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From: Scott C. <sc...@sc...> - 2018-07-18 15:32:30
|
Hi Vaneet, Now that I've reread your email and also tried it myself to remind me how it works--it does not prompt you for a name or location. It assigns a name based on the track and location and puts a file in your default download location. Scott On Wed, Jul 18, 2018 at 11:26 AM, Scott Cain <sc...@sc...> wrote: > Hi Vaneet, > > Can you check the javascript console when you're doing that to see if it > gives any useful feedback? > > Thanks, > Scott > > > On Tue, Jul 17, 2018 at 7:04 PM, Vaneet Lotay <van...@uc...> > wrote: > >> Hello, >> >> >> >> I’m having trouble saving track data to capture sequence data in FASTA >> format, model data in GFF3 or any other track and format. >> >> >> >> I click on the drop down arrow next to the track label and then ‘Save >> track data’. Whether I click on the visible region or the whole reference >> sequence and no matter which output format I select it doesn’t work. When I >> click on ‘Save’ the dialog box always closes and nothing happens. >> >> >> >> I assume there should be another box popping up asking where to save the >> file and also how to name it? >> >> >> >> I’ve tested this on both Firefox and Chrome browsers, still the same >> problem. I’ve also tested both browsers while disabling the pop-up >> blocker, in case that was interfering but still the same problem remained. >> >> >> >> Please let me know if anyone can resolve this issue. >> >> >> >> Thanks, >> >> >> >> Vaneet >> >> >> >> >> >> *Vaneet Lotay* >> >> *Xenbase Bioinformatician* >> >> *716 ICT Building - University of Calgary* >> >> *2500 University Drive NW* >> >> *Calgary AB T2N 1N4* >> >> *CANADA* >> >> >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> >> > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain > dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
|
From: Scott C. <sc...@sc...> - 2018-07-18 15:26:35
|
Hi Vaneet, Can you check the javascript console when you're doing that to see if it gives any useful feedback? Thanks, Scott On Tue, Jul 17, 2018 at 7:04 PM, Vaneet Lotay <van...@uc...> wrote: > Hello, > > > > I’m having trouble saving track data to capture sequence data in FASTA > format, model data in GFF3 or any other track and format. > > > > I click on the drop down arrow next to the track label and then ‘Save > track data’. Whether I click on the visible region or the whole reference > sequence and no matter which output format I select it doesn’t work. When I > click on ‘Save’ the dialog box always closes and nothing happens. > > > > I assume there should be another box popping up asking where to save the > file and also how to name it? > > > > I’ve tested this on both Firefox and Chrome browsers, still the same > problem. I’ve also tested both browsers while disabling the pop-up > blocker, in case that was interfering but still the same problem remained. > > > > Please let me know if anyone can resolve this issue. > > > > Thanks, > > > > Vaneet > > > > > > *Vaneet Lotay* > > *Xenbase Bioinformatician* > > *716 ICT Building - University of Calgary* > > *2500 University Drive NW* > > *Calgary AB T2N 1N4* > > *CANADA* > > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
|
From: Vaneet L. <van...@uc...> - 2018-07-17 23:04:11
|
Hello, I'm having trouble saving track data to capture sequence data in FASTA format, model data in GFF3 or any other track and format. I click on the drop down arrow next to the track label and then 'Save track data'. Whether I click on the visible region or the whole reference sequence and no matter which output format I select it doesn't work. When I click on 'Save' the dialog box always closes and nothing happens. I assume there should be another box popping up asking where to save the file and also how to name it? I've tested this on both Firefox and Chrome browsers, still the same problem. I've also tested both browsers while disabling the pop-up blocker, in case that was interfering but still the same problem remained. Please let me know if anyone can resolve this issue. Thanks, Vaneet Vaneet Lotay Xenbase Bioinformatician 716 ICT Building - University of Calgary 2500 University Drive NW Calgary AB T2N 1N4 CANADA |
|
From: Loraine G. <lor...@sb...> - 2018-07-12 09:45:12
|
ok, this would be great! Thanks Le 10/07/2018 18:34, Colin a écrit : > This would be a good feature. I would envision it being added to this > "enhanced gene detail view" issue > https://github.com/GMOD/jbrowse/issues/174 > > If you have any special comments feel free to add it there! > > > -Colin > > On Mon, Jul 9, 2018 at 10:13 AM Loraine Guéguen > <lor...@sb... <mailto:lor...@sb...>> > wrote: > > Dear JBrowse team and list, > > Is it possible to get the peptide sequence of a feature of type > CanvasFeatures, for BLAST purpose for example ? > (like in Apollo with right-click > get sequence on a user-created > annotation) > > Regards, > > Loraine Guéguen > > -- > Loraine Guéguen > > UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models) > Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences) > > Station Biologique de Roscoff - CNRS | Sorbonne Université > Place Georges Teissier - CS 90074 > 29688 Roscoff cedex > tel: ++33 (0)2 98 29 56 46 (interne : 415) > http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models > http://abims.sb-roscoff.fr/ > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > <mailto:Gmo...@li...> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > -- Loraine Guéguen UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models) Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences) Station Biologique de Roscoff - CNRS | Sorbonne Université Place Georges Teissier - CS 90074 29688 Roscoff cedex tel: ++33 (0)2 98 29 56 46 (interne : 415) http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models http://abims.sb-roscoff.fr/ |
|
From: Colin <col...@gm...> - 2018-07-10 16:35:07
|
Note also that I think plugins such as SeqLighter and FeatureSequence can do this but I know you mentioned wanting built-ins :) -Colin On Tue, Jul 10, 2018 at 12:34 PM Colin <col...@gm...> wrote: > This would be a good feature. I would envision it being added to this > "enhanced gene detail view" issue > https://github.com/GMOD/jbrowse/issues/174 > > If you have any special comments feel free to add it there! > > > -Colin > > On Mon, Jul 9, 2018 at 10:13 AM Loraine Guéguen < > lor...@sb...> wrote: > >> Dear JBrowse team and list, >> >> Is it possible to get the peptide sequence of a feature of type >> CanvasFeatures, for BLAST purpose for example ? >> (like in Apollo with right-click > get sequence on a user-created >> annotation) >> >> Regards, >> >> Loraine Guéguen >> >> -- >> Loraine Guéguen >> >> UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models) >> Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences) >> >> Station Biologique de Roscoff - CNRS | Sorbonne Université >> Place Georges Teissier - CS 90074 >> 29688 Roscoff cedex >> tel: ++33 (0)2 98 29 56 46 (interne : 415) >> http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models >> http://abims.sb-roscoff.fr/ >> >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > |
|
From: Colin <col...@gm...> - 2018-07-10 16:34:41
|
This would be a good feature. I would envision it being added to this "enhanced gene detail view" issue https://github.com/GMOD/jbrowse/issues/174 If you have any special comments feel free to add it there! -Colin On Mon, Jul 9, 2018 at 10:13 AM Loraine Guéguen < lor...@sb...> wrote: > Dear JBrowse team and list, > > Is it possible to get the peptide sequence of a feature of type > CanvasFeatures, for BLAST purpose for example ? > (like in Apollo with right-click > get sequence on a user-created > annotation) > > Regards, > > Loraine Guéguen > > -- > Loraine Guéguen > > UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models) > Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences) > > Station Biologique de Roscoff - CNRS | Sorbonne Université > Place Georges Teissier - CS 90074 > 29688 Roscoff cedex > tel: ++33 (0)2 98 29 56 46 (interne : 415) > http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models > http://abims.sb-roscoff.fr/ > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
|
From: Scott C. <sc...@sc...> - 2018-07-09 16:30:52
|
