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documentation on configuration file?
by Ryan Golhar
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Is there documentation on the configuration file? I can't seem to find
it from gbrowse.org. Also, I've removed everything related to track configurations and default features thinking I would have a clean display with no tracks. However, I consistently get Genes listed unnder the General for available tracks and Restriction Sites under Analysis. I don't have any mention of these tracks in my configuration file. Is this defaulting from somewhere? ------------------------------------------------------------------------------ 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: documentation on configuration file?
by Jan-Ole Christian
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I not experienced with gbrowse (yet), but I've got the experience, that
you sometimes have to delete the temporary files if you want to see the effects of changes in the configuration. You could also scroll/zoom to an area of you genome, that you never visited. This will enforce a new display of the tracks. Ryan Golhar schrieb: > Is there documentation on the configuration file? I can't seem to find > it from gbrowse.org. > > Also, I've removed everything related to track configurations and > default features thinking I would have a clean display with no tracks. > However, I consistently get Genes listed unnder the General for > available tracks and Restriction Sites under Analysis. > > I don't have any mention of these tracks in my configuration file. Is > this defaulting from somewhere? > > ------------------------------------------------------------------------------ > 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 > ------------------------------------------------------------------------------ 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: documentation on configuration file?
by Ryan Golhar
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I've tried that already. I've used the reset button, moving to a new
region, adding and removing other tracks in my config file but those two tracks consistently stay there and I have no idea how to get rid of them. Jan-Ole Christian wrote: > I not experienced with gbrowse (yet), but I've got the experience, that > you sometimes have to delete the temporary files if you want to see the > effects of changes in the configuration. > You could also scroll/zoom to an area of you genome, that you never > visited. This will enforce a new display of the tracks. > > > Ryan Golhar schrieb: >> Is there documentation on the configuration file? I can't seem to find >> it from gbrowse.org. >> >> Also, I've removed everything related to track configurations and >> default features thinking I would have a clean display with no tracks. >> However, I consistently get Genes listed unnder the General for >> available tracks and Restriction Sites under Analysis. >> >> I don't have any mention of these tracks in my configuration file. Is >> this defaulting from somewhere? >> >> ------------------------------------------------------------------------------ >> 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 >> > > > ------------------------------------------------------------------------------ > 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 > ------------------------------------------------------------------------------ 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: documentation on configuration file?
by Scott Cain-4
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Hello Ryan,
If you go to http://localhost/gbrowse (i.e., the computer where you have GBrowse installed local to you), you will find a page that points to several documentation items, including the link to the GBrowse Configuration HOWTO on gmod.org: http://gmod.org/wiki/CONFIGURE_HOWTO As for your specific questions, two things: * the Analysis section, that comes from plugins. Remove RestrictionAnnotator from the list of plugins. * For the Genes track, I suspect that you may not be looking at the correct url for the configuration file you are editing, or perhaps the page is being cached. Scott On Oct 27, 2009, at 12:41 PM, Ryan Golhar wrote: > Is there documentation on the configuration file? I can't seem to > find > it from gbrowse.org. > > Also, I've removed everything related to track configurations and > default features thinking I would have a clean display with no tracks. > However, I consistently get Genes listed unnder the General for > available tracks and Restriction Sites under Analysis. > > I don't have any mention of these tracks in my configuration file. Is > this defaulting from somewhere? > > ------------------------------------------------------------------------------ > 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: documentation on configuration file?
by Ryan Golhar
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Thanks Scott. Removing the RestrictionAnnotator did the trick for the
Restriction Sites. I don't think the Genes track is being cached, only because the Restriction sites came off and I've been adding other tracks and they show up. I've tried viewing the site from another computer and I still see Genes. Could it be from another plugin? Scott Cain wrote: > Hello Ryan, > > If you go to http://localhost/gbrowse (i.e., the computer where you have > GBrowse installed local to you), you will find a page that points to > several documentation items, including the link to the GBrowse > Configuration HOWTO on gmod.org: > > http://gmod.org/wiki/CONFIGURE_HOWTO > > As for your specific questions, two things: > > * the Analysis section, that comes from plugins. Remove > RestrictionAnnotator from the list of plugins. > > * For the Genes track, I suspect that you may not be looking at the > correct url for the configuration file you are editing, or perhaps the > page is being cached. > > Scott > > > On Oct 27, 2009, at 12:41 PM, Ryan Golhar wrote: > >> Is there documentation on the configuration file? I can't seem to find >> it from gbrowse.org. >> >> Also, I've removed everything related to track configurations and >> default features thinking I would have a clean display with no tracks. >> However, I consistently get Genes listed unnder the General for >> available tracks and Restriction Sites under Analysis. >> >> I don't have any mention of these tracks in my configuration file. Is >> this defaulting from somewhere? >> >> ------------------------------------------------------------------------------ >> >> 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: documentation on configuration file?
by Scott Cain-4
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Hi Ryan,
You can send the configuration file to the mailing list for us to look at if you want. Debugging without it is difficult. Scott On Tuesday, October 27, 2009, Ryan Golhar <golharam@...> wrote: > Thanks Scott. Removing the RestrictionAnnotator did the trick for the > Restriction Sites. > > I don't think the Genes track is being cached, only because the > Restriction sites came off and I've been adding other tracks and they > show up. I've tried viewing the site from another computer and I still > see Genes. Could it be from another plugin? > > Scott Cain wrote: >> Hello Ryan, >> >> If you go to http://localhost/gbrowse (i.e., the computer where you have >> GBrowse installed local to you), you will find a page that points to >> several documentation items, including the link to the GBrowse >> Configuration HOWTO on gmod.org: >> >> http://gmod.org/wiki/CONFIGURE_HOWTO >> >> As for your specific questions, two things: >> >> * the Analysis section, that comes from plugins. Remove >> RestrictionAnnotator from the list of plugins. >> >> * For the Genes track, I suspect that you may not be looking at the >> correct url for the configuration file you are editing, or perhaps the >> page is being cached. >> >> Scott >> >> >> On Oct 27, 2009, at 12:41 PM, Ryan Golhar wrote: >> >>> Is there documentation on the configuration file? I can't seem to find >>> it from gbrowse.org. >>> >>> Also, I've removed everything related to track configurations and >>> default features thinking I would have a clean display with no tracks. >>> However, I consistently get Genes listed unnder the General for >>> available tracks and Restriction Sites under Analysis. >>> >>> I don't have any mention of these tracks in my configuration file. Is >>> this defaulting from somewhere? >>> >>> ------------------------------------------------------------------------------ >>> >>> 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 > -- ------------------------------------------------------------------------ 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: documentation on configuration file?
