gbrowse v2 and blast graphics tool
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gbrowse v2 and blast graphics tool
by Biliards
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Hi all,
I'm testing blast graphics 0.02 tool with gbrowse v2. so that I discovered that old paths didn't work with gbrowse v2. this is an example that with gbrowse v1.68 worked: http://gbrowse.cribi.unipd.it/public/gbrowse/vitis_vinifera_8x/?ref=chr15_random;start=1592829;stop=1596888;add=chr15_random%20BLASTN%20HSP4%201594829..1594888;h_region=chr15_random:1594829..1594888; Can you help me about it? Alessandra. ------------------------------------------------------------------------------ Come build with us! The BlackBerry® 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/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: gbrowse v2 and blast graphics tool
by Dave Clements, GMOD Help Desk
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Hi Shuai,
Has there been any work done to test the BLAST Graphic Viewer with GBrowse 2? Thanks, Dave C. On Thu, Sep 17, 2009 at 10:20 AM, Alessandra <alessandra.bilardi@...> wrote: > Hi all, > > I'm testing blast graphics 0.02 tool with gbrowse v2. > so that I discovered that old paths didn't work with gbrowse v2. > this is an example that with gbrowse v1.68 worked: > > http://gbrowse.cribi.unipd.it/public/gbrowse/vitis_vinifera_8x/?ref=chr15_random;start=1592829;stop=1596888;add=chr15_random%20BLASTN%20HSP4%201594829..1594888;h_region=chr15_random:1594829..1594888; > > Can you help me about it? > > Alessandra. > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry® 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/devconf > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > -- * Please keep responses on the list! * Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback ------------------------------------------------------------------------------ Come build with us! The BlackBerry® 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/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: [Gmod-help] Re: gbrowse v2 and blast graphics tool
by Biliards
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Hi all,
I tested this url: http://gbrowse.cribi.unipd.it/public/gbrowse/escherichia_coli/?name=NC_000913:0..2720;h_region=NC_000913:661..720;add=NC_000913 BLASTN HSP1 661..720; next url works: http://gbrowse.cribi.unipd.it/public/gbrowse/escherichia_coli/?name=NC_000913:0..2720;h_region=NC_000913:661..720; when I run this url: http://gbrowse.cribi.unipd.it/public/gbrowse/escherichia_coli/?name=NC_000913:0..2720;h_region=NC_000913:661..720;add=NC_000913 BLASTN HSP1 661..720; I have got these apache error log: Use of uninitialized value $proposed_source in exists at /usr/local/lib/perl/5.10.0/Bio/Graphics/Browser.pm line 258. [Fri Sep 18 23:34:03 2009] [error] Not an ARRAY reference at /usr/local/lib/perl/5.10.0/Bio/Graphics/Browser/Render.pm line 1673.\n I use v1.995 release. Next weekend I will test this url with last version. I hope that this could be an help. Best, Alessandra. On Fri, Sep 18, 2009 at 8:04 PM, Dave Clements, GMOD Help Desk <gmodhelp@...> wrote: > Lincoln, (and the rest of the list) > > Shuai hasn't had a chance to look at using BLAST Graphic Viewer in > GBrowse 2. Do you know enough about the viewer to expect that it > would be broken in GBrowse 2? I'm trying to figure out if Alessandra > should keep working on trying to get this to work, or if BLAST Graphic > Viewer just won't work with GBrowse 2 until it is upgraded. > > Has anyone got the BLAST graphic viewer to work with GBrowse 2? > > Thanks, > > Dave C. > > On Fri, Sep 18, 2009 at 10:53 AM, Shuai Weng <shuai@...> wrote: >> >> Hi Dave, >> >> Sorry, I didn't get chance to do anything with BLAST Graphic Viewer >> recently. >> >> Shuai >> >> On Fri, 18 Sep 2009, Dave Clements, GMOD Help Desk wrote: >> >>> Hi Shuai, >>> >>> Has there been any work done to test the BLAST Graphic Viewer with GBrowse >>> 2? >>> >>> Thanks, >>> >>> Dave C. >>> >>> On Thu, Sep 17, 2009 at 10:20 AM, Alessandra >>> <alessandra.bilardi@...> wrote: >>>> >>>> Hi all, >>>> >>>> I'm testing blast graphics 0.02 tool with gbrowse v2. >>>> so that I discovered that old paths didn't work with gbrowse v2. >>>> this is an example that with gbrowse v1.68 worked: >>>> >>>> >>>> http://gbrowse.cribi.unipd.it/public/gbrowse/vitis_vinifera_8x/?ref=chr15_random;start=1592829;stop=1596888;add=chr15_random%20BLASTN%20HSP4%201594829..1594888;h_region=chr15_random:1594829..1594888; >>>> >>>> Can you help me about it? >>>> >>>> Alessandra. >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Come build with us! The BlackBerry® 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/devconf >>>> _______________________________________________ >>>> Gmod-gbrowse mailing list >>>> Gmod-gbrowse@... >>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>> >>> >>> >>> >>> -- >>> * Please keep responses on the list! >>> * Was this helpful? Let us know at >>> http://gmod.org/wiki/Help_Desk_Feedback >>> >> > > > > -- > * Please keep responses on the list! > * Was this helpful? Let us know at http://gmod.org/wiki/Help_Desk_Feedback > -- 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® 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/devconf _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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