Hi Chris, Thanks for asking. There isn't really, though such a document was a goal some time ago. It's difficult to write a generic document, particularly when it comes down to individual track configs. Even though that part of the document would probably have some hand waving, we should be able to make at least an outline to help people. I'll try to make a skeleton document on the wiki this week. Scott On Mon, Jul 9, 2018 at 11:10 AM, Fields, Christopher J < cjf...@il...> wrote: > Just curious, but is there any documentation I can point others to for > migrating from GBrowse to JBrowse (even if it is essentially dumping > everything to GFF + FASTA)? This pops up now and again and I know of a few > similar GBrowse instances in the wild. > > chris > > On July 9, 2018 at 10:01:32 AM, Scott Cain (sc...@sc...) wrote: > > Hi Jase, > > There is this document specifically for porting from GBrowse 1 to 2: > > http://gmod.org/wiki/Migrating_from_GBrowse_1.X_to_2.X > > Generally when people ask about installing GBrowse I suggest considering > JBrowse, since it's easier to install and configure, and I still think that > is a worthwhile thing for you think about. Basically, I suspect you've got > a fair amount of work in front of you, with moving servers and upgrading > software. Unless you have the original GFF used to create your current > GBrowse instance though, the path of least resistance will likely be to > upgrade to GBrowse 2. > > You'll note I didn't offer as an option just taking the software you have > and moving it: I suspect that will be too hard, since getting the ancient > perl prerequisites installed on the new server would be a herculean task. > Instead, I'd suggest setting up an Ubuntu server (if you have a choice) > since you can use apt to install GBrowse2 and all of the prerequisites. > You can then copy over databases from the old server and then you are just > left with the task of porting old configuration files, which is what the > link above is good for. If you can't use Ubuntu but can use Docker, you > could take a Dockerfile I've been working on for WormBase and modify it for > your own use: > > https://github.com/WormBase/website-genome-browsers/tree/ > staging/gbrowse-docker > > Finally, if you want to post a url for your GBrowse instance, I can take a > look and see if I have any more suggestions and confirm your assumption > that it's GBrowse 1. If you don't want to post it on the list you can > email me a link directly as well. > > Good luck! > Scott > > > On Sun, Jul 8, 2018 at 9:42 PM, Jason.Weber <Jas...@ca...> > wrote: > >> Good Morning, >> >> >> >> I just “inherited” a server running GBrowse (I believe version 1) >> >> However the server its sitting on is slowly dying, and thus I need to >> migrate it to a new server. >> >> However I’d struggling to find any documentation on this process. >> >> Any help/pointing in the right direction would be greatly appreciated. >> >> >> >> - Jase >> >> >> >> >> >> >> *Jason Weber **IT Manager* >> >> *Faculty of Science and Technology* >> >> >> *Institute for Applied Ecology **University of Canberra,* ACT 2601 >> *T* >> *+61 (0)2 620 15572 **F* *+61 (0)2 6201 5231* >> >> *M* *+61 (0) 407999230* >> *E* *jas...@ca... <jas...@ca...>* >> >> *Location: **Building 6 Rm B09* >> >> >> >> “My life flashed before my eyes and all I got was a progress bar” >> >> - Dirk >> >> >> >> Australian Government Higher Education Registered Provider number >> (CRICOS): #00212K >> >> ************************NOTICE & DISCLAIMER******************** >> ************** >> This email and any files transmitted with it may contain confidential >> or copyright material and are for the attention of the addressee only. >> If you have received This email in error please notify us by email reply >> and delete it from your system. The University of Canberra accepts >> >> >> >> <https://www.facebook.com/UniversityOfCanberra> >> <https://twitter.com/UniCanberra> <http://instagram.com/unicanberra> >> <https://www.youtube.com/user/uniofcanberra> >> <https://www.canberra.edu.au> >> >> Australian Government Higher Education Registered Provider number >> (CRICOS):#00212K >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmo...@li... >> 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 > ------------------------------------------------------------------------------ > > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot______ > _________________________________________ > Gmod-gbrowse mailing list > Gmo...@li... > 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 |
|
From: Loraine G. <lor...@sb...> - 2018-07-09 14:12:57
|
Dear JBrowse team and list, Is it possible to get the peptide sequence of a feature of type CanvasFeatures, for BLAST purpose for example ? (like in Apollo with right-click > get sequence on a user-created annotation) Regards, Loraine Guéguen -- Loraine Guéguen UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models) Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences) Station Biologique de Roscoff - CNRS | Sorbonne Université Place Georges Teissier - CS 90074 29688 Roscoff cedex tel: ++33 (0)2 98 29 56 46 (interne : 415) http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models http://abims.sb-roscoff.fr/ |
|
From: Ke J. <bio...@gm...> - 2018-07-05 21:13:06
|
I'd suggest to try plugins like MultiBigWig or ProportionalMultiBW. Both of
them would give you the coverage plots, the later would also give the
SNP/variants. I found the demand to see every individual read is pretty
rare. I used the later for extra-high coverage amplicon data and it worked
very well.
Ke
On Thu, Jul 5, 2018 at 8:17 AM Loraine Guéguen <
lor...@sb...> wrote:
> Dear JBrowse team,
>
> I am experiencing some difficulties to correctly display a BAM file
> (JBrowse 1.14.1): some areas (not all) do not display, whatever I zoom
> in ("Too many BAM features"). See enclosed screenshots.
> They display if I increase the chunkSizeLimit, but this is not a
> solution because the browser rapidly blows up, and I have areas with
> chunk sizes of more than 20 and even 40 MiB (even if I zoom in until
> nucleotide level).
>
> I have also tried to configure storeTimeout for the track, but with no
> visible effect.
>
> What do you suggest ?
>
> Thanks,
>
> Loraine Guéguen
>
>
> --
> Loraine Guéguen
>
> UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
> Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
>
> Station Biologique de Roscoff - CNRS | Sorbonne Université
> Place Georges Teissier - CS 90074
> 29688 Roscoff cedex
> tel: ++33 (0)2 98 29 56 46 (interne : 415)
> http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
> http://abims.sb-roscoff.fr/
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
|
|
From: Robert B. <rb...@gm...> - 2018-07-05 21:00:25
|
This is a tough one. It sounds like your BAM file is just too dense to
display with JBrowse as it's currently implemented. Perhaps you could
consider filtering the BAM file to get a smaller set of reads that are more
likely to be of interest?
On Thu, Jul 5, 2018 at 6:17 AM Loraine Guéguen <
lor...@sb...> wrote:
> Dear JBrowse team,
>
> I am experiencing some difficulties to correctly display a BAM file
> (JBrowse 1.14.1): some areas (not all) do not display, whatever I zoom
> in ("Too many BAM features"). See enclosed screenshots.
> They display if I increase the chunkSizeLimit, but this is not a
> solution because the browser rapidly blows up, and I have areas with
> chunk sizes of more than 20 and even 40 MiB (even if I zoom in until
> nucleotide level).
>
> I have also tried to configure storeTimeout for the track, but with no
> visible effect.
>
> What do you suggest ?
>
> Thanks,
>
> Loraine Guéguen
>
>
> --
> Loraine Guéguen
>
> UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
> Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
>
> Station Biologique de Roscoff - CNRS | Sorbonne Université
> Place Georges Teissier - CS 90074
> 29688 Roscoff cedex
> tel: ++33 (0)2 98 29 56 46 <+33%202%2098%2029%2056%2046> (interne : 415)
> http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
> http://abims.sb-roscoff.fr/
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
|
|
From: Loraine G. <lor...@sb...> - 2018-07-05 13:17:20
|
Dear JBrowse team,
I am experiencing some difficulties to correctly display a BAM file
(JBrowse 1.14.1): some areas (not all) do not display, whatever I zoom
in ("Too many BAM features"). See enclosed screenshots.
They display if I increase the chunkSizeLimit, but this is not a
solution because the browser rapidly blows up, and I have areas with
chunk sizes of more than 20 and even 40 MiB (even if I zoom in until
nucleotide level).
I have also tried to configure storeTimeout for the track, but with no
visible effect.
What do you suggest ?
Thanks,
Loraine Guéguen
--
Loraine Guéguen
UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Station Biologique de Roscoff - CNRS | Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/
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From: Robert B. <rb...@gm...> - 2018-06-29 23:50:17
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This is great Keiran, these scripts should make it a lot easier for people to get running quickly if their genome is in Ensembl! Thanks so much for putting these out there! On Fri, Jun 29, 2018 at 3:17 PM Keiran Raine <kr...@sa...> wrote: > Hi, > > > > We've moved some code from our stack out into the GMOD repo for helping > setup JBrowse instances from Ensembl data dumps. > > > > https://github.com/GMOD/ensembl-to-jbrowse > > > > There's a little left to do, but I've a plane to catch. > > > > If you're still at Reed College you can't use it on the network as they > don't allow FTP. > > > > Regards, > > > > Keiran Raine, M.Sc., MBCS > > Principal Bioinformatician > > Cancer, Ageing and Somatic Mutation > > Wellcome Sanger Institute > > > > kr...@sa... > > Tel:+44 (0)1223 834244 Ext: 4983 > > Office: H104 > > > > Please note that due to childcare I don't work from 14:00 on Tuesdays and > 14:50 on Wednesdays. > -- The Wellcome Sanger Institute is operated by Genome Research Limited, a > charity registered in England with number 1021457 and a company registered > in England with number 2742969, whose registered office is 215 Euston Road, > London, NW1 2BE. > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Keiran R. <kr...@sa...> - 2018-06-29 22:17:34
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Hi, We've moved some code from our stack out into the GMOD repo for helping setup JBrowse instances from Ensembl data dumps. https://github.com/GMOD/ensembl-to-jbrowse There's a little left to do, but I've a plane to catch. If you're still at Reed College you can't use it on the network as they don't allow FTP. Regards, Keiran Raine, M.Sc., MBCS Principal Bioinformatician Cancer, Ageing and Somatic Mutation Wellcome Sanger Institute kr...@sa... Tel:+44 (0)1223 834244 Ext: 4983 Office: H104 Please note that due to childcare I don't work from 14:00 on Tuesdays and 14:50 on Wednesdays. -- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. |
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From: Loraine G. <lor...@sb...> - 2018-06-28 11:48:27
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I thank you for your answer. I will use 2 separate bigwig files (positive and negative) in two different tracks, for now. I prefer to be (over)careful and limit the use of plugins to have a robust display over time, because long-term maintenance is less ensured I suppose. But the multibigwig plugin from the screenshot gives a really nice view. Regards, Loraine Le 22/06/2018 19:38, Colin a écrit : > > I guess it does seem to make sense to make a positive coverage and a > negative coverage bigwig file. There is not really a fileformat even > that can represent multiple bigwig type signals in a single file > annoyingly enough. > > The multibigwig plugin can handle the positive and negative at the > same time though (e.g. you just load two bigwigs and use the XYPlot), > and there is also bhofmei's strandedplot > https://github.com/bhofmei/jbplugin-strandedplot > > I think the effect of both plugins is similar in this case > > It doesn't look like this is something that is part of default > JBrowse, but the "subtrack" concept is on the todo list in github > https://github.com/GMOD/jbrowse/issues/68. > > I guess the plugins offer a way forward for now but I'd be interested > to hear why you are not interested in using plugins. I attached a > screenshot of how positive and negative looks like in multibigwig > > -Colin > > On Tue, Jun 19, 2018 at 3:17 AM Loraine Guéguen > <lor...@sb... <mailto:lor...@sb...>> > wrote: > > Dear JBrowse team, > > I have huge paired-end RNAseq BAM files (e.g. 1.6Go for 2.4Mbp), for > which the whole amount of reads is too big to be visualized in most > locations ("too many features" and "max height reached"), despite a > small glyph height and a compact display mode. And increasing > chunkSizeLimit to 10 MiB is not sufficient and tends to blow up > the browser. > I also have coverage bigwig files that display the overall > coverage but > not the strand-specific coverage. > > My challenge is to offer a display that give a glimpse of the > positive > and negative strand coverage. > So, I wonder what is the best way in JBrowse to display positive > strand > coverage and negative strand coverage from a BAM file (or Bigwig) for > RNAseq data. > > A solution would be to display 2 bigwig files (positive and negative > strand) into the same track, wouldn't it ? I have seen in the JBrowse > FAQ that a "multibigwig" plugin is available > (https://github.com/elsiklab/multibigwig), but is it possible to use > subtracks with the core code of JBrowse ? (I am not keen of using > plugins for maintenance reasons) > > Do you see any other solutions ? > > Thanks, > > Loraine Guéguen > > -- > Loraine Guéguen > > UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models) > Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences) > > Station Biologique de Roscoff - CNRS | Sorbonne Université > Place Georges Teissier - CS 90074 > 29688 Roscoff cedex > tel: ++33 (0)2 98 29 56 46 (interne : 415) > http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models > http://abims.sb-roscoff.fr/ > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! > http://sdm.link/slashdot_______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > <mailto:Gmo...@li...> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > -- Loraine Guéguen UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models) Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences) Station Biologique de Roscoff - CNRS | Sorbonne Université Place Georges Teissier - CS 90074 29688 Roscoff cedex tel: ++33 (0)2 98 29 56 46 (interne : 415) http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models http://abims.sb-roscoff.fr/ |
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From: Nathan D. <nat...@lb...> - 2018-06-22 23:49:29
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1 - Apollo 2.1.0 has been released! https://github.com/GMOD/Apollo/releases/tag/2.1.0 <https://github.com/GMOD/Apollo/releases/tag/2.1.0> 2 - Members of the Apollo and JBrowse teams will be at the Galaxy BOSC conference at the end of next week with an Apollo talk and poster and a few birds of a feather sessions for JBrowse and a Thursday / Friday hackathon with both teams there as well as tons of GMODers and of course lots of brilliant Galaxy folks: https://gccbosc2018.sched.com/ <https://gccbosc2018.sched.com/>. It would be a great time to add features, get bugs fixed, etc. Please reply to the lists directly or email me if you have any further questions or project ideas. Cheers, The Apollo team = More on the Apollo 2.1.0 release = Thanks for the testing, patching, requests and bug reporting. Other availability: - There should be an Amazon Web Service Community image available on most AWS zones called “Apollo 2.1.0 Template” - I updated our docker image to support 2.1.0 as a starting point for your own docker integrations: http://github.com/GMOD/docker-apollo <http://github.com/GMOD/docker-apollo> It is built on both docker hub https://hub.docker.com/r/gmod/apollo/ <https://hub.docker.com/r/gmod/apollo/> (still building) and quay https://quay.io/repository/gmod/docker-apollo?tab=tags <https://quay.io/repository/gmod/docker-apollo?tab=tags> (working now). Some of the new features include: Added ability to annotate a variant from VCF evidence tracks 1892 <https://github.com/GMOD/Apollo/pull/1892> Allow forced assignment of transcript to a gene #1851 <https://github.com/GMOD/Apollo/pull/1851> Added proper Instructor and Organism Admin permission level #1178 <https://github.com/GMOD/Apollo/issues/1178> Indicate start / stop codons with color #1852 <https://github.com/GMOD/Apollo/pull/1852> Set the default biotype on track #1861 <https://github.com/GMOD/Apollo/issues/1861> Some important bug fixes: Prevents setting bad translation starts and ends #1838 <https://github.com/GMOD/Apollo/issues/1838> Fixed descriptor leak when loading bulk loading GFF3 #1187 <https://github.com/GMOD/Apollo/pull/1887> Fixed adding ability to create sequence alterations of uneven length #1883 <https://github.com/GMOD/Apollo/issues/1883> Fixed problem where canonical splice-sites were not recognized if sequence was being shown in lower-case #1879 <https://github.com/GMOD/Apollo/issues/1879> In some cases when the name store is not properly configured, the location is not remembered #1895 <https://github.com/GMOD/Apollo/issues/1895> Note You will need to install node 6 or better <https://nodejs.org/en/download/package-manager/>. Note If updating your jbrowse settings from previous versions in apollo-config.groovy you will need to set the JBrowse to use the currently tagged version or better <https://github.com/GMOD/Apollo/blob/master/sample-postgres-apollo-config.groovy#L113>. If this is commented out, however, the default will work <https://github.com/GMOD/Apollo/blob/master/grails-app/conf/Config.groovy#L388-L433>. Note Some issues with new tomcat and addStore / addTracks RFC 7230 and RFC 3986. See http://genomearchitect.readthedocs.io/en/latest/Setup.html?highlight=RFC#json-in-the-url-with-newer-versions-of-tomcat <http://genomearchitect.readthedocs.io/en/latest/Setup.html?highlight=RFC#json-in-the-url-with-newer-versions-of-tomcat> The complete change log can be found at: https://github.com/GMOD/Apollo/blob/master/ChangeLog.md <https://github.com/GMOD/Apollo/blob/master/ChangeLog.md> Please review the documentation pages for more details: http://genomearchitect.readthedocs.io/en/stable/ <http://genomearchitect.readthedocs.io/en/stable/> Note: You can find a guide upgrading existing Apollo installations here: http://genomearchitect.readthedocs.io/en/stable/Migration.html <http://genomearchitect.readthedocs.io/en/stable/Migration.html> Please open a GitHub issue if you find any problems: https://github.com/GMOD/Apollo/issues/ <https://github.com/GMOD/Apollo/issues/> Active mailing list (ap...@li... <mailto:ap...@li...>) and archive <http://gmod.827538.n3.nabble.com/Apollo-f815553.html>. |
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From: Colin <col...@gm...> - 2018-06-22 17:38:21
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I guess it does seem to make sense to make a positive coverage and a negative coverage bigwig file. There is not really a fileformat even that can represent multiple bigwig type signals in a single file annoyingly enough. The multibigwig plugin can handle the positive and negative at the same time though (e.g. you just load two bigwigs and use the XYPlot), and there is also bhofmei's strandedplot https://github.com/bhofmei/jbplugin-strandedplot I think the effect of both plugins is similar in this case It doesn't look like this is something that is part of default JBrowse, but the "subtrack" concept is on the todo list in github https://github.com/GMOD/jbrowse/issues/68. I guess the plugins offer a way forward for now but I'd be interested to hear why you are not interested in using plugins. I attached a screenshot of how positive and negative looks like in multibigwig -Colin On Tue, Jun 19, 2018 at 3:17 AM Loraine Guéguen < lor...@sb...> wrote: > Dear JBrowse team, > > I have huge paired-end RNAseq BAM files (e.g. 1.6Go for 2.4Mbp), for > which the whole amount of reads is too big to be visualized in most > locations ("too many features" and "max height reached"), despite a > small glyph height and a compact display mode. And increasing > chunkSizeLimit to 10 MiB is not sufficient and tends to blow up the > browser. > I also have coverage bigwig files that display the overall coverage but > not the strand-specific coverage. > > My challenge is to offer a display that give a glimpse of the positive > and negative strand coverage. > So, I wonder what is the best way in JBrowse to display positive strand > coverage and negative strand coverage from a BAM file (or Bigwig) for > RNAseq data. > > A solution would be to display 2 bigwig files (positive and negative > strand) into the same track, wouldn't it ? I have seen in the JBrowse > FAQ that a "multibigwig" plugin is available > (https://github.com/elsiklab/multibigwig), but is it possible to use > subtracks with the core code of JBrowse ? (I am not keen of using > plugins for maintenance reasons) > > Do you see any other solutions ? > > Thanks, > > Loraine Guéguen > > -- > Loraine Guéguen > > UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models) > Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences) > > Station Biologique de Roscoff - CNRS | Sorbonne Université > Place Georges Teissier - CS 90074 > 29688 Roscoff cedex > tel: ++33 (0)2 98 29 56 46 (interne : 415) > http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models > http://abims.sb-roscoff.fr/ > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Colin <col...@gm...> - 2018-06-21 21:02:33
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I guess I am not sure what to say. If you have zlib-devel it clearly should not give an error that "zlib.h not found". If you can try a different system, I would do that. It is not really within the realm of jbrowse to debug such things. Note that I did install CentOS 6.9 minimal in a virtualbox and had JBrowse's setup.sh work fine with the instructions above :) -Colin On Thu, Jun 21, 2018 at 6:27 AM Onkar Nath <onk...@gm...> wrote: > I had updated my system with yum update, > I tried installing that manually but still the same error comes. I even > tried forcefully installing but none worked. This same error occurs > every-time. > > -- > > ONKAR NATH > Senior Research Fellow > National Institute of Plant Genome Research > Aruna Asaf Ali Marg, New Delhi- 110067 > Email- onk...@gm... > Mob: +91-9136065766 > skype id: onkarnath89 > > > On Tue, Jun 19, 2018 at 11:36 AM, Colin <col...@gm...> wrote: > >> The steps that are listed have been tested on CentOS 6.9 so it's sort of >> hard to see what the issue is. You could try manually installing this >> module to the system with just "cpan PerlIO::gzip" to see what happens >> Could also try rebooting or yum update? (you didnt include yum update in >> your list of commands that you replied with) >> >> >> >> -Colin >> >> On Mon, Jun 18, 2018 at 11:33 PM Onkar Nath <onk...@gm...> >> wrote: >> >>> I have tried these and found them installed. I am getting error of >>> PerlIO::gzip library. >>> >>> when installig PerlIO::gzip >>> error that I get is >>> >>> gzip.xs:16:10: fatal error: zlib.h: No such file or directory >>> #include <zlib.h> >>> ^~~~~~~~ >>> compilation terminated. >>> make: *** [gzip.o] Error 1 >>> >>> I have tried many solutions from web but none of them worked. some of >>> them are as below: >>> >>> *yum install libpng libpng-devel* >>> Package 2:libpng-1.2.49-2.el6_7.x86_64 already installed and latest >>> version >>> Package 2:libpng-devel-1.2.49-2.el6_7.x86_64 already installed and >>> latest version >>> >>> *yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker* >>> >>> Package 2:libpng-devel-1.2.49-2.el6_7.x86_64 already installed and >>> latest version >>> Package gd-devel-2.0.35-11.el6.x86_64 already installed and latest >>> version >>> Package zlib-devel-1.2.3-29.el6.x86_64 already installed and latest >>> version >>> Package perl-ExtUtils-MakeMaker-6.55-144.el6.x86_64 already installed >>> and latest version >>> >>> *yum groupinstall "Development Tools"* >>> Package flex-2.5.35-9.el6.x86_64 already installed and latest version >>> Package gcc-4.4.7-18.el6_9.2.x86_64 already installed and latest version >>> Package redhat-rpm-config-9.0.3-51.el6.centos.noarch already installed >>> and latest version >>> Package rpm-build-4.8.0-55.el6.x86_64 already installed and latest >>> version >>> Package 1:make-3.81-23.el6.x86_64 already installed and latest version >>> Package patch-2.6-8.el6_9.x86_64 already installed and latest version >>> Package 1:pkgconfig-0.23-9.1.el6.x86_64 already installed and latest >>> version >>> Package gettext-0.17-18.el6.x86_64 already installed and latest version >>> Package automake-1.11.1-4.el6.noarch already installed and latest version >>> Package bison-2.4.1-5.el6.x86_64 already installed and latest version >>> Package libtool-2.2.6-15.5.el6.x86_64 already installed and latest >>> version >>> Package autoconf-2.63-5.1.el6.noarch already installed and latest version >>> Package gcc-c++-4.4.7-18.el6_9.2.x86_64 already installed and latest >>> version >>> Package binutils-2.20.51.0.2-5.47.el6_9.1.x86_64 already installed and >>> latest version >>> Package patchutils-0.3.1-3.1.el6.x86_64 already installed and latest >>> version >>> Package byacc-1.9.20070509-7.el6.x86_64 already installed and latest >>> version >>> Package indent-2.2.10-7.el6.x86_64 already installed and latest version >>> Package systemtap-2.9-7.el6.x86_64 already installed and latest version >>> Package diffstat-1.51-2.el6.x86_64 already installed and latest version >>> Package elfutils-0.164-2.el6.x86_64 already installed and latest version >>> Package cvs-1.11.23-16.el6.x86_64 already installed and latest version >>> Package rcs-5.7-37.el6.x86_64 already installed and latest version >>> Package subversion-1.6.11-15.el6_7.x86_64 already installed and latest >>> version >>> Package gcc-gfortran-4.4.7-18.el6_9.2.x86_64 already installed and >>> latest version >>> Package 1:doxygen-1.6.1-6.el6.x86_64 already installed and latest version >>> Package intltool-0.41.0-1.1.el6.noarch already installed and latest >>> version >>> Package git-1.7.1-9.el6_9.x86_64 already installed and latest version >>> Package ctags-5.8-2.el6.x86_64 already installed and latest version >>> Package cscope-15.6-7.el6.x86_64 already installed and latest version >>> Package swig-1.3.40-6.el6.x86_64 already installed and latest version >>> Warning: Group development does not have any packages. >>> No packages in any requested group available to install or update >>> >>> But Still the error persists. >>> >>> >>> >>> -- >>> >>> ONKAR NATH >>> Senior Research Fellow >>> National Institute of Plant Genome Research >>> Aruna Asaf Ali Marg, New Delhi- 110067 >>> Email- onk...@gm... >>> Mob: +91-9136065766 >>> skype id: onkarnath89 >>> >>> >>> On Mon, Jun 18, 2018 at 9:07 PM, Colin <col...@gm...> wrote: >>> >>>> Ah ok, centos :) >>>> >>>> From this link >>>> http://www.gmod.org/wiki/JBrowse_Troubleshooting#Linux_-_Red_Hat_.2F_Fedora_.2F_CentOS >>>> >>>> I'd recommend >>>> >>>> yum update >>>> yum groupinstall "Development Tools" >>>> yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker >>>> >>>> >>>> -Colin >>>> >>>> On Mon, Jun 18, 2018 at 1:01 AM Onkar Nath <onk...@gm...> >>>> wrote: >>>> >>>>> I had Ran this command and found all these installed >>>>> >>>>> yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker >>>>> >>>>> Details: >>>>> [root@localhost JBrowse-1.14.2]# yum install libpng-devel gd-devel >>>>> zlib-devel perl-ExtUtils-MakeMaker >>>>> Loaded plugins: fastestmirror, refresh-packagekit, security >>>>> Setting up Install Process >>>>> Loading mirror speeds from cached hostfile >>>>> * base: mirror.dhakacom.com >>>>> * epel: ftp.riken.jp >>>>> * extras: mirror.dhakacom.com >>>>> * updates: mirror.dhakacom.com >>>>> Package 2:libpng-devel-1.2.49-2.el6_7.x86_64 already installed and >>>>> latest version >>>>> Package gd-devel-2.0.35-11.el6.x86_64 already installed and latest >>>>> version >>>>> Package zlib-devel-1.2.3-29.el6.x86_64 already installed and latest >>>>> version >>>>> Package perl-ExtUtils-MakeMaker-6.55-144.el6.x86_64 already installed >>>>> and latest version >>>>> Nothing to do >>>>> [root@localhost JBrowse-1.14.2]# >>>>> >>>>> Still this error occurs. >>>>> >>>>> >>>>> -- >>>>> >>>>> ONKAR NATH >>>>> Senior Research Fellow >>>>> National Institute of Plant Genome Research >>>>> Aruna Asaf Ali Marg, New Delhi- 110067 >>>>> Email- onk...@gm... >>>>> Mob: +91-9136065766 >>>>> skype id: onkarnath89 >>>>> >>>>> >>>>> On Sun, Jun 17, 2018 at 5:54 AM, Colin <col...@gm...> wrote: >>>>> >>>>>> It is recommended to install zlib and some basic dependencies for >>>>>> your linux setup >>>>>> >>>>>> A command you can run is here >>>>>> >>>>>> http://gmod.org/wiki/JBrowse_Configuration_Guide#Making_a_New_JBrowse >>>>>> >>>>>> >>>>>> sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev >>>>>> build-essential >>>>>> >>>>>> >>>>>> -Colin >>>>>> >>>>>> On Sat, Jun 16, 2018 at 7:38 AM Onkar Nath <onk...@gm...> >>>>>> wrote: >>>>>> >>>>>>> Dear JBrowse team, >>>>>>> I want to imbed JBrowse into my html page. So I tried installing it >>>>>>> on my system. But I am getting an error of zlib.h. I have tried the >>>>>>> instructions available on your wikipage and some others by google search. >>>>>>> But none has worked. Kindly Consider the related log file. >>>>>>> Any support will be helpful. >>>>>>> Waiting eagerly for your reply. >>>>>>> >>>>>>> Regards >>>>>>> -- >>>>>>> >>>>>>> ONKAR NATH >>>>>>> Senior Research Fellow >>>>>>> National Institute of Plant Genome Research >>>>>>> Aruna Asaf Ali Marg, New Delhi- 110067 >>>>>>> Email- onk...@gm... >>>>>>> Mob: +91-9136065766 >>>>>>> skype id: onkarnath89 >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>>>>>> Check out the vibrant tech community on one of the world's most >>>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>>>>> _______________________________________________ >>>>>>> Gmod-ajax mailing list >>>>>>> Gmo...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>>>> >>>>>> >>>>> >>> > |
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From: Onkar N. <onk...@gm...> - 2018-06-21 10:27:37
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I had updated my system with yum update, I tried installing that manually but still the same error comes. I even tried forcefully installing but none worked. This same error occurs every-time. -- ONKAR NATH Senior Research Fellow National Institute of Plant Genome Research Aruna Asaf Ali Marg, New Delhi- 110067 Email- onk...@gm... Mob: +91-9136065766 skype id: onkarnath89 On Tue, Jun 19, 2018 at 11:36 AM, Colin <col...@gm...> wrote: > The steps that are listed have been tested on CentOS 6.9 so it's sort of > hard to see what the issue is. You could try manually installing this > module to the system with just "cpan PerlIO::gzip" to see what happens > Could also try rebooting or yum update? (you didnt include yum update in > your list of commands that you replied with) > > > > -Colin > > On Mon, Jun 18, 2018 at 11:33 PM Onkar Nath <onk...@gm...