Nabble - Generic Model Organism System Database

Re: chado editor

2008-10-06T09:30:25Z

Hello Jay

the link you gave me leads to the same Manatee installation I have
(2.4.1). I can see modules that have 'chado' in it, so obviously
somebody tried, but I cannot find any doc on how this is supposed to
work.

So again: can somebody provide any information for getting Manatee to
work with Chado?

I really would appreciate it!

Isabelle

> -----Original Message-----
> From: Jay Sundaram [mailto:sundaram@...]
> Sent: Saturday, October 04, 2008 3:43 PM
> To: Isabelle Phan
> Cc: gmod-schema@...
> Subject: Re: [Gmod-schema] chado editor
>
> Hi Isabelle,
>
> TIGR did.
> Our friends at IGS-SOM continue the chado-Manatee development effort:
> http://www.igs.umaryland.edu/
>
> Jay
>
>
> Isabelle Phan wrote:
>
> >Hello
> >
> >has anybody used Manatee with Chado? I can't find anything
> on the web and the manatee mailing lists on sourceforge seem
> to be completely swamped with spam messages.
> >
> >thanks
> >
> >
> >Isabelle
> >
> >--
> >Isabelle Phan, DPhil
> >Seattle Biomedical Research Institute
> >+1(206)256 7113
> >
> >
> >-------------------------------------------------------------
> ------------
> >This SF.Net email is sponsored by the Moblin Your Move
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> >
> >
>
>
> --
> Jay Sundaram
> Senior Bioinformatics Engineer
> Annotation Engineering Team
> Informatics Department
> J. Craig Venter Institute
> 9704 Medical Center Rockville, Maryland, 20850
> B1/1st FL/room 125
> 301-795-7983
> sundaram@...
> http://www.jcvi.org/
>
>

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From forum: gmod-schema

Re: track citation/popup balloons

2008-10-06T08:34:32Z

Baloon is a good option to give brief introduction to external database and a link from there to the external site, but some of our end users does not like baloons much, as sometime it will pop-up automatically where you do not want. So direct external link will be very useful.

Thanks,
Mustafa.

--- On Wed, 10/1/08, Smithies, Russell <Russell.Smithies@...> wrote:

> From: Smithies, Russell <Russell.Smithies@...>
> Subject: Re: [Gmod-gbrowse] track citation/popup balloons
> To: "Lincoln Stein" <lincoln.stein@...>, "Scott Cain" <cain.cshl@...>
> Cc: "Sheldon McKay" <mckays@...>, gmod-gbrowse@...
> Date: Wednesday, October 1, 2008, 1:13 AM
> It works in 1.65 as I use it often.
>
> Here's an example:
>
>
>
> citation = This track shows predictions from the <a
> href="http://genes.mit.edu/GENSCAN.html"
> target="_blank">Genscan</a>
> program written by Chris Burge. The predictions are based
> on
> transcriptional, translational, and donor/acceptor splicing
> signals, as
> well as the length and compositional distributions of
> exons, introns and
> intergenic regions.
>
>
>
>
>
> No special escaping required.
>
>
>
> Russell
>
>
>
>
>
> From: Lincoln Stein [mailto:lincoln.stein@...]
> Sent: Wednesday, 1 October 2008 5:00 a.m.
> To: Scott Cain
> Cc: Sheldon McKay; gmod-gbrowse@...
> Subject: Re: [Gmod-gbrowse] track citation/popup balloons
>
>
>
> It's odd that that doesn't work. This should be
> fixed.
>
> Lincoln
>
> On Tue, Sep 30, 2008 at 11:57 AM, Scott Cain
> <cain.cshl@...>
> wrote:
>
> OK, I thought not. I was going to suggest putting an html
> link in the
> citation, like this:
>
> citation = <a
> href="http://scottcain.net/">Track
> details</a>
>
> but unfortunately, that doesn't work either.
>
> Scott
>
>
>
> On Tue, Sep 30, 2008 at 11:36 AM, Lincoln Stein
> <lincoln.stein@...> wrote:
> > The current version does not support this
> functionality.
> >
> > Lincoln
> >
> > On Tue, Sep 30, 2008 at 11:34 AM, Scott Cain
> <cain.cshl@...>
> wrote:
> >>
> >> Hi Mustafa,
> >>
> >> I'm not sure this is possible with the current
> implementation of
> >> gbrowse. While the pop up balloons can fetch a
> url and display it
> >> inside a balloon, I don't think the citation
> method will do that for
> >> you. Sheldon, is this accurate?
> >>
> >> Scott
> >>
> >>
> >> On Mon, Sep 29, 2008 at 4:09 PM, Syed Mustafa
> Hussain
> >> <comp_sea@...> wrote:
> >> > Hi,
> >> >
> >> > I am trying to give external link for track
> citation, therefore, I
> have
> >> > URL as a value of citation. But it still
> generate text description
> page
> >> > instead of invoking corressponding URL
> directly. How should I put
> citation
> >> > value so that it invokes URL directly without
> generating text page?
> >> >
> >> > Thanks,
> >> > Mustafa.
> >> >
> >> >
> >> >
> >> >
> >> >
> >> >
> ------------------------------------------------------------------------
> -
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> >> >
> _______________________________________________
> >> > Gmod-gbrowse mailing list
> >> > Gmod-gbrowse@...
> >> >
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> >> >
> >>
> >>
> >>
> >> --
> >>
> ------------------------------------------------------------------------
> >> Scott Cain, Ph. D.
> cain.cshl@...
> >> GMOD Coordinator (http://gmod.org/)
> 216-392-3087
> >> Cold Spring Harbor Laboratory
> >>
> >>
> ------------------------------------------------------------------------
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> >>
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> >
> >
> >
> > --
> > Lincoln D. Stein
> >
> > Ontario Institute for Cancer Research
> > 101 College St., Suite 800
> > Toronto, ON, Canada M5G0A3
> > 416 673-8514
> > Assistant: Stacey Quinn
> <Stacey.Quinn@...>
> >
> > Cold Spring Harbor Laboratory
> > 1 Bungtown Road
> > Cold Spring Harbor, NY 11724 USA
> > (516) 367-8380
> > Assistant: Sandra Michelsen <michelse@...>
> >
>
>
>
>
> --
>
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.
> cain.cshl@...
> GMOD Coordinator (http://gmod.org/)
> 216-392-3087
>
> Ontario Institute for Cancer Research
>
>
>
>
> --
> Lincoln D. Stein
>
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Stacey Quinn <Stacey.Quinn@...>
>
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724 USA
> (516) 367-8380
> Assistant: Sandra Michelsen <michelse@...>
>
>
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From forum: gmod-gbrowse

Re: error

2008-10-06T08:25:19Z

Lincoln,

Yes, it was because of permissions on tmp. It is working now.

Thanks,
Mustafa Syed.

--- On Tue, 9/30/08, Lincoln Stein <lincoln.stein@...> wrote:

> From: Lincoln Stein <lincoln.stein@...>
> Subject: Re: [Gmod-gbrowse] error
> To: comp_sea@...
> Cc: gmod-gbrowse@...
> Date: Tuesday, September 30, 2008, 8:35 PM
> You can fix this by making the tmp directory and its
> subdirectories owned by
> the user account under which apache runs. For example, if
> apache runs as
> user "www", then run the command:
>
> chown -R www /srv/www/htdocs/gbrowse/tmp
>
> Lincoln
>
> On Mon, Sep 29, 2008 at 3:51 PM, Syed Mustafa Hussain
> <comp_sea@...>wrote:
>
> > Hi,
> >
> > I can see selection tracks but image is not comming. I
> checked error log
> > and I am getting following error in log:
> >
> >
> /srv/www/htdocs//gbrowse/tmp/xxxxx/panel_cache/fb/46/fb46daf0d59367dea53a95b5ac965bb9/size:
> > Permission denied at
> >
> /usr/lib/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser.pm
> > line 2662., referer:
> http://xxxxx/cgi-bin/gbrowse/xxxxx/
> >
> > Is the image not comming up because of this error?
> >
> > Mustafa.
> >
> >
> >
> >
> >
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> >
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
> >
>
>
>
> --
> Lincoln D. Stein
>
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Stacey Quinn <Stacey.Quinn@...>
>
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724 USA
> (516) 367-8380
> Assistant: Sandra Michelsen <michelse@...>

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From forum: gmod-gbrowse

Re: possible bug when using track names that start with a number?