by Ryan Golhar
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Here is the config file I'm using. There are no tracks listed, its a
blank template, yet Genes is still listed under General Scott Cain wrote: > Hi Ryan, > > You can send the configuration file to the mailing list for us to look > at if you want. Debugging without it is difficult. > > Scott > > > On Tuesday, October 27, 2009, Ryan Golhar <golharam@...> wrote: >> Thanks Scott. Removing the RestrictionAnnotator did the trick for the >> Restriction Sites. >> >> I don't think the Genes track is being cached, only because the >> Restriction sites came off and I've been adding other tracks and they >> show up. I've tried viewing the site from another computer and I still >> see Genes. Could it be from another plugin? >> >> Scott Cain wrote: >>> Hello Ryan, >>> >>> If you go to http://localhost/gbrowse (i.e., the computer where you have >>> GBrowse installed local to you), you will find a page that points to >>> several documentation items, including the link to the GBrowse >>> Configuration HOWTO on gmod.org: >>> >>> http://gmod.org/wiki/CONFIGURE_HOWTO >>> >>> As for your specific questions, two things: >>> >>> * the Analysis section, that comes from plugins. Remove >>> RestrictionAnnotator from the list of plugins. >>> >>> * For the Genes track, I suspect that you may not be looking at the >>> correct url for the configuration file you are editing, or perhaps the >>> page is being cached. >>> >>> Scott >>> >>> >>> On Oct 27, 2009, at 12:41 PM, Ryan Golhar wrote: >>> >>>> Is there documentation on the configuration file? I can't seem to find >>>> it from gbrowse.org. >>>> >>>> Also, I've removed everything related to track configurations and >>>> default features thinking I would have a clean display with no tracks. >>>> However, I consistently get Genes listed unnder the General for >>>> available tracks and Restriction Sites under Analysis. >>>> >>>> I don't have any mention of these tracks in my configuration file. Is >>>> this defaulting from somewhere? >>>> >>>> ------------------------------------------------------------------------------ >>>> >>>> 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 >> > [GENERAL] description = Arabidopsis thaliana TAIR9 db_adaptor = Bio::DB::SeqFeature::Store db_args = -adaptor DBI::mysql -dsn dbi:mysql:database=arabidopsis:cicdb2 -user apache aggretators = plugins = BatchDumper FastaDumper FilterTest Submitter # Web site configuration info gbrowse root = gbrowse stylesheet = gbrowse.css buttons = images/buttons js = js tmpimages = tmp region segment = 100000 initial landmark = chr1:143000..180000 # advanced features balloon tips = 1 drag and drop = 1 # one hour cache time = 1 # where to link to when user clicks in detailed view link = AUTO # what image widths to offer image widths = 450 640 800 1024 # color of the selection rectangle hilite fill = beige hilite outline = red # default width of detailed view (pixels) default width = 800 default features = # The class of the feature that is used as the reference for all others # "Sequence" is the default - change it if you use something else reference class = Sequence # max and default segment sizes for detailed view max segment = 500000 default segment = 50000 # zoom levels zoom levels = 50 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000 # whether to show the sources popup menu (0=false, 1=true; defaults to true) show sources = 1 # colors of the overview, detailed map and key overview bgcolor = lightgrey detailed bgcolor = lightgoldenrodyellow key bgcolor = beige # examples to show in the introduction examples = AT1G01040 AT3G52910.1 ABC11_171G2 AtMRP11 Chr1:1504365..1514364 ChrC:63781..68780 # "automatic" classes to try when an unqualified identifier is given automatic classes = Symbol Gene Clone chromosome gene five_prime_UTR mRNA mRNA_TE_gene exon three_prime_UTR ncRNA pseudogene pseudogenic_exon pseudogenic_transcript CA1mRNA CA1exon CA1cds CA1gene CA2mRNA CA2exon CA3mRNA CA3CDS_Eugene CA4mRNA CA4exon ### HTML TO INSERT AT VARIOUS STRATEGIC LOCATIONS ### # inside the <head></head> section head = # at the top... header = # a footer footer = <hr> <table width="100%"> <TR> <TD align="LEFT" class="databody"> For the source code for this browser, see the <a href="http://www.gmod.org"> Generic Model Organism Database Project.</a> For other questions, send mail to <a href="mailto:lstein@...">lstein@...</a>. </TD> </TR> </table> <hr> <pre>$Id: yeast.conf,v 1.4.2.9 2009/05/12 02:21:50 scottcain Exp $</pre> # Various places where you can insert your own HTML -- see configuration docs html1 = html2 = html3 = html4 = html5 = html6 = # Advanced feature: custom balloons custom balloons = [balloon] delayTime = 500 [balloon500] maxWidth = 500 delayTime = 50 # Advanced feature: an example of callbacks to be run remotely # by gbrowse_details for AJAX/iframe balloons [TOOLTIPS] intro = sub { my $args = shift; my $feat = $args->{feature}; my $name = $feat->display_name; my $type = $feat->primary_tag; my $class = $feat->class; my $extra = join(' ',$feat->each_tag_value('Note')) if $feat->has_tag('Note'); my $n = $type =~ /^[AEIOU]/i ? 'n' : ''; my $msg = "Hello, I am $name, a$n $type of class $class"; $msg .= "<br>I am described as a <i><b>$extra</b></i>" if $extra; $msg .= "<br>Click to see the sequence of $name"; return "<table><tr><th bgcolor='lightsteelblue'>$name</th><tr>" . "<tr><td>$msg</td></tr></table>"; } full_sequence = sub { my $args = shift; my $feat = $args->{feature}; my $name = $feat->display_name; my $seq = $feat->seq->seq; $seq =~ s/(\S{75})/$1\n/g; return "<pre style='font-size:8pt'>>$name\n$seq</pre>"; } # Advanced feature: an example of a customized popup mentu for rubber band selection [OVERVIEW SELECT MENU] width = 100 html = <table style="width:100%"> <tr> <th style="background:lightgrey"> Overview </span> </th> </tr> <tr> <td> <span style="color:blue;cursor:pointer" onclick="SelectArea.prototype.clearAndSubmit()"> Zoom </span> </td> </tr> <tr> <td> <span style="color:blue;cursor:pointer" onclick="SelectArea.prototype.cancelRubber()"> Cancel </span> </td> </tr> </table> [DETAIL SELECT MENU] width = 250 html = <table style="width:100%"> <tr> <th style="background:lightgrey;cell-padding:5"> SELECTION <span style="right:0px;position:absolute;color:blue;cursor:pointer" onclick="SelectArea.prototype.cancelRubber()"> [X] </span> </th> </tr> <tr> <td> <span style="color:blue;cursor:pointer" onclick="SelectArea.prototype.clearAndSubmit()"> Zoom in </span> </td> </tr> <tr> <td> <span style="color:blue;cursor:pointer" onclick="SelectArea.prototype.clearAndRecenter()"> Recenter on this region </span> </td> </tr> <tr> <td onmouseup="SelectArea.prototype.cancelRubber()"> <a href="?plugin=FastaDumper;plugin_action=Go;name=SELECTION" target="_BLANK"> Dump selection as FASTA </a> </td> </tr> <tr> <td onmouseup="SelectArea.prototype.cancelRubber()"> <a href="?name=SELECTION;plugin=Submitter;plugin_do=Go;Submitter.target=UCSC_BLAT" target="_BLANK"> Submit selection to UCSC BLAT </a> </td> </tr> <tr> <td onmouseup="SelectArea.prototype.cancelRubber()"> <a href="?name=SELECTION;plugin=Submitter;plugin_do=Go;Submitter.target=NCBI_BLAST" target="_BLANK"> Submit selection to NCBI BLAST </a> </td> </tr> </table> # Configuration for submitter plugin (used in above menu) [Submitter:plugin] submitter = [UCSC_BLAT] url = http://genome.ucsc.edu/cgi-bin/hgBlat seq_label = userSeq output = hyperlink type = DNA extra_html = Genome: <SELECT name=org> <OPTION VALUE="Human">Human</OPTION> <OPTION VALUE="Chimp">Chimp</OPTION> <OPTION VALUE="Rhesus">Rhesus</OPTION> <OPTION VALUE="Mouse">Mouse</OPTION> <OPTION VALUE="Stickleback">Stickleback</OPTION> <OPTION VALUE="Medaka">Medaka</OPTION> <OPTION VALUE="C. intestinalis">C. intestinalis</OPTION> <OPTION VALUE="S. purpuratus">S. purpuratus</OPTION> <OPTION VALUE="D. persimilis">D. persimilis</OPTION> <OPTION VALUE="D. virilis">D. virilis</OPTION> <OPTION VALUE="D. mojavensis">D. mojavensis</OPTION> <OPTION VALUE="D. grimshawi">D. grimshawi</OPTION> <OPTION VALUE="A. gambiae">A. gambiae</OPTION> <OPTION VALUE="A. mellifera">A. mellifera</OPTION> <OPTION SELECTED VALUE="S. cerevisiae">S. cerevisiae</OPTION> <OPTION VALUE="SARS">SARS</OPTION> </SELECT> [NCBI_BLAST] confirm = 1 url = http://www.ncbi.nlm.nih.gov/blast/Blast.cgi seq_label = QUERY PAGE = Nucleotides PROGRAM = blastn DATABASE = nr CLIENT = web CMD = put # Default glyph settings [TRACK DEFAULTS] glyph = generic height = 8 bgcolor = cyan fgcolor = cyan label density = 25 bump density = 100 # default pop-up balloon balloon hover = <b>$name</b> is a $type spanning $ref from $start to $end. Click for more details. ### TRACK CONFIGURATION #### # the remainder of the sections configure individual tracks ------------------------------------------------------------------------------ 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: documentation on configuration file?
by Scott Cain-4
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Hi Ryan,
Just so you know, you're not crazy: I reproduced the same behavior with the phantom Genes track. It looks like I have a homework assignment for tonight. I'll let you know what I find. I have a question for you as an aside: what email client are you using? While I assume you sent that conf file as an attachment, both the Apple mail client and the Google web interface put the files inline, so there was no "download this file" option. Strange. Scott On Oct 27, 2009, at 4:34 PM, Ryan Golhar wrote: > Here is the config file I'm using. There are no tracks listed, its > a blank template, yet Genes is still listed under General > > > > Scott Cain wrote: >> Hi Ryan, >> You can send the configuration file to the mailing list for us to >> look >> at if you want. Debugging without it is difficult. >> Scott >> On Tuesday, October 27, 2009, Ryan Golhar <golharam@...> wrote: >>> Thanks Scott. Removing the RestrictionAnnotator did the trick for >>> the >>> Restriction Sites. >>> >>> I don't think the Genes track is being cached, only because the >>> Restriction sites came off and I've been adding other tracks and >>> they >>> show up. I've tried viewing the site from another computer and I >>> still >>> see Genes. Could it be from another plugin? >>> >>> Scott Cain wrote: >>>> Hello Ryan, >>>> >>>> If you go to http://localhost/gbrowse (i.e., the computer where >>>> you have >>>> GBrowse installed local to you), you will find a page that points >>>> to >>>> several documentation items, including the link to the GBrowse >>>> Configuration HOWTO on gmod.org: >>>> >>>> http://gmod.org/wiki/CONFIGURE_HOWTO >>>> >>>> As for your specific questions, two things: >>>> >>>> * the Analysis section, that comes from plugins. Remove >>>> RestrictionAnnotator from the list of plugins. >>>> >>>> * For the Genes track, I suspect that you may not be looking at the >>>> correct url for the configuration file you are editing, or >>>> perhaps the >>>> page is being cached. >>>> >>>> Scott >>>> >>>> >>>> On Oct 27, 2009, at 12:41 PM, Ryan Golhar wrote: >>>> >>>>> Is there documentation on the configuration file? I can't seem >>>>> to find >>>>> it from gbrowse.org. >>>>> >>>>> Also, I've removed everything related to track configurations and >>>>> default features thinking I would have a clean display with no >>>>> tracks. >>>>> However, I consistently get Genes listed unnder the General for >>>>> available tracks and Restriction Sites under Analysis. >>>>> >>>>> I don't have any mention of these tracks in my configuration >>>>> file. Is >>>>> this defaulting from somewhere? >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> >>>>> 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 >>> > [GENERAL] > description = Arabidopsis thaliana TAIR9 > db_adaptor = Bio::DB::SeqFeature::Store > db_args = -adaptor DBI::mysql > -dsn dbi:mysql:database=arabidopsis:cicdb2 > -user apache > > aggretators = > plugins = BatchDumper FastaDumper FilterTest Submitter > > # Web site configuration info > gbrowse root = gbrowse > stylesheet = gbrowse.css > buttons = images/buttons > js = js > tmpimages = tmp > > region segment = 100000 > initial landmark = chr1:143000..180000 > > # advanced features > balloon tips = 1 > drag and drop = 1 > > # one hour > cache time = 1 > > # where to link to when user clicks in detailed view > link = AUTO > > # what image widths to offer > image widths = 450 640 800 1024 > > # color of the selection rectangle > hilite fill = beige > hilite outline = red > > # default width of detailed view (pixels) > default width = 800 > default features = > > # The class of the feature that is used as the reference for all > others > # "Sequence" is the default - change it if you use something else > reference class = Sequence > > # max and default segment sizes for detailed view > max segment = 500000 > default segment = 50000 > > # zoom levels > zoom levels = 50 100 200 1000 2000 5000 10000 20000 40000 100000 > 200000 500000 1000000 > > # whether to show the sources popup menu (0=false, 1=true; defaults > to true) > show sources = 1 > > # colors of the overview, detailed map and key > overview bgcolor = lightgrey > detailed bgcolor = lightgoldenrodyellow > key bgcolor = beige > > # examples to show in the introduction > examples = AT1G01040 AT3G52910.1 ABC11_171G2 AtMRP11 > Chr1:1504365..1514364 ChrC:63781..68780 > > # "automatic" classes to try when an unqualified identifier is given > automatic classes = Symbol Gene Clone chromosome gene five_prime_UTR > mRNA mRNA_TE_gene exon three_prime_UTR ncRNA pseudogene > pseudogenic_exon pseudogenic_transcript CA1mRNA CA1exon CA1cds > CA1gene CA2mRNA CA2exon CA3mRNA CA3CDS_Eugene CA4mRNA CA4exon > > ### HTML TO INSERT AT VARIOUS STRATEGIC LOCATIONS ### > # inside the <head></head> section > head = > > # at the top... > header = > > # a footer > footer = <hr> > <table width="100%"> > <TR> > <TD align="LEFT" class="databody"> > For the source code for this browser, see the <a href="http://www.gmod.org > "> > Generic Model Organism Database Project.</a> For other questions, > send > mail to <a href="mailto:lstein@...">lstein@...</a>. > </TD> > </TR> > </table> > <hr> > <pre>$Id: yeast.conf,v 1.4.2.9 2009/05/12 02:21:50 scottcain Exp $</ > pre> > > # Various places where you can insert your own HTML -- see > configuration docs > html1 = > html2 = > html3 = > html4 = > html5 = > html6 = > > # Advanced feature: custom balloons > custom balloons = [balloon] > delayTime = 500 > > [balloon500] > maxWidth = 500 > delayTime = 50 > > > # Advanced feature: an example of callbacks to be run remotely > # by gbrowse_details for AJAX/iframe balloons > [TOOLTIPS] > intro = sub { > my $args = shift; > my $feat = $args->{feature}; > my $name = $feat->display_name; > my $type = $feat->primary_tag; > my $class = $feat->class; > my $extra = join(' ',$feat->each_tag_value('Note')) > if $feat->has_tag('Note'); > my $n = $type =~ /^[AEIOU]/i ? 'n' : ''; > my $msg = "Hello, I am $name, a$n $type of class > $class"; > $msg .= "<br>I am described as a <i><b>$extra</ > b></i>" if $extra; > $msg .