> wrote: > >> I have tried these and found them installed. I am getting error of >> PerlIO::gzip library. >> >> when installig PerlIO::gzip >> error that I get is >> >> gzip.xs:16:10: fatal error: zlib.h: No such file or directory >> #include <zlib.h> >> ^~~~~~~~ >> compilation terminated. >> make: *** [gzip.o] Error 1 >> >> I have tried many solutions from web but none of them worked. some of >> them are as below: >> >> *yum install libpng libpng-devel* >> Package 2:libpng-1.2.49-2.el6_7.x86_64 already installed and latest >> version >> Package 2:libpng-devel-1.2.49-2.el6_7.x86_64 already installed and >> latest version >> >> *yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker* >> >> Package 2:libpng-devel-1.2.49-2.el6_7.x86_64 already installed and >> latest version >> Package gd-devel-2.0.35-11.el6.x86_64 already installed and latest version >> Package zlib-devel-1.2.3-29.el6.x86_64 already installed and latest >> version >> Package perl-ExtUtils-MakeMaker-6.55-144.el6.x86_64 already installed >> and latest version >> >> *yum groupinstall "Development Tools"* >> Package flex-2.5.35-9.el6.x86_64 already installed and latest version >> Package gcc-4.4.7-18.el6_9.2.x86_64 already installed and latest version >> Package redhat-rpm-config-9.0.3-51.el6.centos.noarch already installed >> and latest version >> Package rpm-build-4.8.0-55.el6.x86_64 already installed and latest version >> Package 1:make-3.81-23.el6.x86_64 already installed and latest version >> Package patch-2.6-8.el6_9.x86_64 already installed and latest version >> Package 1:pkgconfig-0.23-9.1.el6.x86_64 already installed and latest >> version >> Package gettext-0.17-18.el6.x86_64 already installed and latest version >> Package automake-1.11.1-4.el6.noarch already installed and latest version >> Package bison-2.4.1-5.el6.x86_64 already installed and latest version >> Package libtool-2.2.6-15.5.el6.x86_64 already installed and latest version >> Package autoconf-2.63-5.1.el6.noarch already installed and latest version >> Package gcc-c++-4.4.7-18.el6_9.2.x86_64 already installed and latest >> version >> Package binutils-2.20.51.0.2-5.47.el6_9.1.x86_64 already installed and >> latest version >> Package patchutils-0.3.1-3.1.el6.x86_64 already installed and latest >> version >> Package byacc-1.9.20070509-7.el6.x86_64 already installed and latest >> version >> Package indent-2.2.10-7.el6.x86_64 already installed and latest version >> Package systemtap-2.9-7.el6.x86_64 already installed and latest version >> Package diffstat-1.51-2.el6.x86_64 already installed and latest version >> Package elfutils-0.164-2.el6.x86_64 already installed and latest version >> Package cvs-1.11.23-16.el6.x86_64 already installed and latest version >> Package rcs-5.7-37.el6.x86_64 already installed and latest version >> Package subversion-1.6.11-15.el6_7.x86_64 already installed and latest >> version >> Package gcc-gfortran-4.4.7-18.el6_9.2.x86_64 already installed and >> latest version >> Package 1:doxygen-1.6.1-6.el6.x86_64 already installed and latest version >> Package intltool-0.41.0-1.1.el6.noarch already installed and latest >> version >> Package git-1.7.1-9.el6_9.x86_64 already installed and latest version >> Package ctags-5.8-2.el6.x86_64 already installed and latest version >> Package cscope-15.6-7.el6.x86_64 already installed and latest version >> Package swig-1.3.40-6.el6.x86_64 already installed and latest version >> Warning: Group development does not have any packages. >> No packages in any requested group available to install or update >> >> But Still the error persists. >> >> >> >> -- >> >> ONKAR NATH >> Senior Research Fellow >> National Institute of Plant Genome Research >> Aruna Asaf Ali Marg, New Delhi- 110067 >> Email- onk...@gm... >> Mob: +91-9136065766 >> skype id: onkarnath89 >> >> >> On Mon, Jun 18, 2018 at 9:07 PM, Colin <col...@gm...> wrote: >> >>> Ah ok, centos :) >>> >>> From this link http://www.gmod.org/wiki/JBrowse_Troubleshooting#Linux_ >>> -_Red_Hat_.2F_Fedora_.2F_CentOS >>> >>> I'd recommend >>> >>> yum update >>> yum groupinstall "Development Tools" >>> yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker >>> >>> >>> -Colin >>> >>> On Mon, Jun 18, 2018 at 1:01 AM Onkar Nath <onk...@gm...> >>> wrote: >>> >>>> I had Ran this command and found all these installed >>>> >>>> yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker >>>> >>>> Details: >>>> [root@localhost JBrowse-1.14.2]# yum install libpng-devel gd-devel >>>> zlib-devel perl-ExtUtils-MakeMaker >>>> Loaded plugins: fastestmirror, refresh-packagekit, security >>>> Setting up Install Process >>>> Loading mirror speeds from cached hostfile >>>> * base: mirror.dhakacom.com >>>> * epel: ftp.riken.jp >>>> * extras: mirror.dhakacom.com >>>> * updates: mirror.dhakacom.com >>>> Package 2:libpng-devel-1.2.49-2.el6_7.x86_64 already installed and >>>> latest version >>>> Package gd-devel-2.0.35-11.el6.x86_64 already installed and latest >>>> version >>>> Package zlib-devel-1.2.3-29.el6.x86_64 already installed and latest >>>> version >>>> Package perl-ExtUtils-MakeMaker-6.55-144.el6.x86_64 already installed >>>> and latest version >>>> Nothing to do >>>> [root@localhost JBrowse-1.14.2]# >>>> >>>> Still this error occurs. >>>> >>>> >>>> -- >>>> >>>> ONKAR NATH >>>> Senior Research Fellow >>>> National Institute of Plant Genome Research >>>> Aruna Asaf Ali Marg, New Delhi- 110067 >>>> Email- onk...@gm... >>>> Mob: +91-9136065766 >>>> skype id: onkarnath89 >>>> >>>> >>>> On Sun, Jun 17, 2018 at 5:54 AM, Colin <col...@gm...> wrote: >>>> >>>>> It is recommended to install zlib and some basic dependencies for your >>>>> linux setup >>>>> >>>>> A command you can run is here >>>>> >>>>> http://gmod.org/wiki/JBrowse_Configuration_Guide#Making_a_New_JBrowse >>>>> >>>>> >>>>> sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev >>>>> build-essential >>>>> >>>>> >>>>> -Colin >>>>> >>>>> On Sat, Jun 16, 2018 at 7:38 AM Onkar Nath <onk...@gm...> >>>>> wrote: >>>>> >>>>>> Dear JBrowse team, >>>>>> I want to imbed JBrowse into my html page. So I tried installing it >>>>>> on my system. But I am getting an error of zlib.h. I have tried the >>>>>> instructions available on your wikipage and some others by google search. >>>>>> But none has worked. Kindly Consider the related log file. >>>>>> Any support will be helpful. >>>>>> Waiting eagerly for your reply. >>>>>> >>>>>> Regards >>>>>> -- >>>>>> >>>>>> ONKAR NATH >>>>>> Senior Research Fellow >>>>>> National Institute of Plant Genome Research >>>>>> Aruna Asaf Ali Marg, New Delhi- 110067 >>>>>> Email- onk...@gm... >>>>>> Mob: +91-9136065766 >>>>>> skype id: onkarnath89 >>>>>> >>>>>> ------------------------------------------------------------ >>>>>> ------------------ >>>>>> Check out the vibrant tech community on one of the world's most >>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______ >>>>>> _________________________________________ >>>>>> Gmod-ajax mailing list >>>>>> Gmo...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>>> >>>>> >>>> >> |
|
From: Loraine G. <lor...@sb...> - 2018-06-19 09:17:20
|
Dear JBrowse team,
I have huge paired-end RNAseq BAM files (e.g. 1.6Go for 2.4Mbp), for
which the whole amount of reads is too big to be visualized in most
locations ("too many features" and "max height reached"), despite a
small glyph height and a compact display mode. And increasing
chunkSizeLimit to 10 MiB is not sufficient and tends to blow up the browser.
I also have coverage bigwig files that display the overall coverage but
not the strand-specific coverage.
My challenge is to offer a display that give a glimpse of the positive
and negative strand coverage.
So, I wonder what is the best way in JBrowse to display positive strand
coverage and negative strand coverage from a BAM file (or Bigwig) for
RNAseq data.
A solution would be to display 2 bigwig files (positive and negative
strand) into the same track, wouldn't it ? I have seen in the JBrowse
FAQ that a "multibigwig" plugin is available
(https://github.com/elsiklab/multibigwig), but is it possible to use
subtracks with the core code of JBrowse ? (I am not keen of using
plugins for maintenance reasons)
Do you see any other solutions ?
Thanks,
Loraine Guéguen
--
Loraine Guéguen
UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Station Biologique de Roscoff - CNRS | Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/
|
|
From: Colin <col...@gm...> - 2018-06-19 06:06:30
|
The steps that are listed have been tested on CentOS 6.9 so it's sort of hard to see what the issue is. You could try manually installing this module to the system with just "cpan PerlIO::gzip" to see what happens Could also try rebooting or yum update? (you didnt include yum update in your list of commands that you replied with) -Colin On Mon, Jun 18, 2018 at 11:33 PM Onkar Nath <onk...@gm...> wrote: > I have tried these and found them installed. I am getting error of > PerlIO::gzip library. > > when installig PerlIO::gzip > error that I get is > > gzip.xs:16:10: fatal error: zlib.h: No such file or directory > #include <zlib.h> > ^~~~~~~~ > compilation terminated. > make: *** [gzip.o] Error 1 > > I have tried many solutions from web but none of them worked. some of them > are as below: > > *yum install libpng libpng-devel* > Package 2:libpng-1.2.49-2.el6_7.x86_64 already installed and latest version > Package 2:libpng-devel-1.2.49-2.el6_7.x86_64 already installed and latest > version > > *yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker* > > Package 2:libpng-devel-1.2.49-2.el6_7.x86_64 already installed and latest > version > Package gd-devel-2.0.35-11.el6.x86_64 already installed and latest version > Package zlib-devel-1.2.3-29.el6.x86_64 already installed and latest version > Package perl-ExtUtils-MakeMaker-6.55-144.el6.x86_64 already installed and > latest version > > *yum groupinstall "Development Tools"* > Package flex-2.5.35-9.el6.x86_64 already installed and latest version > Package gcc-4.4.7-18.el6_9.2.x86_64 already installed and latest version > Package redhat-rpm-config-9.0.3-51.el6.centos.noarch already installed and > latest version > Package rpm-build-4.8.0-55.el6.x86_64 already installed and latest version > Package 1:make-3.81-23.el6.x86_64 already installed and latest version > Package patch-2.6-8.el6_9.x86_64 already installed and latest version > Package 1:pkgconfig-0.23-9.1.el6.x86_64 already installed and latest > version > Package gettext-0.17-18.el6.x86_64 already installed and latest version > Package automake-1.11.1-4.el6.noarch already installed and latest version > Package bison-2.4.1-5.el6.x86_64 already installed and latest version > Package libtool-2.2.6-15.5.el6.x86_64 already installed and latest version > Package autoconf-2.63-5.1.el6.noarch already installed and latest version > Package gcc-c++-4.4.7-18.el6_9.2.x86_64 already installed and latest > version > Package binutils-2.20.51.0.2-5.47.el6_9.1.x86_64 already installed and > latest version > Package patchutils-0.3.1-3.1.el6.x86_64 already installed and latest > version > Package byacc-1.9.20070509-7.el6.x86_64 already installed and latest > version > Package indent-2.2.10-7.el6.x86_64 already installed and latest version > Package systemtap-2.9-7.el6.x86_64 already installed and latest version > Package diffstat-1.51-2.el6.x86_64 already installed and latest version > Package elfutils-0.164-2.el6.x86_64 already installed and latest version > Package cvs-1.11.23-16.el6.x86_64 already installed and latest version > Package rcs-5.7-37.el6.x86_64 already installed and latest version > Package subversion-1.6.11-15.el6_7.x86_64 already installed and latest > version > Package gcc-gfortran-4.4.7-18.el6_9.2.x86_64 already installed and latest > version > Package 1:doxygen-1.6.1-6.el6.x86_64 already installed and latest version > Package intltool-0.41.0-1.1.el6.noarch already installed and latest version > Package git-1.7.1-9.el6_9.x86_64 already installed and latest version > Package ctags-5.8-2.el6.x86_64 already installed and latest version > Package cscope-15.6-7.el6.x86_64 already installed and latest version > Package swig-1.3.40-6.el6.x86_64 already installed and latest version > Warning: Group development does not have any packages. > No packages in any requested group available to install or update > > But Still the error persists. > > > > -- > > ONKAR NATH > Senior Research Fellow > National Institute of Plant Genome Research > Aruna Asaf Ali Marg, New Delhi- 110067 > Email- onk...@gm... > Mob: +91-9136065766 > skype id: onkarnath89 > > > On Mon, Jun 18, 2018 at 9:07 PM, Colin <col...@gm...> wrote: > >> Ah ok, centos :) >> >> From this link >> http://www.gmod.org/wiki/JBrowse_Troubleshooting#Linux_-_Red_Hat_.2F_Fedora_.2F_CentOS >> >> I'd recommend >> >> yum update >> yum groupinstall "Development Tools" >> yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker >> >> >> -Colin >> >> On Mon, Jun 18, 2018 at 1:01 AM Onkar Nath <onk...@gm...> wrote: >> >>> I had Ran this command and found all these installed >>> >>> yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker >>> >>> Details: >>> [root@localhost JBrowse-1.14.2]# yum install libpng-devel gd-devel >>> zlib-devel perl-ExtUtils-MakeMaker >>> Loaded plugins: fastestmirror, refresh-packagekit, security >>> Setting up Install Process >>> Loading mirror speeds from cached hostfile >>> * base: mirror.dhakacom.com >>> * epel: ftp.riken.jp >>> * extras: mirror.dhakacom.com >>> * updates: mirror.dhakacom.com >>> Package 2:libpng-devel-1.2.49-2.el6_7.x86_64 already installed and >>> latest version >>> Package gd-devel-2.0.35-11.el6.x86_64 already installed and latest >>> version >>> Package zlib-devel-1.2.3-29.el6.x86_64 already installed and latest >>> version >>> Package perl-ExtUtils-MakeMaker-6.55-144.el6.x86_64 already installed >>> and latest version >>> Nothing to do >>> [root@localhost JBrowse-1.14.2]# >>> >>> Still this error occurs. >>> >>> >>> -- >>> >>> ONKAR NATH >>> Senior Research Fellow >>> National Institute of Plant Genome Research >>> Aruna Asaf Ali Marg, New Delhi- 110067 >>> Email- onk...@gm... >>> Mob: +91-9136065766 >>> skype id: onkarnath89 >>> >>> >>> On Sun, Jun 17, 2018 at 5:54 AM, Colin <col...@gm...> wrote: >>> >>>> It is recommended to install zlib and some basic dependencies for your >>>> linux setup >>>> >>>> A command you can run is here >>>> >>>> http://gmod.org/wiki/JBrowse_Configuration_Guide#Making_a_New_JBrowse >>>> >>>> >>>> sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev >>>> build-essential >>>> >>>> >>>> -Colin >>>> >>>> On Sat, Jun 16, 2018 at 7:38 AM Onkar Nath <onk...@gm...> >>>> wrote: >>>> >>>>> Dear JBrowse team, >>>>> I want to imbed JBrowse into my html page. So I tried installing it on >>>>> my system. But I am getting an error of zlib.h. I have tried the >>>>> instructions available on your wikipage and some others by google search. >>>>> But none has worked. Kindly Consider the related log file. >>>>> Any support will be helpful. >>>>> Waiting eagerly for your reply. >>>>> >>>>> Regards >>>>> -- >>>>> >>>>> ONKAR NATH >>>>> Senior Research Fellow >>>>> National Institute of Plant Genome Research >>>>> Aruna Asaf Ali Marg, New Delhi- 110067 >>>>> Email- onk...@gm... >>>>> Mob: +91-9136065766 >>>>> skype id: onkarnath89 >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Check out the vibrant tech community on one of the world's most >>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>>> _______________________________________________ >>>>> Gmod-ajax mailing list >>>>> Gmo...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>> >>>> >>> > |
|
From: Onkar N. <onk...@gm...> - 2018-06-19 03:33:46
|
