Installing Gbrowse2 ....

classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|

Installing Gbrowse2 ....

bosborne
gmod-gbrowse,

 I'm installing GBrowse2, and I have a question. Using SVN from sourceforge, or using CPAN, I see:

WARNING: the following files are missing in your kit:
        lib/Bio/Graphics/Browser2/DataLoader/bigwig.pm
Please inform the author.

However, as far as I can tell there is no such module, bigwig.pm, in CPAN. I have the latest Bio::Graphics, but not bigwig.pm:

ls /usr/local//perl/lib/site_perl/5.10.0/darwin-2level/Bio/Graphics/Browser2/DataLoader
total 48
8 bam.pm  4 bed.pm  8 featurefile.pm  8 generic.pm  4 gff.pm  4 gff3.pm  4 sam.pm  8 wiggle.pm

Your thoughts?

Thanks again,

BIO
------------------------------------------------------------------------------
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Installing Gbrowse2 ....

Lincoln Stein
Hi Brian,

Sorry about that. I had added bigwig.pm to the manifest but not to SVN. Try doing an svn update.

A new release is on its way. I am just ironing out a few remaining issues with the built-in DAS server.

Lincoln

On Tue, Jun 29, 2010 at 10:14 AM, Brian Osborne <[hidden email]> wrote:
gmod-gbrowse,

 I'm installing GBrowse2, and I have a question. Using SVN from sourceforge, or using CPAN, I see:

WARNING: the following files are missing in your kit:
       lib/Bio/Graphics/Browser2/DataLoader/bigwig.pm
Please inform the author.

However, as far as I can tell there is no such module, bigwig.pm, in CPAN. I have the latest Bio::Graphics, but not bigwig.pm:

ls /usr/local//perl/lib/site_perl/5.10.0/darwin-2level/Bio/Graphics/Browser2/DataLoader
total 48
8 bam.pm  4 bed.pm  8 featurefile.pm  8 generic.pm  4 gff.pm  4 gff3.pm  4 sam.pm  8 wiggle.pm

Your thoughts?

Thanks again,

BIO
------------------------------------------------------------------------------
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
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 <[hidden email]>

------------------------------------------------------------------------------
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Installing Gbrowse2 ....

bosborne
Lincoln,

Thank you for that, cleared it up of course. Now I seem to be having trouble making images (Perl 5.10.0, Darwin 10.4.0):

767 ~/Generic-Genome-Browser>sudo perl Build.PL 
Checking prerequisites...
  recommends:
    *  Bio::DB::BigFile is not installed
    *  DBD::Pg is not installed
    *  DBD::SQLite is not installed
    *  DB_File::Lock is not installed
    *  File::NFSLock is not installed
    *  GD::SVG is not installed
    *  Net::OpenID::Consumer is not installed
    *  Net::SMTP::SSL is not installed
  * Do not worry if some optional preqrequisites are missing. You can install *
  * them later if you need the features they provide. Do not proceed with the *
  * install if any of REQUIRED prerequisites are missing.                     *
  *                                                                           *
  * The optional Safe::World module does not currently run on Perl 5.10 or    *
  * higher, and so cannot be installed.                                       *

Creating new 'MYMETA.yml' with configuration results
Creating new 'Build' script for 'GBrowse' version '2.11'
Now run:
  ./Build test
  ./Build demo          (optional)
  ./Build install       (as superuser/administrator)
        -or-
  ./Build install_slave (optional, for slave installations)

Other useful targets:
  ./Build register      (to register your copy of GBrowse)
  ./Build reconfig      (to reconfigure install locations)
  ./Build demostop      (to stop the demo)

768 ~/Generic-Genome-Browser>sudo ./Build reconfig
NOTE: Run ./Build reconfig to change existing configuration.
Reuse previous configuration as defaults? [y ]n

**Beginning interactive configuration**
Directory for GBrowse's config and support files? [/etc/gbrowse2] 
Directory for GBrowse's static images & HTML files? [/usr/local/apache2/htdocs] 
Directory for GBrowse's temporary data [/var/tmp/gbrowse2] 
Directory for GBrowse's example databases [/usr/local/apache2/htdocs/databases] 
Directory for GBrowse's CGI script executables? [/usr/local/apache2/cgi-bin] 
Internet port to run demo web site on (for demo)? [80] 
Apache loadable module directory (for demo)? [/usr/local/apache2/modules] 
User account under which Apache daemon runs? [www] daemon
Automatically update Apache config files to run GBrowse? [y] 
Automatically update system config files to run gbrowse-slave? [y] n

**Interactive configuration done. Run './Build reconfig' to reconfigure**

**Paths reconfigured. Running "Build clean".
Cleaning up build files

769 ~/Generic-Genome-Browser>sudo ./Build test
NOTE: Run ./Build reconfig to change existing configuration.
cc -I/Users/bosborne/Generic-Genome-Browser/libalign -I/usr/local/perl/lib/5.10.0/darwin-2level/CORE -DXS_VERSION="2.11" -DVERSION="2.11" -c -fno-common -DPERL_DARWIN -no-cpp-precomp -fno-strict-aliasing -pipe -I/usr/local/include -O3 -o lib/Bio/Graphics/Browser2/CAlign.o lib/Bio/Graphics/Browser2/CAlign.c
ExtUtils::Mkbootstrap::Mkbootstrap('blib/arch/auto/Bio/Graphics/Browser2/CAlign/CAlign.bs')
env MACOSX_DEPLOYMENT_TARGET=10.3 cc -bundle -undefined dynamic_lookup -L/usr/local/lib -o blib/arch/auto/Bio/Graphics/Browser2/CAlign/CAlign.bundle lib/Bio/Graphics/Browser2/CAlign.o
Performing variable substitutions in blib/conf/detail_select_menu.conf
Performing variable substitutions in blib/conf/enzymes.txt
Performing variable substitutions in blib/conf/GBrowse.conf
/etc/gbrowse2/GBrowse.conf conf file is already installed. New version will be installed as /etc/gbrowse2/GBrowse.conf.new
Performing variable substitutions in blib/conf/log4perl.conf
Performing variable substitutions in blib/conf/MobyServices/moby.conf
Performing variable substitutions in blib/conf/pop_demo.conf
/etc/gbrowse2/pop_demo.conf conf file is already installed. New version will be installed as /etc/gbrowse2/pop_demo.conf.new
Performing variable substitutions in blib/conf/slave_preload.conf
/etc/gbrowse2/slave_preload.conf conf file is already installed. New version will be installed as /etc/gbrowse2/slave_preload.conf.new
Performing variable substitutions in blib/conf/submitter_plugin.conf
Performing variable substitutions in blib/conf/synteny/rice_synteny.conf
/etc/gbrowse2/synteny/rice_synteny.conf conf file is already installed. New version will be installed as /etc/gbrowse2/synteny/rice_synteny.conf.new
Performing variable substitutions in blib/conf/synteny/wild_rice_synteny.conf
/etc/gbrowse2/synteny/wild_rice_synteny.conf conf file is already installed. New version will be installed as /etc/gbrowse2/synteny/wild_rice_synteny.conf.new
Performing variable substitutions in blib/conf/themes/solid_gray_colors
Performing variable substitutions in blib/conf/themes/transparent_colors
Performing variable substitutions in blib/conf/themes/warm_colors
Performing variable substitutions in blib/conf/yeast_chr1+2.conf
/etc/gbrowse2/yeast_chr1+2.conf conf file is already installed. New version will be installed as /etc/gbrowse2/yeast_chr1+2.conf.new
Performing variable substitutions in blib/conf/yeast_renderfarm.conf
/etc/gbrowse2/yeast_renderfarm.conf conf file is already installed. New version will be installed as /etc/gbrowse2/yeast_renderfarm.conf.new
Performing variable substitutions in blib/conf/yeast_simple.conf
/etc/gbrowse2/yeast_simple.conf conf file is already installed. New version will be installed as /etc/gbrowse2/yeast_simple.conf.new
Performing variable substitutions in blib/htdocs/annotation_help.html
Performing variable substitutions in blib/htdocs/gbrowse_karyotype_help.html
Performing variable substitutions in blib/htdocs/gbrowse_syn_help.html
Performing variable substitutions in blib/htdocs/general_help.html
Performing variable substitutions in blib/htdocs/index.html
Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_core.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/elegans_extra.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/HEADER.html
Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_final_withPhylo.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_halfway.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_Phylo.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_quarter.conf
Performing variable substitutions in blib/htdocs/tutorial/conf_files/volvox_refactored.conf
Performing variable substitutions in blib/htdocs/tutorial/data_files/HEADER.html
Performing variable substitutions in blib/htdocs/tutorial/tutorial.html
Performing variable substitutions in blib/htdocs/tutorial/tutorial.phyTreeEdit.html
/etc/apache2/other/gbrowse2.conf is already installed. Please run ./Build apache_conf to see this file's recommended contents.
t/01yeast.t ............... ok   
t/02.rearchitecture.t ..... ok     
t/03.render.t ............. 110/138 Use of uninitialized value in concatenation (.) or string at /Users/bosborne/Generic-Genome-Browser/t/../lib/Bio/Graphics/Browser2/Render/HTML.pm line 1330.
Use of uninitialized value in concatenation (.) or string at /Users/bosborne/Generic-Genome-Browser/t/../lib/Bio/Graphics/Browser2/Render/HTML.pm line 1341.
t/03.render.t ............. 121/138 Use of uninitialized value $png in substitution (s///) at t/03.render.t line 444.
Use of uninitialized value $png in -e at t/03.render.t line 445.
t/03.render.t ............. 124/138 Use of uninitialized value $png in substitution (s///) at t/03.render.t line 455.
Use of uninitialized value $png in -e at t/03.render.t line 456.
t/03.render.t ............. Failed 6/138 subtests 
t/04.remoteserver.t ....... Failed 5/43 subtests 
t/05.deferredrendering.t .. 4/19 Use of uninitialized value $images[0] in -e at t/05.deferredrendering.t line 147.
t/05.deferredrendering.t .. Failed 2/19 subtests 
t/06.featuresearch.t ...... Failed 3/26 subtests 
t/07.karyotype.t .......... ok   
t/08.calign.t ............. ok   