2008-10-06T07:36:10Z

Hi Kara,

Ok, I believe the bug is fixed, but it is a bioperl issue, so you will have to use the latest and greatest bioperl-live from subversion. I also suggest that you try using GBrowse version 1.69, which fixes a couple of related bugs.

Give it a try and let me know if it works for you.

Lincoln

On Mon, Oct 6, 2008 at 10:31 AM, Lincoln Stein <lincoln.stein@...> wrote:

Hi Kara,

I can confirm this bug. If it is an easy fix I'll get it into the 1.70 release; otherwise I'll change the documentation to say "don't do that!".

Thanks for reporting it.

Lincoln

On Thu, Sep 25, 2008 at 3:13 PM, Kara Dolinski <kara@...> wrote:

Hello,

We found a possible bug when using track names that start with a number.

When we use a track name that starts with a number, for example:

[273614N_Peaks]
feature = 273614N_PEAK
glyph = \&snp_glyph
parallel = 0

fgcolor = black
bgcolor = black
key = 273614N Peaks
description = 0
link = AUTO
title = $description
category = SNPscanner Peaks (Schacherer and Shapiro et al 2008)

and select that track on the web interface for viewing, the map display did not load, and we saw the following in the error log:

Can't call method "isa" without a package or object reference at /usr/local/perl/5.80/Library/darwin/Bio/Graphics/Browser.pm line 2444.

Use of uninitialized value in print at gbrowse line 426.

When we change the track name to the following, all is well:

[Peaks_273614N]
feature = 273614N_PEAK

glyph = \&snp_glyph
parallel = 0
fgcolor = black
bgcolor = black
key = 273614N Peaks
description = 0
link = AUTO
title = $description
category = SNPscanner Peaks (Schacherer and Shapiro et al 2008)

We're using Gbrowse 1.68.

-Kara

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--
Lincoln D. Stein

Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Stacey Quinn <Stacey.Quinn@...>

Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724 USA
(516) 367-8380
Assistant: Sandra Michelsen <michelse@...>

--
Lincoln D. Stein

Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Stacey Quinn <Stacey.Quinn@...>

Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724 USA
(516) 367-8380
Assistant: Sandra Michelsen <michelse@...>

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From forum: gmod-gbrowse

Re: possible bug when using track names that start with a number?

2008-10-06T07:31:28Z

Hi Kara,

I can confirm this bug. If it is an easy fix I'll get it into the 1.70 release; otherwise I'll change the documentation to say "don't do that!".

Thanks for reporting it.

Lincoln

On Thu, Sep 25, 2008 at 3:13 PM, Kara Dolinski <kara@...> wrote:

Hello,

We found a possible bug when using track names that start with a number.

When we use a track name that starts with a number, for example:

[273614N_Peaks]
feature = 273614N_PEAK
glyph = \&snp_glyph
parallel = 0

fgcolor = black
bgcolor = black
key = 273614N Peaks
description = 0
link = AUTO
title = $description
category = SNPscanner Peaks (Schacherer and Shapiro et al 2008)

and select that track on the web interface for viewing, the map display did not load, and we saw the following in the error log:

Can't call method "isa" without a package or object reference at /usr/local/perl/5.80/Library/darwin/Bio/Graphics/Browser.pm line 2444.

Use of uninitialized value in print at gbrowse line 426.

