Using DAS with gbrowse2

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Using DAS with gbrowse2

Wes Barris
I would like to add a track which uses a DAS source.  I was trying to
find information on the gmod web site but keep running into dead ends.
The GBrowse_2.0_HOWTO page has a link to a "GBrowse DAS HOWTO" page
but the link does not work.

I tried downloading and building the latest Bio::Das (v1.14) from CPAN
but it fails its test:

wes@bioweb> make test
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01das.t .. 35/36
#   Failed test 'got genes'
#   at t/01das.t line 121.
Can't call method "get_SeqFeatures" on an undefined value at t/01das.t line 122.
# Looks like you planned 36 tests but ran 35.
# Looks like you failed 1 test of 35 run.
# Looks like your test exited with 255 just after 35.
t/01das.t .. Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 2/36 subtests

Test Summary Report
-------------------
t/01das.t (Wstat: 65280 Tests: 35 Failed: 1)
   Failed test:  35
   Non-zero exit status: 255
   Parse errors: Bad plan.  You planned 36 tests but ran 35.
Files=1, Tests=35, 11 wallclock secs ( 0.06 usr  0.01 sys +  1.29 cusr  0.07 csys =  1.43 CPU)
Result: FAIL
Failed 1/1 test programs. 1/35 subtests failed.
make: *** [test_dynamic] Error 255

Is anyone using DAS with GBrowse2?  Do you configure a DAS track
with a "remote feature" or just define a separate DAS database?
--
Wes Barris

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Re: Using DAS with gbrowse2

Lincoln Stein
Hi Wes,

DAS is working with GBrowse 2 as of release 2.08. There is information on configuring DAS in the GBrowse2 tutorial.

I am also seeing regression errors on Bio::Das. This seems to be new, and is probably related to something changing on the online database that is used for the regression tests. For now, you should go ahead and force the Bio::Das install and I will try to fix the tests and/or regression server.

Lincoln

On Sun, Jun 6, 2010 at 8:13 PM, Wes Barris <[hidden email]> wrote:
I would like to add a track which uses a DAS source.  I was trying to
find information on the gmod web site but keep running into dead ends.
The GBrowse_2.0_HOWTO page has a link to a "GBrowse DAS HOWTO" page
but the link does not work.

I tried downloading and building the latest Bio::Das (v1.14) from CPAN
but it fails its test:

wes@bioweb> make test
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01das.t .. 35/36
#   Failed test 'got genes'
#   at t/01das.t line 121.
Can't call method "get_SeqFeatures" on an undefined value at t/01das.t line 122.
# Looks like you planned 36 tests but ran 35.
# Looks like you failed 1 test of 35 run.
# Looks like your test exited with 255 just after 35.
t/01das.t .. Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 2/36 subtests

Test Summary Report
-------------------
t/01das.t (Wstat: 65280 Tests: 35 Failed: 1)
  Failed test:  35
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 36 tests but ran 35.
Files=1, Tests=35, 11 wallclock secs ( 0.06 usr  0.01 sys +  1.29 cusr  0.07 csys =  1.43 CPU)
Result: FAIL
Failed 1/1 test programs. 1/35 subtests failed.
make: *** [test_dynamic] Error 255

Is anyone using DAS with GBrowse2?  Do you configure a DAS track
with a "remote feature" or just define a separate DAS database?
--
Wes Barris

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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]>

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
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Re: Using DAS with gbrowse2

Lincoln Stein
I take it back. DAS configuration is not described in the tutorial.  The information in the old version 1.0 tutorial still is valid, however.

Lincoln

On Mon, Jun 7, 2010 at 12:44 PM, Lincoln Stein <[hidden email]> wrote:
Hi Wes,

DAS is working with GBrowse 2 as of release 2.08. There is information on configuring DAS in the GBrowse2 tutorial.

I am also seeing regression errors on Bio::Das. This seems to be new, and is probably related to something changing on the online database that is used for the regression tests. For now, you should go ahead and force the Bio::Das install and I will try to fix the tests and/or regression server.

Lincoln


On Sun, Jun 6, 2010 at 8:13 PM, Wes Barris <[hidden email]> wrote:
I would like to add a track which uses a DAS source.  I was trying to
find information on the gmod web site but keep running into dead ends.
The GBrowse_2.0_HOWTO page has a link to a "GBrowse DAS HOWTO" page
but the link does not work.

I tried downloading and building the latest Bio::Das (v1.14) from CPAN
but it fails its test:

wes@bioweb> make test
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/01das.t .. 35/36
#   Failed test 'got genes'
#   at t/01das.t line 121.
Can't call method "get_SeqFeatures" on an undefined value at t/01das.t line 122.
# Looks like you planned 36 tests but ran 35.
# Looks like you failed 1 test of 35 run.
# Looks like your test exited with 255 just after 35.
t/01das.t .. Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 2/36 subtests

Test Summary Report
-------------------
t/01das.t (Wstat: 65280 Tests: 35 Failed: 1)
  Failed test:  35
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 36 tests but ran 35.
Files=1, Tests=35, 11 wallclock secs ( 0.06 usr  0.01 sys +  1.29 cusr  0.07 csys =  1.43 CPU)
Result: FAIL
Failed 1/1 test programs. 1/35 subtests failed.
make: *** [test_dynamic] Error 255

Is anyone using DAS with GBrowse2?  Do you configure a DAS track
with a "remote feature" or just define a separate DAS database?
--
Wes Barris

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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]>



--
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]>

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse