Re: github error

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Re: github error

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Re: github error

Thanks Lincoln but it turns out my problem was specific my build of
CentOS having an old certificate authority bundle.
credit to: http://eric.lubow.org/2011/security/fixing-centos-root-certificate-authority-issues

What fixed it was this:

$ cd /etc/pki/tls/certs
$ sudo su
# cp ca-bundle.crt ca-bundle.crt.bak
# curl http://curl.haxx.se/ca/cacert.pem -o /etc/pki/tls/certs/ca-bundle.crt

Then the git clone worked fine.

Sheldon McKay, PhD
Scientific Lead, Tree of Life engagement Team
iPlant Collaborative, BIO5 Institute, University of Arizona
Email: mckays@...
Google Voice:  (203) 701-9204

On Wed, Aug 31, 2011 at 4:22 PM, Lincoln Stein
<lincoln.stein@...> wrote:
> If you first get an account on github, then you can also use this method:
> git clone git@...:GMOD/GBrowse.git
>
> On Wed, Aug 31, 2011 at 6:31 PM, Sheldon McKay <sheldon.mckay@...>
> wrote:
>>
>> Hi all,
>>
>> I am trying to grab GB2 using the incantation described in the wiki
>> but am failing with this error message:
>>
>> $ git clone https://github.com/GMOD/GBrowse.git
>> Cloning into GBrowse...
>> error: SSL certificate problem, verify that the CA cert is OK. Details:
>> error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate
>> verify failed while accessing
>> https://github.com/GMOD/GBrowse.git/info/refs
>>
>> Any suggestions?
>>
>> Thanks
>>
>> Sheldon McKay, PhD
>> Scientific Lead, Tree of Life engagement Team
>> iPlant Collaborative, BIO5 Institute, University of Arizona
>> Email: mckays@...
>> Google Voice:  (203) 701-9204
>>
>>
>> ------------------------------------------------------------------------------
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>> Finally, a world-class log management solution at an even better
>> price-free! And you'll get a free "Love Thy Logs" t-shirt when you
>> download Logger. Secure your free ArcSight Logger TODAY!
>> http://p.sf.net/sfu/arcsisghtdev2dev
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse@...
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <Renata.Musa@...>
>

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gbrowse_syn add NGS data(bam,coverage)

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Re: gbrowse re-install -- bioperl problem?

Zhiliang wrote on 2011-08-31:

> Wes - It is odd but repeatable on my site.
> 
> To repeat: I copy an existing species.conf to, say "odd.conf", in the
> same location; Modify the "odd.conf" by only remove '=' in one of its
> name/value pairs - the GBrowse then quits working by return "boo boo"
> on the web.
> GBrowse resumes normal work when I put '=' back to "odd.conf" or I
> simply delete "odd.conf" file.

Then you cannot be running GBrowse-2.xx

GBrowse-2 would not try to read odd.conf unless you also edited the
main GBrowse.conf file and configured a datasource definition for odd.conf.

> I will try to get v2.39 to work on a different server.
> 
> Zhiliang
> 
> 
> On Wed, 31 Aug 2011, Barris, Wes wrote:
> 
>> Date: Wed, 31 Aug 2011 13:13:28 -0500
>> From: "Barris, Wes" <Wes.Barris@...>
>> To: Zhiliang <hu@...>
>> Cc: GBrowse Group <gmod-gbrowse@...>
>> Subject: RE: [Gmod-gbrowse] gbrowse re-install -- bioperl problem?
>> 
>> Zhiliang wrote on 2011-08-31:
>> 
>>> Thank you Wes - that brings me for a more aggressive hack on the
>>> problem.
>>> 
>>> Actually I had noticed that; The problem was - it is not in any of the
>>> species/config I tested (we are hosting multiple species/tracks);
>>> rather, it is in an unused config that sits in the /conf/ folder.
>>> Apparently the new GBrowse is now checking the syntax for all conf
>>> files by default.
>> 
>> That is odd.  The behaviour of the old GBrowse-1.7 was to parse each
>> and every .conf file in the gbrowse.conf directory.  The new
>> GBrowse-2.xx parses only the "active" .conf file in the conf directory.
>>  I just did a test where I removed the '=' in a key/value pair in one
>> .conf file and then used GBrowse to view another.  I got no error.  I
>> only saw the error shown in your example when I tried to directly view
>> the .conf file with the missing '=' character.
>> 
>> I am running GBrowse-2.39.
>> 
>>> Thanks,
>>> Zhiliang
>>> 
>>> 
>>> On Tue, 30 Aug 2011, Barris, Wes wrote:
>>> 
>>>> Date: Tue, 30 Aug 2011 12:18:31 -0500
>>>> From: "Barris, Wes" <Wes.Barris@...>
>>>> To: Zhiliang <hu@...>,
>>>>     GBrowse Group <gmod-gbrowse@...>
>>>> Subject: RE: [Gmod-gbrowse] gbrowse re-install -- bioperl problem?
>>>> 
>>>> Zhiliang wrote on 2011-08-29:
>>>> 
>>>>> [Mon Aug 29 15:25:30 2011] [error] [client 127.0.0.1] ------------ -
>>>>> EXCEPTION: Bio::Root::Exception ------------- [Mon Aug 29 15:25:30
>>>>> 2011] [error] [client 127.0.0.1] MSG: syntax error at line 134: 'key
>>>>> DNA/GC Content' [Mon Aug 29 15:25:30 2011] [error] [client
>>> 127.0.0.1]
>>>> 
>>>> It looks like the error above (which is mangled in this email) is due
>>>> to an error in your .conf file.  A "key = value" pair is missing the
>>>> equals sign.  Search for this:
>>>> 
>>>> key        DNA/GC Content
>>>> 
>>>> and change it to
>>>> 
>>>> key      = DNA/GC Content
>>>> 
>>>> 
>>>>> STACK: Error::throw [Mon Aug 29 15:25:30 2011] [error] [client
>>>>> 127.0.0.1] STACK: Bio::Root::Root::throw
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:472 [Mon Aug 29
>>>>> 15:25:30 2011] [error] [client 127.0.0.1] STACK:
>>>>> Bio::DB::SeqFeature::Store::FeatureFileLoader::_make_feature
>>>>> 
>>>>> 
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/FeatureFileL
>>>>> oa de r.pm:629 [Mon Aug 29 15:25:30 2011] [error] [client 127.0.0.1]
>>>>> STACK:
>>>>> 
>>>>> Bio::DB::SeqFeature::Store::FeatureFileLoader::_make_indexed_featur e
>>>>> 
>>>>> 
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/FeatureFileL
>>>>> oa de r.pm:616 [Mon Aug 29 15:25:30 2011] [error] [client 127.0.0.1]
>>>>> STACK: Bio::DB::SeqFeature::Store::FeatureFileLoader::handle_feature
>>>>> 
>>>>> 
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/FeatureFileL
>>>>> oa de r.pm:579 [Mon Aug 29 15:25:30 2011] [error] [client 127.0.0.1]
>>>>> STACK: Bio::DB::SeqFeature::Store::FeatureFileLoader::load_line
>>>>> 
>>>>> 
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/FeatureFileL
>>>>> oa de r.pm:430 [Mon Aug 29 15:25:30 2011] [error] [client 127.0.0.1]
>>>>> STACK: Bio::Graphics::FeatureFile::parse_data_line
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/FeatureFile.pm:902 [Mon
>>>>> Aug 29 15:25:30 2011] [error] [client 127.0.0.1] STACK:
>>>>> Bio::Graphics::FeatureFile::parse_line
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/FeatureFile.pm:820 [Mon
>>>>> Aug 29 15:25:30 2011] [error] [client 127.0.0.1] STACK:
>>>>> Bio::Graphics::FeatureFile::parse_fh
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/FeatureFile.pm:771 [Mon
>>>>> Aug 29 15:25:30 2011] [error] [client 127.0.0.1] STACK:
>>>>> Bio::Graphics::FeatureFile::parse_file
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/FeatureFile.pm:758 [Mon
>>>>> Aug 29 15:25:30 2011] [error] [client 127.0.0.1] STACK:
>>>>> Bio::Graphics::FeatureFile::_new
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/FeatureFile.pm:396 [Mon
>>>>> Aug 29 15:25:30 2011] [error] [client 127.0.0.1] STACK:
>>>>> Bio::Graphics::FeatureFile::new
>>>>> /usr/lib/perl5/site_perl/5.8.8/Bio/Graphics/FeatureFile.pm:358 [Mon
>>>>> Aug 29 15:25:30 2011] [error] [client 127.0.0.1] STACK:
>>>>> Bio::Graphics::Browser::read_configuration
>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-
>>>>> multi/Bio/Graphics/Browser.pm:187 [Mon Aug 29 15:25:30 2011] [error]
>>>>> [client 127.0.0.1] STACK: Bio::Graphics::Browser::Util::open_config
>>>>> /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-
>>>>> multi/Bio/Graphics/Browser/Util.pm:152 [Mon Aug 29 15:25:30 2011]
>>>>> [error] [client 127.0.0.1] STACK:
>>>>> /usr/local/apache/cgi-bin/gbrowse:134 [Mon Aug 29 15:25:30 2011]
>>>>> [error] [client 127.0.0.1]
>>>>> ----------------------------------------------------------- [Mon Aug
>>>>> 29 15:25:30 2011] [error] [client 127.0.0.1] Premature end of script
>>>>> headers: gbrowse
>>>>> 
>>>>> Thanks in advance,
>>>>> 
>>>>> Zhiliang
>> 
>> 
>> --
>> Wes Barris
>> 
>> This email and any files transmitted with it are confidential and
>> intended solely for the use of the addressee. If you are not the
>> intended addressee, then you have received this email in error and any
>> use, dissemination, forwarding, printing, or copying of this email is
>> strictly prohibited. Please notify us immediately of your unintended
>> receipt by reply and then delete this email and your reply.
>> Cobb-Vantress, Inc. and its subsidiaries and affiliates will not be
>> held liable to any person resulting from the unintended or unauthorized
>> use of any information contained in this email or as a
> result of any additions or deletions of information originally
> contained in this email.
>>

--
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This email and any files transmitted with it are confidential and intended solely for the use of the
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Remote source coordinates

Hi,

I have a gbrowse 2.26 server set up using mysql. All of the coordinates that I have in the database are in the
form 'chr1','chr2' etc. I would like to link to a remote source. From the remote source I copy/paste the URL
into my gbrowse server but nothing is rendered. The coordinates that are used on the remote server are
'1','2' etc. Could this difference cause this problem? Is there any way that I can modify the outgoing
coordinates so that I can use the remote data?

Thanks,

- Christopher

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Re: trouble with session and param method

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Re: trouble with session and param method

Thank you for the suggestions.

I am installing Gbrowse2.39 on an old Dell desktop running RedHat Enterprise Linux 5.1.19.6 which also
lists Red Hat linux 2.6.18-274.el5 as it boots.

When I build the demo as you suggested, I can connect and it does work. I turned it off and then I rebuilt my
bioperl and dependencies and tried to delete all the GB2 directories then rebult GB2. At the end of this GB2
rebuild I see:

All tests successful.
Files=9, Tests=439, 69 wallclock secs ( 0.29 usr  0.05 sys + 37.99 cusr  7.17 csys = 45.50 CPU)
Result: PASS

Connecting to this fresh GB2  ( <at>   http://localhost/cgi-bin/gb2) gives these lines in the error_log:

[Fri Sep 02 10:07:44 2011] [error] [client 127.0.0.1] couldn't create lock file
'/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at
/usr/lib/perl5/site_perl/5.8.8/CGI/Session/Driver/db_file.pm line 98., referer: http://localhost/gbrowse2/tutorial/tutorial.html
[Fri Sep 02 10:07:44 2011] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer: http://localhost/gbrowse2/tutorial/tutorial.html

If make  /var/lib/gbrowse2/sessions  writtable then these 'permission denied' errors are avoided but
then I  return to these 'method param  undefined' errors

[Fri Sep 02 10:26:59 2011] [error] [client 128.23.6.30] Can't call method "param" on an undefined value at
/usr/lib/perl5/site_perl/5.8.8/i386-linux-thread-multi/Bio/Graphics/Browser2/Session.pm
line 316., referer: http://localhost/index.html.en
[Fri Sep 02 10:26:59 2011] [error] [client 128.23.6.30] Premature end of script headers: gbrowse,
referer: http://localhost/index.html.en

If I then ./Build demo I can connect to  http://localhost:8000/cgi-bin/gb2/gbrowse/yeast/ and
manipulate the display.

http://localhost/cgi-bin/gb2 does not work

http://localhost:8000/cgi-bin/gb2/ does work

So I'm stumped at the moment.

Starr

From: Lincoln Stein [lincoln.stein@...]
Sent: Wednesday, August 31, 2011 11:50 AM
To: Hazard, E. Starr
Cc: gmod-gbrowse@...
Subject: Re: [Gmod-gbrowse] trouble with session and param method

Could you try the following from within the distribution directory:

 perl Build.PL
 ./Build clean
 ./Build demo

Then try to connect to the demo server (the URL will print out when you run Build demo).

I do not know what's going on, but this procedure will ensure that you don't have any conflicting libraries
or configuration directives from within GBrowse. Also you didn't mention what operating
system/distribution you're using.

Lincoln

On Tue, Aug 30, 2011 at 5:39 PM, Hazard, E. Starr
<hazards@...<mailto:hazards@...>> wrote:
Folks,

I have been trying to get an instance GBrowse2 up and running. I had a screen showing at one point but clicking
on any objects to change gave a series of errors[

Tue Aug 30 15:54:06 2011] [error] [client 128.23.6.30] couldn't create lock file
'/var/lib/gbrowse2/sessions/cgisess.db.lck': Permission denied at
/usr/lib/perl5/site_perl/5.8.8/CGI/Session/Driver/db_file.pm<http://db_file.pm> line 98.,
referer: http://pchazards-linux.csb.mu/var/lib/gbrowse2/sessions/sc.edu/cgi-bin/gb2/gbrowse/yeast/
[Tue Aug 30 15:54:06 2011] [error] [client 128.23.6.30] Premature end of script headers: gbrowse,
referer: http://pchazards-linux.csb.musc.edu/cgi-bin/gb2/gbrowse/yeast/

When I altered the write permission for the
/var/lib/gbrowse2/sessions/

directory began to see the following error in my apache error_log

[Tue Aug 30 17:21:45 2011] [error] [client 128.23.6.30]
Can't call method "param" on an undefined value at
/usr/lib/perl5/site_perl/5.8.8/i386-linux-thread-multi/Bio/Graphics/Browser2/Session.pm
line 316., referer: http://pchazards-linux.csb.musc.edu/index.html.en
[Tue Aug 30 17:21:45 2011] [error] [client 128.23.6.30] Premature end of script headers: gbrowse,
referer: http://pchazards-linux.csb.musc.edu/index.html.en

I have CGI-Session-4.48 installed

here's my "z_gbrowse.conf" file content
cat /etc/httpd/conf.d/z_gbrowse2.conf
Alias        "/gbrowse2/i/" "/tmp/gbrowse2/images/"
Alias        "/gbrowse2"    "/var/www/html/gbrowse2"
ScriptAlias  "/gb2"      "/var/www/cgi-bin/gb2"

<Directory "/var/www/html/gbrowse2">
 AllowOverride Options
 Options -Indexes -MultiViews +FollowSymLinks
 Order allow,deny
 Allow from all
</Directory>

<Directory "/var/www/html/gbrowse2/tutorial">
 Options +Indexes
</Directory>

<Directory "/tmp/gbrowse2/images/">
 Order allow,deny
 Allow from all
</Directory>

<Directory "/var/lib/gbrowse2/databases">
 Order allow,deny
 Deny from all
</Directory>

<Directory "/var/www/cgi-bin/gb2">

 Options ExecCGI
 SetEnv GBROWSE_CONF   "/etc/gbrowse2"
</Directory>

<IfModule mod_fcgid.c>
 Alias /fgb2 "/var/www/cgi-bin/gb2"
 <Location /fgb2>
   SetHandler   fcgid-script
 </Location>
 FcgidInitialEnv GBROWSE_CONF /etc/gbrowse2
 # these directives prevent idle/busy timeouts and may need to be
 # adjusted up or down
 FcgidMinProcessesPerClass 6
 FcgidIOTimeout   600
 FcgidBusyTimeout 600

</IfModule>

<IfModule mod_fastcgi.c>
 Alias /fgb2 "/var/www/cgi-bin/gb2"
 <Location /fgb2>
   SetHandler   fastcgi-script
 </Location>
 # Note: you may need to increase -idle-timeout if file uploads are timing out and returning server
 # errors.
 FastCgiConfig -idle-timeout 600 -maxClassProcesses 20  -initial-env GBROWSE_CONF=/etc/gbrowse2
</IfModule>

<IfModule mod_perl.c>
  Alias /mgb2 "/var/www/cgi-bin/gb2"

  <Location /mgb2>
    SetHandler perl-script
    PerlResponseHandler ModPerl::Registry
    PerlOptions +ParseHeaders
  </Location>
</IfModule>

What should I fix to make the basic setup work?

Starr

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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <Renata.Musa@...<mailto:Renata.Musa@...>>

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"File does not exist" problem

Hi,

I've updated GBrowse2.26 to 2.39 via CPAN, but track images are not 
displayed. In my apache error log I can see that gbrowse is searching  
images at "/var/tmp/gbrowse2/images/yeast/..." but images are created in 
"/tmp/gbrowse2/images/yeast/..." as defined in the GBrowse.conf  
(tmp_base = /tmp/gbrowse2).

Any ideas about how can I address this issue? could it be a conflict 
with the previous installed version?

cheers

--

-- 
Miquel Ràmia Jesús
PhD. student (PIF)
Evolutionary Bioinformatics Group
(Genomics, Bioinformatics and Evolution Group)
Lab MRB/014 - 93 586 89 58
MRB - Institut de Biologia i Biomedicina (IBB)
Universitat Autònoma de Barcelona (UAB)
08193, Cerdanyola del Vallès
Barcelona (Spain)

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Re: "File does not exist" problem

Solved!

My apache2 conf.d/gbrowse.conf was not modified by the CPAN update, I 
only had to correct the alias

Alias        "/gbrowse2/i/" "/tmp/gbrowse2/images/"

hope this helps anyone upgrading from a 2.2x version for the first time

cheers!

On 09/05/2011 05:45 PM, Miquel Ràmia wrote:
> Hi,
>
> I've updated GBrowse2.26 to 2.39 via CPAN, but track images are not
> displayed. In my apache error log I can see that gbrowse is searching
> images at "/var/tmp/gbrowse2/images/yeast/..." but images are created in
> "/tmp/gbrowse2/images/yeast/..." as defined in the GBrowse.conf
> (tmp_base = /tmp/gbrowse2).
>
> Any ideas about how can I address this issue? could it be a conflict
> with the previous installed version?
>
> cheers
>
>

--

-- 
Miquel Ràmia Jesús
PhD. student (PIF)
Evolutionary Bioinformatics Group
(Genomics, Bioinformatics and Evolution Group)
Lab MRB/014 - 93 586 89 58
MRB - Institut de Biologia i Biomedicina (IBB)
Universitat Autònoma de Barcelona (UAB)
08193, Cerdanyola del Vallès
Barcelona (Spain)

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