When we change the track name to the following, all is well:

[Peaks_273614N]
feature = 273614N_PEAK

glyph = \&snp_glyph
parallel = 0
fgcolor = black
bgcolor = black
key = 273614N Peaks
description = 0
link = AUTO
title = $description
category = SNPscanner Peaks (Schacherer and Shapiro et al 2008)

We're using Gbrowse 1.68.

-Kara

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From forum: gmod-gbrowse

Re: Controlling label_features default//Solution

2008-10-05T17:27:25Z

Hi Ben,
I have managed to reproduce the behaviour I don't like in Firefox & IE
like so:
-select a map in VIEWER
-click on a marker
-select VIEW MAP DETAILS

This sets view to SHOW LANDMARKS as it is coded in feature_detail.tmpl
and seems to affect this setting via cookies,as deleting cookies
resents to SHOW ALL

So...I have just deleted the SHOW FEATURES string from the URL in the
template file to get the behaviour I want.

Regards
John

>>> Ben Faga <faga.cshl@...> 9:01 a.m. 05-Oct-08 >>>
Hi John,

Without looking at code, I can tell you how this is supposed to work.

If you have never been to the site, the config option should set the
labels to "all".

Since you have visited the site, your cookie remembers which option
you
selected.

Try deleting the cookie with your browser and then visiting again. If
there isn't a bug, then it should be fine.

If there is a bug then let Ken know.

Ben

On Mon, 2008-09-29 at 14:13 +1300, John McCallum wrote:
> Im struggling to work out how to better control the default genetic
map
> drawing behaviour in terms of showing ALL feature labels vs Landmark
> features only.
>
> In my database config file the option set is 'label_features all'
>
> but on first selecting a map the behaviour is to just show landmark
> feature labels.
>
> I definitely don't want new users getting this (and having to
manually

> change this themselves)
>
> Im sure I can change this by hacking the templates but that seems a
> little extreme!
>
>
>
>
>
> Dr. John A. McCallum
> Crop & Food Research
> Private Bag 4704
> Christchurch
> New Zealand
> Work Ph 64 3 325 6400
> Home 64 3 328 7420
> Mobile 027 443 9033
> Fax 64 3 325 2074
> Email MCCALLUMJ@...
>
>
> Visit our website at http://www.crop.cri.nz
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From forum: gmod-cmap

Re: chado editor

2008-10-04T15:42:58Z

Hi Isabelle,

TIGR did.
Our friends at IGS-SOM continue the chado-Manatee development effort:
http://www.igs.umaryland.edu/

Jay

Isabelle Phan wrote:

>Hello
>
>has anybody used Manatee with Chado? I can't find anything on the web and the manatee mailing lists on sourceforge seem to be completely swamped with spam messages.
>
>thanks
>
>
>Isabelle
>
>--
>Isabelle Phan, DPhil
>Seattle Biomedical Research Institute
>+1(206)256 7113
>
>
>-------------------------------------------------------------------------
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>_______________________________________________
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>
>

--
Jay Sundaram
Senior Bioinformatics Engineer
Annotation Engineering Team
Informatics Department
J. Craig Venter Institute
9704 Medical Center Rockville, Maryland, 20850
B1/1st FL/room 125
301-795-7983
sundaram@...
http://www.jcvi.org/

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From forum: gmod-schema

Re: CMap-1.01 Map.pm issue

2008-10-04T13:17:10Z

Hi Anil,

I'm cc'ing to the list since I've moved on to a different job.

My guess is that you have maps of zero length (although, I thought we
had a fix for that). If so, you need to set the map_start and map_stop
for the map in the database.

Ben

On Sat, 2008-10-04 at 13:01 -0400, asuryan@... wrote:

> Hi Ben,
>
> This is Anil, graduate student from Clemson University. I had interacted
> with you during the CMap-1.01 installation. Currently, I am running into
> few issues with it, so please help me out if you have some time for this.
>
> - CMap is in: http://www.cottonmarker.org/cmap/
> - Issue is that, in the recently uploaded data, when I try to compare
> maps(left or right), I get an error saying:
> Illegal division by zero at
> /gnb/blenda/sites/www.cottonmarker.org/cmap-1.01/lib/Bio/GMOD/CMap/Drawer/Map.pm
> line 2451.
>
> - The URL for this data is:
> http://www.cottonmarker.org/cgi-bin/cmap/viewer?ref_map_set_acc=11;ref_map_accs=359
>
> - This is the first set of data I uploaded after installing CMap.
>
> I was not sure what was going wrong in Map.pm module. Please let me know
> if you can figure out the issue here.
>
> Thanks a lot.
> Anil

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From forum: gmod-cmap

Re: Controlling label_features default

2008-10-04T13:01:48Z

Hi John,

Without looking at code, I can tell you how this is supposed to work.

If you have never been to the site, the config option should set the
labels to "all".

Since you have visited the site, your cookie remembers which option you
selected.

Try deleting the cookie with your browser and then visiting again. If
there isn't a bug, then it should be fine.

If there is a bug then let Ken know.

Ben

On Mon, 2008-09-29 at 14:13 +1300, John McCallum wrote:

> Im struggling to work out how to better control the default genetic map
> drawing behaviour in terms of showing ALL feature labels vs Landmark
> features only.
>
> In my database config file the option set is 'label_features all'
>
> but on first selecting a map the behaviour is to just show landmark
> feature labels.
>
> I definitely don't want new users getting this (and having to manually
> change this themselves)
>
> Im sure I can change this by hacking the templates but that seems a
> little extreme!
>
>
>
>
>
> Dr. John A. McCallum
> Crop & Food Research
> Private Bag 4704
> Christchurch
> New Zealand
> Work Ph 64 3 325 6400
> Home 64 3 328 7420
> Mobile 027 443 9033
> Fax 64 3 325 2074
> Email MCCALLUMJ@...
>
>
> Visit our website at http://www.crop.cri.nz
> ______________________________________________________
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From forum: gmod-cmap

Re: PhP in the conf file?

2008-10-04T12:35:37Z

'Can of worms' is the phrase that springs to mind.

chris

On Sep 26, 2008, at 5:28 PM, Dave Clements, GMOD Help Desk wrote:

> Hi Taner,
>
> The thought of running PHP inside Perl gives me the cold pricklies.
> However, that doesn't mean it can't be done.
>
> You could try something like PHP::Interpreter:
>
> http://search.cpan.org/~gschloss/PHP-Interpreter-1.0.1/lib/PHP/Interpreter.pm
> http://www.linuxjournal.com/article/9282
>
> However, I don't think we would enthusiastically support doing this.
> If at all possible I would think about rewriting the code in Perl.
>
> Thanks,
> Dave C.
> GMOD Help Desk
>
> On Fri, Sep 26, 2008 at 3:21 PM, Taner Z. Sen <taner@...>
> wrote:
>> Hi,
>>
>> Is there a way to insert php code in the conf file? (something like
>> header =
>> <?PHP ...)
>>
>> Thanks,
>> Taner
>>
>> Taner Z. Sen, Ph.D.
>> Computational Biologist, USDA-Agricultural Research Service
>> Collaborator Assistant Professor, Dept. of Genetics, Development
>> and Cell
>> Biology
>> Bioinformatics and Computational Biology Program
>> Iowa State University
>> 1025 Crop Genome Informatics Lab
>> Ames, IA 50011
>> Phone: (515) 294-5326
>> Fax: (515) 294-8280
>> taner@iastate. edu
>> http://www.public.iastate.edu/~taner/
>>
>> -------------------------------------------------------------------------
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>
>
>
> --
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign

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From forum: gmod-gbrowse

[SPAM] You havee 1 new message

2008-10-04T09:50:48Z

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three shafts of his, thy son uttered his operations, he
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From forum: gmod-schema-cmts

Re: Chado compatible Schema for Pato

2008-10-03T18:36:35Z

Hi Jeff,

I've learned more too. This is what my understanding is now:

There was an original FlyBase extension for phenotypes in their
instance of Chado, but it wasn't a GMOD-able solution.