Test Summary Report
-------------------
t/03.render.t           (Wstat: 0 Tests: 138 Failed: 6)
  Failed tests:  95-96, 122-123, 125-126
t/04.remoteserver.t     (Wstat: 0 Tests: 39 Failed: 1)
  Failed test:  39
  Parse errors: Bad plan.  You planned 43 tests but ran 39.
t/05.deferredrendering.t (Wstat: 0 Tests: 19 Failed: 2)
  Failed tests:  16-17
t/06.featuresearch.t    (Wstat: 0 Tests: 26 Failed: 3)
  Failed tests:  21-23
Files=8, Tests=328, 71 wallclock secs ( 0.11 usr  0.06 sys + 15.21 cusr  6.47 csys = 21.85 CPU)
Result: FAIL
Failed 4/8 test programs. 12/328 subtests failed.


In fact, when I open the yeast1+2 page after the install there are no images, just text. I should that GBrowse 1.6* was working well, so GD was working with the older GBrowse.

What do you think?

Thanks again,

BIO

On Jun 29, 2010, at 10:57 AM, Lincoln Stein wrote:

Hi Brian,

Sorry about that. I had added bigwig.pm to the manifest but not to SVN. Try doing an svn update.

A new release is on its way. I am just ironing out a few remaining issues with the built-in DAS server.

Lincoln

On Tue, Jun 29, 2010 at 10:14 AM, Brian Osborne <[hidden email]> wrote:
gmod-gbrowse,

 I'm installing GBrowse2, and I have a question. Using SVN from sourceforge, or using CPAN, I see:

WARNING: the following files are missing in your kit:
       lib/Bio/Graphics/Browser2/DataLoader/bigwig.pm
Please inform the author.

However, as far as I can tell there is no such module, bigwig.pm, in CPAN. I have the latest Bio::Graphics, but not bigwig.pm:

ls /usr/local//perl/lib/site_perl/5.10.0/darwin-2level/Bio/Graphics/Browser2/DataLoader
total 48
8 bam.pm  4 bed.pm  8 featurefile.pm  8 generic.pm  4 gff.pm  4 gff3.pm  4 sam.pm  8 wiggle.pm

Your thoughts?

Thanks again,

BIO
------------------------------------------------------------------------------
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
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 <[hidden email]>


------------------------------------------------------------------------------
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
Reply | Threaded
Open this post in threaded view
|

Re: Installing Gbrowse2 ....

bosborne
In reply to this post by Lincoln Stein
Lincoln,

Please disregard that second post, GBrowse2 displays now! Not sure why but I made a few tweaks including opening up permissions on /var/tmp/gbrowse2.

Still getting the errors in "./Build test" though.

Thanks again,

BIO

On Jun 29, 2010, at 10:57 AM, Lincoln Stein wrote:

Hi Brian,

Sorry about that. I had added bigwig.pm to the manifest but not to SVN. Try doing an svn update.

A new release is on its way. I am just ironing out a few remaining issues with the built-in DAS server.

Lincoln

On Tue, Jun 29, 2010 at 10:14 AM, Brian Osborne <[hidden email]> wrote:
gmod-gbrowse,

 I'm installing GBrowse2, and I have a question. Using SVN from sourceforge, or using CPAN, I see:

WARNING: the following files are missing in your kit:
       lib/Bio/Graphics/Browser2/DataLoader/bigwig.pm
Please inform the author.

However, as far as I can tell there is no such module, bigwig.pm, in CPAN. I have the latest Bio::Graphics, but not bigwig.pm:

ls /usr/local//perl/lib/site_perl/5.10.0/darwin-2level/Bio/Graphics/Browser2/DataLoader
total 48
8 bam.pm  4 bed.pm  8 featurefile.pm  8 generic.pm  4 gff.pm  4 gff3.pm  4 sam.pm  8 wiggle.pm

Your thoughts?

Thanks again,

BIO
------------------------------------------------------------------------------
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
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 <[hidden email]>


------------------------------------------------------------------------------
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse