Hi,<br>The sample (yeast) database works good for me.However,myself not.Event simplest database do not work(not coordinate show nor can not search).<br>For the general GBrowse.conf part.I only add lines:<br><br>[annoproject]<br>
description = annoproject<br>path = annoproject.conf<br><br>For annoproject.conf content is :<br>[GENERAL]<br>description = annoproject<br>
database = annoproject <br>default tracks = CYT:overview<br>default width = 800<br>automatic classes = chromosome Sequence<br>[annoproject:database]<br>db_adaptor = Bio::DB::SeqFeature::Store<br>db_args = -adaptor memory<br>
-dir /var/www/html/gbrowse2/<div class="gmail_quote">databases/annoproject<br>cache_overview = 0<br>[TRACK DEFAULTS]<br>glyph = generic<br>database = annoproject<br>height = 8<br>bgcolor = black<br>
fgcolor = black<br>
label density = 50<br>bump density = 100<br>[CYT:overview]<br>feature = chromosome<br>glyph = generic<br>stranded = 1<br>bgcolor = grey<br>fgcolor = black<br>height = 10<br><br>My .gff data is :<br>
<br>
##gff-version 3<br>chr1 ensembl chromosome 1 245522847 . . . ID=chr1;Name=chr1<br>chr11 ensembl chromosome 1 134452384 . . . ID=chr11;Name=chr11<br>chr12 ensembl chromosome 1 132449811 . . . ID=chr12;Name=chr12</div>
<br>It still have error.<br><div class="gmail_quote">2009/6/11 Dave Clements, GMOD Help Desk <span dir="ltr"><<a href="mailto:gmodhelp@googlemail.com">gmodhelp@googlemail.com</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>Hi Josh,<br></div><div></div><div>The email below implies that you have a single .conf file. If you are running GBrowse 2 you'll need a general .conf and an organism specific .conf file. See <a href="http://gmod.org/wiki/GBrowse_2.0_HOWTO" target="_blank">http://gmod.org/wiki/GBrowse_2.0_HOWTO</a> for more. Please pay particular attention to the part on the GENERAL section.</div>
<div></div><div>If you are running with two conf files, please include more of each in the email and indicate where one stops and the other starts.</div><div></div><div>Thanks,</div><div></div><div>Dave C.</div><br><div class="gmail_quote">
<div><div></div><div class="h5">
On Thu, Jun 11, 2009 at 12:36 PM, ³Â¹Ú»ª <span dir="ltr"><<a href="mailto:cghhust@gmail.com" target="_blank">cghhust@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div class="h5">
Hi,<br>GBrowse2 sample database(yeast) works fine on the server.However,myself not.Event simplest database do not work(not coordinate show nor can not search).<br>My .conf is:<br>[GENERAL]<br>description = annoproject<br>
database = annoproject <br>default tracks = CYT:overview<br>default width = 800<br>automatic classes = chromosome Sequence<br>[annoproject:database]<br>db_adaptor = Bio::DB::SeqFeature::Store<br>db_args = -adaptor memory<br>
-dir /var/www/html/gbrowse2/databases/annoproject<br>cache_overview = 0<br>[TRACK DEFAULTS]<br>glyph = generic<br>database = annoproject<br>height = 8<br>bgcolor = black<br>fgcolor = black<br>
label density = 50<br>bump density = 100<br>[CYT:overview]<br>feature = chromosome<br>glyph = generic<br>stranded = 1<br>bgcolor = grey<br>fgcolor = black<br>height = 10<br><br>.gff data is :<br>
##gff-version 3<br>chr1 ensembl chromosome 1 245522847 . . . ID=chr1;Name=chr1<br>chr11 ensembl chromosome 1 134452384 . . . ID=chr11;Name=chr11<br>chr12 ensembl chromosome 1 132449811 . . . ID=chr12;Name=chr12<br>
<br>See the attachment picture for the detailed error!<br><br>Yours<br>Josh<br>
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