse_img 
> line 217
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] 
> \tGBrowse_img::render_image(GBrowse_img=HASH(0x4e32de0)) called at 
> /home/gbrowse/webapps/GBrowse-2.33/var/www/cgi-bin/gb2/gbrowse_img 
> line 139
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] 
> \tGBrowse_img::run(GBrowse_img=HASH(0x4e32de0)) called at 
> /home/gbrowse/webapps/GBrowse-2.33/var/www/cgi-bin/gb2/gbrowse_img line 73
> [Wed Mar 23 14:13:19 2016] [error] [client 138.102.133.243] Premature 
> end of script headers: gbrowse_img

My GBrowse version is 2.33 and I saw that GFFDumper.pm was deprecated 
since 2.0, so the error message does not helped me a lot...

Best regards,

Thomas

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Scott Cain | 2 Mar 17:32 2016
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Call for Abstracts for BOSC

Hi All,

I'm forwarding this call for abstracts for BOSC (Bioinformatics Open Source Conference) this year in Orlando, Florida:

From Peter Cock (p.j.a.cock at googlemail.com):

As BOSC co-chair I would like to encourage you all to think about
attending BOSC 2016, and if you are working on your own open
source software for bioinformatics please consider submitting an
abstract. See the email below and:

http://news.open-bio.org/2016/03/01/bosc-2016-call-for-abstracts/

Also, as a member of the Open Bioinformatics Foundation (OBF)
Board of Directors, I am delighted to let you know about the new
OBF Travel Fellowship which could be used to attend BOSC:

http://news.open-bio.org/2016/03/01/obf-travel-fellowship-program/

In case you missed the earlier announcement last year, we finally
got rid of the paper forms for OBF membership, see:

http://news.open-bio.org/2015/12/10/online-membership-form/

Thank you,

Peter

[Biopython developer, BOSC co-chair, OBF Secretary, etc.]


--
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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王敏晓 | 24 Feb 13:42 2016
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unable to load fasta sequences

Hi! I’d llke to make our genome dataset visible by gbrowse2. I’m now following the tutorial guide to understand the processing steps of the configuration. Everything seems to be successful except the part on DNA and 3-frame translations. Nothing appeared on the corresponding track. The volvax directory have been made writable worldwide following the instruction.
Thanks in advance.
Yours Wang Minxiao
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Scott Cain | 1 Mar 16:37 2016
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GMOD in Google Summer of Code 2016

Hello,

Very good news!  GMOD (as part of the Open Genome Informatics group along with Reactome) has been accepted into Google Summer of Code this year.  If you are or know of a student that might like to participate, please take a look at


where there are several really interesting project ideas.  It is also possible for students to suggest their own ideas and we will try hard to find them a mentor. 

Please let me know if you have any questions about GSoC.

Scott

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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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Scott Cain | 26 Feb 18:50 2016
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GMOD 2016 meeting

Hello all,

I am pleased to announce that details have been finalized for the 2016 GMOD meeting.  It will take place immediately following the Galaxy Community Conference at Indiana University in Bloomington, IN on June 30 and July 1.  We're still working on agenda details, so if you have suggestions or would like to present, please let me know.

For registration information, please see:


And for other information about the meeting, keep an eye on:


I look forward to seeing you there!
Scott


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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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Florian | 23 Feb 12:44 2016
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Gbrowse 2.50 VM wont start - vboxnet0 (adapter 2) not found

Hi all,

I am trying to set up a GBrowse2 VM on my PC running Ubuntu 14.04.

I downloaded the VM-file from http://gmod.org/wiki/GBrowse2_VMs (Version 2.50) and installed VirtualBox (https://www.virtualbox.org/wiki/Linux_Downloads, 14.04 Version) + Extension Pack.

The import of the .ova file worked and I can start VirtualBox and see it listed there. However if I try to run it I receive following error:

Could not start the machine Growse 2.50, VirtualBox Edition because the following physical network interfaces were not found:

vboxnet0 (adapter 2)

You can either change the machine's network settings or stop the machine.

I have no experience with VirtualBox and a quick google search didnt help me out, so could someone explain to me what I have to do to get this running?


Thanks for any Help,
Florian




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pankaj agrawal | 1 Feb 23:04 2016
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issue with registration

Hi,
I am trying to register to make an entry to the database but the emails sent by you are somehow not reaching me. I tried 2 different email  accounts and both had the same issue. Can you please help?
thanks
Pankaj



Pankaj B. Agrawal, MD MMSC
Attending Neonatologist
Staff Scientist, Division of Genetics and Genomics
Medical Director, Gene Discovery Core, Manton Center for Orphan Disease Research   
Boston Children's Hospital                      
Assistant Professor of Pediatrics, Harvard Medical School

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Andrew ODonnell | 19 Feb 15:23 2016
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Congenie.org genome browser

Hello,

I am having some issues linking the BLAST results on congenie.org with their genome browser locations. 
When I click on "GB" next to each blast hit (I had about BLAST 100 results), the genome browser informs me
that the locus cannot be found with the red letters "Not Found" (please see picture).

I have tried blasting two genomes (Picea abies and Picea sithcensis V4), and neither worked.

I just want to bring it to your attention, and would greatly appreciate it if the problem is fixed.  Or, if it's
not an error, then please let me know if a work-around.

Kind Regards,

-Andrew J O'Donnell

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Sam Hokin | 5 Feb 00:33 2016

Illegible formatting of bases on zoomed-in segments glyph

Hi, I hope I can attach to an email to the list, because without it this is pretty hard to envision. I'm running
a stock GBrowse2 on 
a Google Cloud Debian machine - works great for the most part, all the stuff needed came down from the repo.
The one issue I'm 
running into is that I can't make out the bases of reads when I zoom in. They're made with this section in the
config, 
feature=match, glyph=segments. The glyph works fine when zoomed out, but when zoomed in it shows a lot of
overlapping tiny-font text 
for the bases along with solid color from the overlapping reads.

Any suggestions?

[FC1154_May2014.PollenCL.reads]
feature        = match
category       = Fowler Silk_Pollen_RawRNAseqData:FC1154_May2014
citation       = Fowler Lab, Oregon State, FC1154_May2014 read set. PollenCL: B73 pollen only (techrep2)
database       = FC1154_May2014.PollenCL
key            = PollenCL READS: B73 pollen only (techrep2)
bgcolor        = orange
fgcolor        = orange
glyph          = segments
draw_target    = 1
show_mismatch  = 1
mismatch_color = red
bump           = fast
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Gmane