= "<br>Click to see the sequence of $name"; > return "<table><tr><th bgcolor='lightsteelblue'> > $name</th><tr>" . > "<tr><td>$msg</td></tr></table>"; > } > full_sequence = sub { > my $args = shift; > my $feat = $args->{feature}; > my $name = $feat->display_name; > my $seq = $feat->seq->seq; > $seq =~ s/(\S{75})/$1\n/g; > return "<pre style='font-size:8pt'>>$name\n$seq</pre>"; > } > > # Advanced feature: an example of a customized popup mentu for > rubber band selection > [OVERVIEW SELECT MENU] > width = 100 > html = <table style="width:100%"> > <tr> > <th style="background:lightgrey"> > Overview > </span> > </th> > </tr> > <tr> > <td> > <span style="color:blue;cursor:pointer" > onclick="SelectArea.prototype.clearAndSubmit()"> > Zoom > </span> > </td> > </tr> > <tr> > <td> > <span style="color:blue;cursor:pointer" > onclick="SelectArea.prototype.cancelRubber()"> > Cancel > </span> > </td> > </tr> > </table> > > > [DETAIL SELECT MENU] > width = 250 > html = <table style="width:100%"> > <tr> > <th style="background:lightgrey;cell-padding:5"> > SELECTION > <span style="right: > 0px;position:absolute;color:blue;cursor:pointer" > onclick="SelectArea.prototype.cancelRubber()"> > [X] > </span> > </th> > </tr> > <tr> > <td> > <span style="color:blue;cursor:pointer" > onclick="SelectArea.prototype.clearAndSubmit()"> > Zoom in > </span> > </td> > </tr> > <tr> > <td> > <span style="color:blue;cursor:pointer" > onclick="SelectArea.prototype.clearAndRecenter()"> > Recenter on this region > </span> > </td> > </tr> > <tr> > <td onmouseup="SelectArea.prototype.cancelRubber()"> > <a href="? > plugin=FastaDumper;plugin_action=Go;name=SELECTION" target="_BLANK"> > Dump selection as FASTA > </a> > </td> > </tr> > <tr> > <td onmouseup="SelectArea.prototype.cancelRubber()"> > <a href="? > name > =SELECTION;plugin=Submitter;plugin_do=Go;Submitter.target=UCSC_BLAT" > target="_BLANK"> > Submit selection to UCSC BLAT > </a> > </td> > </tr> > <tr> > <td onmouseup="SelectArea.prototype.cancelRubber()"> > <a href="? > name > = > SELECTION;plugin=Submitter;plugin_do=Go;Submitter.target=NCBI_BLAST" > target="_BLANK"> > Submit selection to NCBI BLAST > </a> > </td> > </tr> > </table> > > # Configuration for submitter plugin (used in above menu) > [Submitter:plugin] > submitter = [UCSC_BLAT] > url = http://genome.ucsc.edu/cgi-bin/hgBlat > seq_label = userSeq > output = hyperlink > type = DNA > extra_html = Genome: > <SELECT name=org> > <OPTION VALUE="Human">Human</OPTION> > <OPTION VALUE="Chimp">Chimp</OPTION> > <OPTION VALUE="Rhesus">Rhesus</OPTION> > <OPTION VALUE="Mouse">Mouse</OPTION> > <OPTION VALUE="Stickleback">Stickleback</ > OPTION> > <OPTION VALUE="Medaka">Medaka</OPTION> > <OPTION VALUE="C. intestinalis">C. > intestinalis</OPTION> > <OPTION VALUE="S. purpuratus">S. purpuratus</ > OPTION> > <OPTION VALUE="D. persimilis">D. persimilis</ > OPTION> > <OPTION VALUE="D. virilis">D. virilis</OPTION> > <OPTION VALUE="D. mojavensis">D. mojavensis</ > OPTION> > <OPTION VALUE="D. grimshawi">D. grimshawi</ > OPTION> > <OPTION VALUE="A. gambiae">A. gambiae</OPTION> > <OPTION VALUE="A. mellifera">A. mellifera</ > OPTION> > <OPTION SELECTED VALUE="S. cerevisiae">S. > cerevisiae</OPTION> > <OPTION VALUE="SARS">SARS</OPTION> > </SELECT> > > [NCBI_BLAST] > confirm = 1 > url = http://www.ncbi.nlm.nih.gov/blast/Blast.cgi > seq_label = QUERY > PAGE = Nucleotides > PROGRAM = blastn > DATABASE = nr > CLIENT = web > CMD = put > > > > # Default glyph settings > [TRACK DEFAULTS] > glyph = generic > height = 8 > bgcolor = cyan > fgcolor = cyan > label density = 25 > bump density = 100 > # default pop-up balloon > balloon hover = <b>$name</b> is a $type spanning $ref from $start to > $end. Click for more details. > > ### TRACK CONFIGURATION #### > # the remainder of the sections configure individual tracks > > > ------------------------------------------------------------------------------ > 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: documentation on configuration file?
by Wes Barris
::
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Ryan Golhar wrote:
> Here is the config file I'm using. There are no tracks listed, its a > blank template, yet Genes is still listed under General Remove the "FilterTest" plugin from the .conf file and your "Gene" track will go away. I don't know what the FilterTest plugin does. I ran into this same problem a while ago. > Scott Cain wrote: >> Hi Ryan, >> >> You can send the configuration file to the mailing list for us to look >> at if you want. Debugging without it is difficult. >> >> Scott >> >> >> On Tuesday, October 27, 2009, Ryan Golhar <golharam@...> wrote: >>> Thanks Scott. Removing the RestrictionAnnotator did the trick for the >>> Restriction Sites. >>> >>> I don't think the Genes track is being cached, only because the >>> Restriction sites came off and I've been adding other tracks and they >>> show up. I've tried viewing the site from another computer and I still >>> see Genes. Could it be from another plugin? >>> >>> Scott Cain wrote: >>>> Hello Ryan, >>>> >>>> If you go to http://localhost/gbrowse (i.e., the computer where you have >>>> GBrowse installed local to you), you will find a page that points to >>>> several documentation items, including the link to the GBrowse >>>> Configuration HOWTO on gmod.org: >>>> >>>> http://gmod.org/wiki/CONFIGURE_HOWTO >>>> >>>> As for your specific questions, two things: >>>> >>>> * the Analysis section, that comes from plugins. Remove >>>> RestrictionAnnotator from the list of plugins. >>>> >>>> * For the Genes track, I suspect that you may not be looking at the >>>> correct url for the configuration file you are editing, or perhaps the >>>> page is being cached. >>>> >>>> Scott >>>> >>>> >>>> On Oct 27, 2009, at 12:41 PM, Ryan Golhar wrote: >>>> >>>>> Is there documentation on the configuration file? I can't seem to find >>>>> it from gbrowse.org. >>>>> >>>>> Also, I've removed everything related to track configurations and >>>>> default features thinking I would have a clean display with no tracks. >>>>> However, I consistently get Genes listed unnder the General for >>>>> available tracks and Restriction Sites under Analysis. >>>>> >>>>> I don't have any mention of these tracks in my configuration file. Is >>>>> this defaulting from somewhere? >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> >>>>> 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 >>> -- Wes Barris <wes.barris@...> ------------------------------------------------------------------------------ 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: documentation on configuration file?
by Scott Cain-4
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Ah, weird. I don't remember seeing that before. Amusingly, if you
are using the yeast sample data, with a track whose "real" name is "Genes" (but whose display name is "Named genes"), the spurious Genes track is not present, but but if the Named genes track is taken out, the FilterTest-derived track appears. Thanks for pointing that out so I can get to sleep at a reasonable hour tonight :-) Scott On Tue, Oct 27, 2009 at 7:47 PM, Wes Barris <wes.barris@...> wrote: > Ryan Golhar wrote: >> Here is the config file I'm using. There are no tracks listed, its a >> blank template, yet Genes is still listed under General > > Remove the "FilterTest" plugin from the .conf file and your "Gene" > track will go away. I don't know what the FilterTest plugin does. > I ran into this same problem a while ago. > >> Scott Cain wrote: >>> Hi Ryan, >>> >>> You can send the configuration file to the mailing list for us to look >>> at if you want. Debugging without it is difficult. >>> >>> Scott >>> >>> >>> On Tuesday, October 27, 2009, Ryan Golhar <golharam@...> wrote: >>>> Thanks Scott. Removing the RestrictionAnnotator did the trick for the >>>> Restriction Sites. >>>> >>>> I don't think the Genes track is being cached, only because the >>>> Restriction sites came off and I've been adding other tracks and they >>>> show up. I've tried viewing the site from another computer and I still >>>> see Genes. Could it be from another plugin? >>>> >>>> Scott Cain wrote: >>>>> Hello Ryan, >>>>> >>>>> If you go to http://localhost/gbrowse (i.e., the computer where you have >>>>> GBrowse installed local to you), you will find a page that points to >>>>> several documentation items, including the link to the GBrowse >>>>> Configuration HOWTO on gmod.org: >>>>> >>>>> http://gmod.org/wiki/CONFIGURE_HOWTO >>>>> >>>>> As for your specific questions, two things: >>>>> >>>>> * the Analysis section, that comes from plugins. Remove >>>>> RestrictionAnnotator from the list of plugins. >>>>> >>>>> * For the Genes track, I suspect that you may not be looking at the >>>>> correct url for the configuration file you are editing, or perhaps the >>>>> page is being cached. >>>>> >>>>> Scott >>>>> >>>>> >>>>> On Oct 27, 2009, at 12:41 PM, Ryan Golhar wrote: >>>>> >>>>>> Is there documentation on the configuration file? I can't seem to find >>>>>> it from gbrowse.org. >>>>>> >>>>>> Also, I've removed everything related to track configurations and >>>>>> default features thinking I would have a clean display with no tracks. >>>>>> However, I consistently get Genes listed unnder the General for >>>>>> available tracks and Restriction Sites under Analysis. >>>>>> >>>>>> I don't have any mention of these tracks in my configuration file. Is >>>>>> this defaulting from somewhere? >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> >>>>>> 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 >>>> > > > -- > Wes Barris <wes.barris@...> > > ------------------------------------------------------------------------------ > 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: documentation on configuration file?
by Ryan Golhar
::
Rate this Message:
Thanks!
Wes Barris wrote: > Ryan Golhar wrote: >> Here is the config file I'm using. There are no tracks listed, its a >> blank template, yet Genes is still listed under General > > Remove the "FilterTest" plugin from the .conf file and your "Gene" > track will go away. I don't know what the FilterTest plugin does. > I ran into this same problem a while ago. > >> Scott Cain wrote: >>> Hi Ryan, >>> >>> You can send the configuration file to the mailing list for us to look >>> at if you want. Debugging without it is difficult. >>> >>> Scott >>> >>> >>> On Tuesday, October 27, 2009, Ryan Golhar <golharam@...> wrote: >>>> Thanks Scott. Removing the RestrictionAnnotator did the trick for the >>>> Restriction Sites. >>>> >>>> I don't think the Genes track is being cached, only because the >>>> Restriction sites came off and I've been adding other tracks and they >>>> show up. I've tried viewing the site from another computer and I still >>>> see Genes. Could it be from another plugin? >>>> >>>> Scott Cain wrote: >>>>> Hello Ryan, >>>>> >>>>> If you go to http://localhost/gbrowse (i.e., the computer where you >>>>> have >>>>> GBrowse installed local to you), you will find a page that points to >>>>> several documentation items, including the link to the GBrowse >>>>> Configuration HOWTO on gmod.org: >>>>> >>>>> http://gmod.org/wiki/CONFIGURE_HOWTO >>>>> >>>>> As for your specific questions, two things: >>>>> >>>>> * the Analysis section, that comes from plugins. Remove >>>>> RestrictionAnnotator from the list of plugins. >>>>> >>>>> * For the Genes track, I suspect that you may not be looking at the >>>>> correct url for the configuration file you are editing, or perhaps the >>>>> page is being cached. >>>>> >>>>> Scott >>>>> >>>>> >>>>> On Oct 27, 2009, at 12:41 PM, Ryan Golhar wrote: >>>>> >>>>>> Is there documentation on the configuration file? I can't seem to >>>>>> find >>>>>> it from gbrowse.org. >>>>>> >>>>>> Also, I've removed everything related to track configurations and >>>>>> default features thinking I would have a clean display with no >>>>>> tracks. >>>>>> However, I consistently get Genes listed unnder the General for >>>>>> available tracks and Restriction Sites under Analysis. >>>>>> >>>>>> I don't have any mention of these tracks in my configuration >>>>>> file. Is >>>>>> this defaulting from somewhere? >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> >>>>>> >>>>>> 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 >>>> > > ------------------------------------------------------------------------------ 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: documentation on configuration file?
by Ryan Golhar
::
Rate this Message:
I'm using Thunderbird on Mac...