ZFIN did develop a phenotype extension for phenotypes and this -is-
included in the GMOD version. Eric Segerdell is probably familiar with
it and it is OBD/EQ compatible. Monte Westerfield at least tells me
that it has been folded into GMOD-Chado (and if it hasn't it should
be). If there are limitations on this one, then any required
modifications should ideally make it back into GMOD-Chado.

And then there is OBD as Chris mentioned. This is a different schema,
but since we're importing data from ZFIN into OBD, we should be able
to have it both ways, or chose one that suits.

Scott can you confirm that GMOD-Chado has the ZFIN phenotype module?

Hope this isn't reaching you too late to make a difference.

-S

On Sep 22, 2008, at 2:39 PM, Jeff Bowes wrote:

> Hi,
>
> I hope I am posting this request to the right place.
>
> I was talking to Suzanna Lewis at the GMOD meeting in July and she
> said that Flybase has been working on a Chado-compatible database
> schema to support PATO-based annotations. My understanding is that
> this is not the same as the phenotypes module that is currently part
> of Chado.
> Can anyone tell me where I could get a copy of this schema?
>
> Thanks very much,
>
> Jeff Bowes
>
>
>
>
> --
> Jeff Bowes M.Sc.
> DBA/Technical Architect, Xenbase
> Department of Biological Sciences
> University of Calgary
> Calgary, Alberta T2N 1N4
> CANADA
> Tel: (403) 220-2824 Fax: (403) 284-4707
>
>
>
>

From forum: gmod-schema

chado editor

2008-10-03T11:54:35Z

Hello

has anybody used Manatee with Chado? I can't find anything on the web and the manatee mailing lists on sourceforge seem to be completely swamped with spam messages.

thanks

Isabelle

--
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Seattle Biomedical Research Institute
+1(206)256 7113

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From forum: gmod-schema

Re: set up QTL track in GBrowse

2008-10-03T11:13:40Z

Hi Zhiliang,

I took a look around and I found lots of places that show the spans of
QTLs but not inner workings. (BovineGenome.org show peaks, but not
within GBrowse.)

The best I could find was a posting from 2006:

http://www.nabble.com/Re:--Gmod-gbrowse--aggregators-issue--td7431347.html

I think that posting is about GenmapDB, and unfortuantely, that
appears not to be up today.

Hope this helps,

On Thu, Oct 2, 2008 at 7:12 AM, Zhiliang Hu <zhu@...> wrote:

> We plan to set up a QTL track in GBrowse for cattle and chicken, aligned
> with their respective genomes. While this seems to be straight forward but
> there are some tricks we may need to work out, such as - is it possible or
> how to show the QTL peak location besides the span, etc.
>
> I didn't find but perhaps someone might have already worked on this? I am
> posting to see if anyone wish to kindly share?
>
> Thanks in advance,
>
> Zhiliang
>
>
> --
> Zhi-Liang Hu (PhD)
> Associate Scientist,
> Department of Animal Science,
> Center for Integrated Animal Genomics,
> National Animal Genome Research Program,
> Iowa State University
> Tel: 901-759-0643
> Mob: 901-212-2820
> Web: http://www.animalgenome.org
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--
Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback

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From forum: gmod-gbrowse

Re: [Gmod-help] Re: gbrowse

2008-10-02T08:04:25Z

Hi,

I fixed both issues: DB_File is fixed for perl 5.8 as I mentioned
below, and the installer now checks for ActiveState perl 5.10 and dies
if it is present (on non-Windows systems, perl 5.10 is fine, but the
current build of ActiveState perl 5.10 lacks DB_File). The installer
can be obtained from:

http://gmod.cvs.sourceforge.net/viewvc/*checkout*/gmod/Generic-Genome-Browser/bin/gbrowse_netinstall.pl?revision=1.1.2.28

If someone other than me could check that this works, I'll copy it to
the main development track so it will be available for everybody.

Thanks,
Scott

On Wed, Oct 1, 2008 at 2:22 PM, Scott Cain <cain.cshl@...> wrote:

> I fixed the DB_File issue by adding the tcool repository to the list of
> repositories that the installer adds but I'm currently unable to commit, so
> I'm attaching the install script to this email. I'll do the check for perl
> 5.10 next.
>
> Scott
>
>
> On Wed, Oct 1, 2008 at 12:45 PM, Scott Cain <cain.cshl@...> wrote:
>>
>> I still don't know what happened to DB_File from ActiveState for perl
>> 5.8--it used to be there and google doesn't turn up and explanation. For
>> perl 5.10, it is supposed to be distributed with core, but it isn't present
>> either. When 5.10 does get DB_File in core, it should support GBrowse
>> fine. Until then, I looks like we'll have to add another repository to the
>> preinstall so that DB_File can be found: there is a ppm version of DB_File
>> at ppm.tcool.org that appears to work. I'll update the installer and do
>> some testing.
>>
>> Scott
>>
>>
>> On Wed, Oct 1, 2008 at 11:12 AM, Scott Cain <cain.cshl@...> wrote:
>>>
>>> Darn it. I tried ActiveState perl 5.10 since I read that there cpan
>>> shell problems were fixed, but it doesn't have a DB_File either. It is
>>> baffling to me that ActiveState could have screwed up such an important
>>> module.
>>>
>>> Scott
>>>
>>>
>>> On Wed, Oct 1, 2008 at 10:40 AM, Chris Fields <cjfields@...>
>>> wrote:
>>>>
>>>> That's scary. I wonder how this might affect bioperl tests and
>>>> installation.
>>>>
>>>> chris
>>>>
>>>> On Oct 1, 2008, at 8:58 AM, Scott Cain wrote:
>>>>
>>>>> Somebody (perhaps Remi) submitted a bug report about this:
>>>>>
>>>>>
>>>>> https://sourceforge.net/tracker/?func=detail&atid=391291&aid=2138884&group_id=27707
>>>>>
>>>>> I was just working on it. The bug report has a link to a suggested fix
>>>>> when DB_File doesn't install.
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> On Wed, Oct 1, 2008 at 9:54 AM, Lincoln Stein <lincoln.stein@...>
>>>>> wrote:
>>>>> Hi Remi,
>>>>>
>>>>> ActivePerl 5.10 has known problems with missing modules. I suggest that
>>>>> you uninstall it and try version 5.8, which is just as good.
>>>>>
>>>>> Lincoln
>>>>>
>>>>> On Wed, Oct 1, 2008 at 9:46 AM, Rémi Emans <remi.emans@...>
>>>>> wrote:
>>>>> Lincoln Stein a écrit :
>>>>>
>>>>> Hi Remi,
>>>>>
>>>>> This means that your version of Perl does not have the DB_File module
>>>>> installed. This is odd, because DB_File is a standard part of most Perl
>>>>> distributions. From your error message, it looks like you are using Perl on
>>>>> a Windows platform. Are you using the ActiveState distribution, or a
>>>>> different one? Which version of the distribution are you using?
>>>>>
>>>>> Lincoln
>>>>> Thank you to answer me so quickly...
>>>>> I've installed Active Perl 5.10 which seem to be the last package...
>>>>>
>>>>> Rémi
>>>>>
>>>>>
>>>>> --
>>>>> Biologie & Ecologie Tropicale & Méditerranéenne
>>>>> Service Informatique UMR 5244
>>>>> CNRS/EPHE/Université de Perpignan
>>>>> 52, Avenue Paul Alduy
>>>>> 66860 Perpignan
>>>>> Tel 33 (0)468662055
>>>>> Fax 33 (0)468503686
>>>>> http://cbetm.univ-perp.fr
>>>>>
>>>>>
>>>>> --
>>>>> Ce message a été vérifié par MailScanner
>>>>> pour des virus ou des polluriels et rien de
>>>>> suspect n'a été trouvé.
>>>>> CRI UPVD http://www.univ-perp.fr
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Lincoln D. Stein
>>>>>
>>>>> Ontario Institute for Cancer Research
>>>>> 101 College St., Suite 800
>>>>> Toronto, ON, Canada M5G0A3
>>>>> 416 673-8514
>>>>> Assistant: Stacey Quinn <Stacey.Quinn@...>
>>>>>
>>>>> Cold Spring Harbor Laboratory
>>>>> 1 Bungtown Road
>>>>> Cold Spring Harbor, NY 11724 USA
>>>>> (516) 367-8380
>>>>> Assistant: Sandra Michelsen <michelse@...>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>>
>>>>> ------------------------------------------------------------------------
>>>>> Scott Cain, Ph. D.
>>>>> cain.cshl@...
>>>>> GMOD Coordinator (http://gmod.org/) 216-392-3087
>>>>> Ontario Institute for Cancer Research
>>>>>
>>>>> -------------------------------------------------------------------------
>>>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>>>> challenge
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>>>>> prizes
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>>>>> world
>>>>>
>>>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/_______________________________________________
>>>>> Gmod-gbrowse mailing list
>>>>> Gmod-gbrowse@...
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>
>>>> Christopher Fields
>>>> Postdoctoral Researcher
>>>> Lab of Dr. Marie-Claude Hofmann
>>>> College of Veterinary Medicine
>>>> University of Illinois Urbana-Champaign
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D. cain.cshl@...
>>> GMOD Coordinator (http://gmod.org/) 216-392-3087
>>> Ontario Institute for Cancer Research
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D. cain.cshl@...
>> GMOD Coordinator (http://gmod.org/) 216-392-3087
>> Ontario Institute for Cancer Research
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D. cain.cshl@...
> GMOD Coordinator (http://gmod.org/) 216-392-3087
> Ontario Institute for Cancer Research
>

