WIG file display problem
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Re: WIG file display problem
by Scott Cain-4
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Hi Ryan,
I don't think the wiggle file itself is the problem; it is more likely a configuration problem. See my comments in the previous email about debugging and let us know if you still can't figure it out. Thanks, Scott On Thu, Oct 22, 2009 at 7:53 AM, Alessandra <alessandra.bilardi@...> wrote: > Hello, > > I receive this question, but I think that Ryan will find here a > complete answer about his problems.. > > Alessandra. > > ---------- Forwarded message ---------- > From: Ryan Golhar <golharam@...> > Date: Thu, Oct 22, 2009 at 12:38 AM > Subject: WIG file display problem > To: info@... > > > Hi, > > I've set up a local instance of Gbrowse on my linux server. It runs > fine with the dataset I've loaded. > > Now, I'm trying to upload my own track in the form of a WIG file. > When I try to display it in Gbrowse, I get the following error in my > apache log: > > > [Wed Oct 21 19:07:09 2009] [error] [client 127.0.0.1] Subroutine > Bio::DB::SeqFeature::Store::berkeleydb::O_RDONLY redefined at > /usr/lib/perl5/5.8.8/Exporter.pm line 65, <F> line 21., referer: > http://localhost:8888/cgi-bin/gbrowse/arabidopsis/ > [Wed Oct 21 19:07:09 2009] [error] [client 127.0.0.1] at > /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm > line 10, referer: http://localhost:8888/cgi-bin/gbrowse/arabidopsis/ > > > I'm not using berkeleydb, I'm using mysql to store my data. If I > remove the WIG file from being displayed, these errors go away. Do > you know what I can do to resolve this? > > > > Here's a subset of the wig file I'm using: > > browser position chr1:1-47500 > browser hide all > browser pack refGene encodeRegions > track type=wiggle_0 name="testwig, chr1 positive strand" > description="testing wig file in gbrowse" visibility=full > color=0,0,255 yLineMark=0 yLineOnOff=on priority=10 > variableStep chrom=1 span=1 > 8429 24 > 8430 24 > 8431 24 > 8432 24 > 8433 24 > 8434 24 > 8435 24 > 8436 24 > 8437 24 > 8438 24 > 8439 24 > 8440 24 > 8441 24 > > > > -- > Alessandra Bilardi, Ph. D. > ---- > CRIBI, University of Padova, Italy > Via Ugo Bassi, 58/B - 35121 Padova > Tel +390498276165 Fax +390498276159 > http://www.linkedin.com/in/bilardi > ---- > La semplicità è la più alta forma di perfezione (Leonardo Da Vinci) > Keep simple, stupid (KISS, IT) > ---- > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Fwd: WIG file display problem
by Scott Cain-4
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HI Vipin,
I don't understand your email--is this related to the email that Alessandra forwarded to the mailing list? Scott On Thu, Oct 22, 2009 at 10:01 AM, Vipin TS <vipin.ts@...> wrote: > Hi Ryan, > > I tried to add the small example mentioned in the previous mail. It is > working fine in my local gbrowse instance. Please find the attached image > file with this mail. > > Here is the configuration stanza > > [ShortReadCoverage] > feature = src > glyph = wiggle_xyplot > glyph_type = boxes > min_score = 0 > max_score = 30 > height = 20 > fgcolor = black > bgcolor = skyblue > scale = right > category = Expression Tracks:Short read coverage experiments > key = Short Read Coverage Exp 1 > > > Regards, > Vipin T S > > > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: WIG file display problem
by Ryan Golhar
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I'm still unable to display my wig file. I've verified my installation
is clean...this is a new machine I set up just for gbrowse. All the other displays seems to work correctly. I'm still getting this error when trying to display a wig file. The display only shows a solid black line. Is this how a wig file is supposed to be displayed? I know the values are varying in the wig file itself, I would expect to see that in the display too. Scott Cain wrote: > Hi Ryan, > > I don't think the wiggle file itself is the problem; it is more likely > a configuration problem. See my comments in the previous email about > debugging and let us know if you still can't figure it out. > > Thanks, > Scott > > > On Thu, Oct 22, 2009 at 7:53 AM, Alessandra > <alessandra.bilardi@...> wrote: >> Hello, >> >> I receive this question, but I think that Ryan will find here a >> complete answer about his problems.. >> >> Alessandra. >> >> ---------- Forwarded message ---------- >> From: Ryan Golhar <golharam@...> >> Date: Thu, Oct 22, 2009 at 12:38 AM >> Subject: WIG file display problem >> To: info@... >> >> >> Hi, >> >> I've set up a local instance of Gbrowse on my linux server. It runs >> fine with the dataset I've loaded. >> >> Now, I'm trying to upload my own track in the form of a WIG file. >> When I try to display it in Gbrowse, I get the following error in my >> apache log: >> >> >> [Wed Oct 21 19:07:09 2009] [error] [client 127.0.0.1] Subroutine >> Bio::DB::SeqFeature::Store::berkeleydb::O_RDONLY redefined at >> /usr/lib/perl5/5.8.8/Exporter.pm line 65, <F> line 21., referer: >> http://localhost:8888/cgi-bin/gbrowse/arabidopsis/ >> [Wed Oct 21 19:07:09 2009] [error] [client 127.0.0.1] at >> /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/berkeleydb.pm >> line 10, referer: http://localhost:8888/cgi-bin/gbrowse/arabidopsis/ >> >> >> I'm not using berkeleydb, I'm using mysql to store my data. If I >> remove the WIG file from being displayed, these errors go away. Do >> you know what I can do to resolve this? >> >> >> >> Here's a subset of the wig file I'm using: >> >> browser position chr1:1-47500 >> browser hide all >> browser pack refGene encodeRegions >> track type=wiggle_0 name="testwig, chr1 positive strand" >> description="testing wig file in gbrowse" visibility=full >> color=0,0,255 yLineMark=0 yLineOnOff=on priority=10 >> variableStep chrom=1 span=1 >> 8429 24 >> 8430 24 >> 8431 24 >> 8432 24 >> 8433 24 >> 8434 24 >> 8435 24 >> 8436 24 >> 8437 24 >> 8438 24 >> 8439 24 >> 8440 24 >> 8441 24 >> >> >> >> -- >> Alessandra Bilardi, Ph. D. >> ---- >> CRIBI, University of Padova, Italy >> Via Ugo Bassi, 58/B - 35121 Padova >> Tel +390498276165 Fax +390498276159 >> http://www.linkedin.com/in/bilardi >> ---- >> La semplicità è la più alta forma di perfezione (Leonardo Da Vinci) >> Keep simple, stupid (KISS, IT) >> ---- >> >> ------------------------------------------------------------------------------ >> Come build with us! The BlackBerry(R) Developer Conference in SF, CA >> is the only developer event you need to attend this year. Jumpstart your >> developing skills, take BlackBerry mobile applications to market and stay >> ahead of the curve. Join us from November 9 - 12, 2009. Register now! >> http://p.sf.net/sfu/devconference >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> > > > ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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