Scott Cain wrote: > Hi Ryan, > > Just so you know, you're not crazy: I reproduced the same behavior with > the phantom Genes track. It looks like I have a homework assignment for > tonight. I'll let you know what I find. > > I have a question for you as an aside: what email client are you using? > While I assume you sent that conf file as an attachment, both the Apple > mail client and the Google web interface put the files inline, so there > was no "download this file" option. Strange. > > Scott > > > On Oct 27, 2009, at 4:34 PM, Ryan Golhar wrote: > >> Here is the config file I'm using. There are no tracks listed, its a >> blank template, yet Genes is still listed under General >> >> >> >> Scott Cain wrote: >>> Hi Ryan, >>> You can send the configuration file to the mailing list for us to look >>> at if you want. Debugging without it is difficult. >>> Scott >>> On Tuesday, October 27, 2009, Ryan Golhar <golharam@...> wrote: >>>> Thanks Scott. Removing the RestrictionAnnotator did the trick for the >>>> Restriction Sites. >>>> >>>> I don't think the Genes track is being cached, only because the >>>> Restriction sites came off and I've been adding other tracks and they >>>> show up. I've tried viewing the site from another computer and I still >>>> see Genes. Could it be from another plugin? >>>> >>>> Scott Cain wrote: >>>>> Hello Ryan, >>>>> >>>>> If you go to http://localhost/gbrowse (i.e., the computer where you >>>>> have >>>>> GBrowse installed local to you), you will find a page that points to >>>>> several documentation items, including the link to the GBrowse >>>>> Configuration HOWTO on gmod.org: >>>>> >>>>> http://gmod.org/wiki/CONFIGURE_HOWTO >>>>> >>>>> As for your specific questions, two things: >>>>> >>>>> * the Analysis section, that comes from plugins. Remove >>>>> RestrictionAnnotator from the list of plugins. >>>>> >>>>> * For the Genes track, I suspect that you may not be looking at the >>>>> correct url for the configuration file you are editing, or perhaps the >>>>> page is being cached. >>>>> >>>>> Scott >>>>> >>>>> >>>>> On Oct 27, 2009, at 12:41 PM, Ryan Golhar wrote: >>>>> >>>>>> Is there documentation on the configuration file? I can't seem to >>>>>> find >>>>>> it from gbrowse.org. >>>>>> >>>>>> Also, I've removed everything related to track configurations and >>>>>> default features thinking I would have a clean display with no >>>>>> tracks. >>>>>> However, I consistently get Genes listed unnder the General for >>>>>> available tracks and Restriction Sites under Analysis. >>>>>> >>>>>> I don't have any mention of these tracks in my configuration >>>>>> file. Is >>>>>> this defaulting from somewhere? >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> >>>>>> >>>>>> 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 >>>> >> [GENERAL] >> description = Arabidopsis thaliana TAIR9 >> db_adaptor = Bio::DB::SeqFeature::Store >> db_args = -adaptor DBI::mysql >> -dsn dbi:mysql:database=arabidopsis:cicdb2 >> -user apache >> >> aggretators = >> plugins = BatchDumper FastaDumper FilterTest Submitter >> >> # Web site configuration info >> gbrowse root = gbrowse >> stylesheet = gbrowse.css >> buttons = images/buttons >> js = js >> tmpimages = tmp >> >> region segment = 100000 >> initial landmark = chr1:143000..180000 >> >> # advanced features >> balloon tips = 1 >> drag and drop = 1 >> >> # one hour >> cache time = 1 >> >> # where to link to when user clicks in detailed view >> link = AUTO >> >> # what image widths to offer >> image widths = 450 640 800 1024 >> >> # color of the selection rectangle >> hilite fill = beige >> hilite outline = red >> >> # default width of detailed view (pixels) >> default width = 800 >> default features = >> >> # The class of the feature that is used as the reference for all others >> # "Sequence" is the default - change it if you use something else >> reference class = Sequence >> >> # max and default segment sizes for detailed view >> max segment = 500000 >> default segment = 50000 >> >> # zoom levels >> zoom levels = 50 100 200 1000 2000 5000 10000 20000 40000 100000 >> 200000 500000 1000000 >> >> # whether to show the sources popup menu (0=false, 1=true; defaults to >> true) >> show sources = 1 >> >> # colors of the overview, detailed map and key >> overview bgcolor = lightgrey >> detailed bgcolor = lightgoldenrodyellow >> key bgcolor = beige >> >> # examples to show in the introduction >> examples = AT1G01040 AT3G52910.1 ABC11_171G2 AtMRP11 >> Chr1:1504365..1514364 ChrC:63781..68780 >> >> # "automatic" classes to try when an unqualified identifier is given >> automatic classes = Symbol Gene Clone chromosome gene five_prime_UTR >> mRNA mRNA_TE_gene exon three_prime_UTR ncRNA pseudogene >> pseudogenic_exon pseudogenic_transcript CA1mRNA CA1exon CA1cds CA1gene >> CA2mRNA CA2exon CA3mRNA CA3CDS_Eugene CA4mRNA CA4exon >> >> ### HTML TO INSERT AT VARIOUS STRATEGIC LOCATIONS ### >> # inside the <head></head> section >> head = >> >> # at the top... >> header = >> >> # a footer >> footer = <hr> >> <table width="100%"> >> <TR> >> <TD align="LEFT" class="databody"> >> For the source code for this browser, see the <a >> href="http://www.gmod.org"> >> Generic Model Organism Database Project.</a> For other questions, >> send >> mail to <a href="mailto:lstein@...">lstein@...</a>. >> </TD> >> </TR> >> </table> >> <hr> >> <pre>$Id: yeast.conf,v 1.4.2.9 2009/05/12 02:21:50 scottcain Exp >> $</pre> >> >> # Various places where you can insert your own HTML -- see >> configuration docs >> html1 = >> html2 = >> html3 = >> html4 = >> html5 = >> html6 = >> >> # Advanced feature: custom balloons >> custom balloons = [balloon] >> delayTime = 500 >> >> [balloon500] >> maxWidth = 500 >> delayTime = 50 >> >> >> # Advanced feature: an example of callbacks to be run remotely >> # by gbrowse_details for AJAX/iframe balloons >> [TOOLTIPS] >> intro = sub { >> my $args = shift; >> my $feat = $args->{feature}; >> my $name = $feat->display_name; >> my $type = $feat->primary_tag; >> my $class = $feat->class; >> my $extra = join(' ',$feat->each_tag_value('Note')) if >> $feat->has_tag('Note'); >> my $n = $type =~ /^[AEIOU]/i ? 'n' : ''; >> my $msg = "Hello, I am $name, a$n $type of class >> $class"; >> $msg .= "<br>I am described as a >> <i><b>$extra</b></i>" if $extra; >> $msg .= "<br>Click to see the sequence of $name"; >> return "<table><tr><th >> bgcolor='lightsteelblue'>$name</th><tr>" . >> "<tr><td>$msg</td></tr></table>"; >> } >> full_sequence = sub { >> my $args = shift; >> my $feat = $args->{feature}; >> my $name = $feat->display_name; >> my $seq = $feat->seq->seq; >> $seq =~ s/(\S{75})/$1\n/g; >> return "<pre style='font-size:8pt'>>$name\n$seq</pre>"; >> } >> >> # Advanced feature: an example of a customized popup mentu for rubber >> band selection >> [OVERVIEW SELECT MENU] >> width = 100 >> html = <table style="width:100%"> >> <tr> >> <th style="background:lightgrey"> >> Overview >> </span> >> </th> >> </tr> >> <tr> >> <td> >> <span style="color:blue;cursor:pointer" >> onclick="SelectArea.prototype.clearAndSubmit()"> >> Zoom >> </span> >> </td> >> </tr> >> <tr> >> <td> >> <span style="color:blue;cursor:pointer" >> onclick="SelectArea.prototype.cancelRubber()"> >> Cancel >> </span> >> </td> >> </tr> >> </table> >> >> >> [DETAIL SELECT MENU] >> width = 250 >> html = <table style="width:100%"> >> <tr> >> <th style="background:lightgrey;cell-padding:5"> >> SELECTION >> <span >> style="right:0px;position:absolute;color:blue;cursor:pointer" >> onclick="SelectArea.prototype.cancelRubber()"> >> [X] >> </span> >> </th> >> </tr> >> <tr> >> <td> >> <span style="color:blue;cursor:pointer" >> onclick="SelectArea.prototype.clearAndSubmit()"> >> Zoom in >> </span> >> </td> >> </tr> >> <tr> >> <td> >> <span style="color:blue;cursor:pointer" >> onclick="SelectArea.prototype.clearAndRecenter()"> >> Recenter on this region >> </span> >> </td> >> </tr> >> <tr> >> <td onmouseup="SelectArea.prototype.cancelRubber()"> >> <a >> href="?plugin=FastaDumper;plugin_action=Go;name=SELECTION" >> target="_BLANK"> >> Dump selection as FASTA >> </a> >> </td> >> </tr> >> <tr> >> <td onmouseup="SelectArea.prototype.cancelRubber()"> >> <a >> href="?name=SELECTION;plugin=Submitter;plugin_do=Go;Submitter.target=UCSC_BLAT" >> target="_BLANK"> >> Submit selection to UCSC BLAT >> </a> >> </td> >> </tr> >> <tr> >> <td onmouseup="SelectArea.prototype.cancelRubber()"> >> <a >> href="?name=SELECTION;plugin=Submitter;plugin_do=Go;Submitter.target=NCBI_BLAST" >> target="_BLANK"> >> Submit selection to NCBI BLAST >> </a> >> </td> >> </tr> >> </table> >> >> # Configuration for submitter plugin (used in above menu) >> [Submitter:plugin] >> submitter = [UCSC_BLAT] >> url = http://genome.ucsc.edu/cgi-bin/hgBlat >> seq_label = userSeq >> output = hyperlink >> type = DNA >> extra_html = Genome: >> <SELECT name=org> >> <OPTION VALUE="Human">Human</OPTION> >> <OPTION VALUE="Chimp">Chimp</OPTION> >> <OPTION VALUE="Rhesus">Rhesus</OPTION> >> <OPTION VALUE="Mouse">Mouse</OPTION> >> <OPTION VALUE="Stickleback">Stickleback</OPTION> >> <OPTION VALUE="Medaka">Medaka</OPTION> >> <OPTION VALUE="C. intestinalis">C. >> intestinalis</OPTION> >> <OPTION VALUE="S. purpuratus">S. >> purpuratus</OPTION> >> <OPTION VALUE="D. persimilis">D. >> persimilis</OPTION> >> <OPTION VALUE="D. virilis">D. virilis</OPTION> >> <OPTION VALUE="D. mojavensis">D. >> mojavensis</OPTION> >> <OPTION VALUE="D. grimshawi">D. >> grimshawi</OPTION> >> <OPTION VALUE="A. gambiae">A. gambiae</OPTION> >> <OPTION VALUE="A. mellifera">A. >> mellifera</OPTION> >> <OPTION SELECTED VALUE="S. cerevisiae">S. >> cerevisiae</OPTION> >> <OPTION VALUE="SARS">SARS</OPTION> >> </SELECT> >> >> [NCBI_BLAST] >> confirm = 1 >> url = http://www.ncbi.nlm.nih.gov/blast/Blast.cgi >> seq_label = QUERY >> PAGE = Nucleotides >> PROGRAM = blastn >> DATABASE = nr >> CLIENT = web >> CMD = put >> >> >> >> # Default glyph settings >> [TRACK DEFAULTS] >> glyph = generic >> height = 8 >> bgcolor = cyan >> fgcolor = cyan >> label density = 25 >> bump density = 100 >> # default pop-up balloon >> balloon hover = <b>$name</b> is a $type spanning $ref from $start to >> $end. Click for more details. >> >> ### TRACK CONFIGURATION #### >> # the remainder of the sections configure individual tracks >> >> >> ------------------------------------------------------------------------------ >> >> 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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