--
------------------------------------------------------------------------
Scott Cain, Ph. D. cain.cshl@...
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research

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From forum: gmod-gbrowse

set up QTL track in GBrowse

2008-10-02T07:12:03Z

We plan to set up a QTL track in GBrowse for cattle and chicken, aligned with their respective genomes. While this seems to be straight forward but there are some tricks we may need to work out, such as - is it possible or how to show the QTL peak location besides the span, etc.

I didn't find but perhaps someone might have already worked on this? I am posting to see if anyone wish to kindly share?

Thanks in advance,

Zhiliang

--
Zhi-Liang Hu (PhD)
Associate Scientist,
Department of Animal Science,
Center for Integrated Animal Genomics,
National Animal Genome Research Program,
Iowa State University
Tel: 901-759-0643
Mob: 901-212-2820
Web: http://www.animalgenome.org
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From forum: gmod-gbrowse

Re: feature filters

2008-10-01T19:24:58Z

Hi Nicole,

I am nearly certain that this is not possible; in fact, I don't think
you could do it with a callback--the problem is that the callback
architecture passes in a feature, so you need a populated feature line
in the track config so that gbrowse knows what features to pass to the
callback, if you follow me. The only way I could think of to do that
would be your first example (what you don't seem to want to do,
presumably because you have too many types).

Sorry,
Scott

On Wed, Oct 1, 2008 at 6:08 PM, Nicole Washington <NLWashington@...> wrote:

> hi there,
>
> is there a way, without callbacks, to get all features of the same
> source, no matter what their type?
>
> meaning, instead of a line in the conf file like (this is not a real
> example):
>
> feature = gene:mySource match:mySource binding_site:mySource
>
> why can't i just say
>
> feature = :mySource ?
>
> or is there a way like this to do it?
>
> thanks,
>
> nicole
>
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From forum: gmod-gbrowse

feature filters

2008-10-01T15:08:00Z

hi there,

is there a way, without callbacks, to get all features of the same
source, no matter what their type?

meaning, instead of a line in the conf file like (this is not a real
example):

feature = gene:mySource match:mySource binding_site:mySource

why can't i just say

feature = :mySource ?

or is there a way like this to do it?

thanks,

nicole

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From forum: gmod-gbrowse