I have tried these and found them installed. I am getting error of PerlIO::gzip library. when installig PerlIO::gzip error that I get is gzip.xs:16:10: fatal error: zlib.h: No such file or directory #include <zlib.h> ^~~~~~~~ compilation terminated. make: *** [gzip.o] Error 1 I have tried many solutions from web but none of them worked. some of them are as below: *yum install libpng libpng-devel* Package 2:libpng-1.2.49-2.el6_7.x86_64 already installed and latest version Package 2:libpng-devel-1.2.49-2.el6_7.x86_64 already installed and latest version *yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker* Package 2:libpng-devel-1.2.49-2.el6_7.x86_64 already installed and latest version Package gd-devel-2.0.35-11.el6.x86_64 already installed and latest version Package zlib-devel-1.2.3-29.el6.x86_64 already installed and latest version Package perl-ExtUtils-MakeMaker-6.55-144.el6.x86_64 already installed and latest version *yum groupinstall "Development Tools"* Package flex-2.5.35-9.el6.x86_64 already installed and latest version Package gcc-4.4.7-18.el6_9.2.x86_64 already installed and latest version Package redhat-rpm-config-9.0.3-51.el6.centos.noarch already installed and latest version Package rpm-build-4.8.0-55.el6.x86_64 already installed and latest version Package 1:make-3.81-23.el6.x86_64 already installed and latest version Package patch-2.6-8.el6_9.x86_64 already installed and latest version Package 1:pkgconfig-0.23-9.1.el6.x86_64 already installed and latest version Package gettext-0.17-18.el6.x86_64 already installed and latest version Package automake-1.11.1-4.el6.noarch already installed and latest version Package bison-2.4.1-5.el6.x86_64 already installed and latest version Package libtool-2.2.6-15.5.el6.x86_64 already installed and latest version Package autoconf-2.63-5.1.el6.noarch already installed and latest version Package gcc-c++-4.4.7-18.el6_9.2.x86_64 already installed and latest version Package binutils-2.20.51.0.2-5.47.el6_9.1.x86_64 already installed and latest version Package patchutils-0.3.1-3.1.el6.x86_64 already installed and latest version Package byacc-1.9.20070509-7.el6.x86_64 already installed and latest version Package indent-2.2.10-7.el6.x86_64 already installed and latest version Package systemtap-2.9-7.el6.x86_64 already installed and latest version Package diffstat-1.51-2.el6.x86_64 already installed and latest version Package elfutils-0.164-2.el6.x86_64 already installed and latest version Package cvs-1.11.23-16.el6.x86_64 already installed and latest version Package rcs-5.7-37.el6.x86_64 already installed and latest version Package subversion-1.6.11-15.el6_7.x86_64 already installed and latest version Package gcc-gfortran-4.4.7-18.el6_9.2.x86_64 already installed and latest version Package 1:doxygen-1.6.1-6.el6.x86_64 already installed and latest version Package intltool-0.41.0-1.1.el6.noarch already installed and latest version Package git-1.7.1-9.el6_9.x86_64 already installed and latest version Package ctags-5.8-2.el6.x86_64 already installed and latest version Package cscope-15.6-7.el6.x86_64 already installed and latest version Package swig-1.3.40-6.el6.x86_64 already installed and latest version Warning: Group development does not have any packages. No packages in any requested group available to install or update But Still the error persists. -- ONKAR NATH Senior Research Fellow National Institute of Plant Genome Research Aruna Asaf Ali Marg, New Delhi- 110067 Email- onk...@gm... Mob: +91-9136065766 skype id: onkarnath89 On Mon, Jun 18, 2018 at 9:07 PM, Colin <col...@gm...> wrote: > Ah ok, centos :) > > From this link http://www.gmod.org/wiki/JBrowse_Troubleshooting#Linux_ > -_Red_Hat_.2F_Fedora_.2F_CentOS > > I'd recommend > > yum update > yum groupinstall "Development Tools" > yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker > > > -Colin > > On Mon, Jun 18, 2018 at 1:01 AM Onkar Nath <onk...@gm...> wrote: > >> I had Ran this command and found all these installed >> >> yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker >> >> Details: >> [root@localhost JBrowse-1.14.2]# yum install libpng-devel gd-devel >> zlib-devel perl-ExtUtils-MakeMaker >> Loaded plugins: fastestmirror, refresh-packagekit, security >> Setting up Install Process >> Loading mirror speeds from cached hostfile >> * base: mirror.dhakacom.com >> * epel: ftp.riken.jp >> * extras: mirror.dhakacom.com >> * updates: mirror.dhakacom.com >> Package 2:libpng-devel-1.2.49-2.el6_7.x86_64 already installed and >> latest version >> Package gd-devel-2.0.35-11.el6.x86_64 already installed and latest version >> Package zlib-devel-1.2.3-29.el6.x86_64 already installed and latest >> version >> Package perl-ExtUtils-MakeMaker-6.55-144.el6.x86_64 already installed >> and latest version >> Nothing to do >> [root@localhost JBrowse-1.14.2]# >> >> Still this error occurs. >> >> >> -- >> >> ONKAR NATH >> Senior Research Fellow >> National Institute of Plant Genome Research >> Aruna Asaf Ali Marg, New Delhi- 110067 >> Email- onk...@gm... >> Mob: +91-9136065766 >> skype id: onkarnath89 >> >> >> On Sun, Jun 17, 2018 at 5:54 AM, Colin <col...@gm...> wrote: >> >>> It is recommended to install zlib and some basic dependencies for your >>> linux setup >>> >>> A command you can run is here >>> >>> http://gmod.org/wiki/JBrowse_Configuration_Guide#Making_a_New_JBrowse >>> >>> >>> sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev >>> build-essential >>> >>> >>> -Colin >>> >>> On Sat, Jun 16, 2018 at 7:38 AM Onkar Nath <onk...@gm...> >>> wrote: >>> >>>> Dear JBrowse team, >>>> I want to imbed JBrowse into my html page. So I tried installing it on >>>> my system. But I am getting an error of zlib.h. I have tried the >>>> instructions available on your wikipage and some others by google search. >>>> But none has worked. Kindly Consider the related log file. >>>> Any support will be helpful. >>>> Waiting eagerly for your reply. >>>> >>>> Regards >>>> -- >>>> >>>> ONKAR NATH >>>> Senior Research Fellow >>>> National Institute of Plant Genome Research >>>> Aruna Asaf Ali Marg, New Delhi- 110067 >>>> Email- onk...@gm... >>>> Mob: +91-9136065766 >>>> skype id: onkarnath89 >>>> >>>> ------------------------------------------------------------ >>>> ------------------ >>>> Check out the vibrant tech community on one of the world's most >>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______ >>>> _________________________________________ >>>> Gmod-ajax mailing list >>>> Gmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>> >>> >> |
|
From: Colin <col...@gm...> - 2018-06-18 15:38:02
|
Ah ok, centos :) >From this link http://www.gmod.org/wiki/JBrowse_Troubleshooting#Linux_-_Red_Hat_.2F_Fedora_.2F_CentOS I'd recommend yum update yum groupinstall "Development Tools" yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker -Colin On Mon, Jun 18, 2018 at 1:01 AM Onkar Nath <onk...@gm...> wrote: > I had Ran this command and found all these installed > > yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker > > Details: > [root@localhost JBrowse-1.14.2]# yum install libpng-devel gd-devel > zlib-devel perl-ExtUtils-MakeMaker > Loaded plugins: fastestmirror, refresh-packagekit, security > Setting up Install Process > Loading mirror speeds from cached hostfile > * base: mirror.dhakacom.com > * epel: ftp.riken.jp > * extras: mirror.dhakacom.com > * updates: mirror.dhakacom.com > Package 2:libpng-devel-1.2.49-2.el6_7.x86_64 already installed and latest > version > Package gd-devel-2.0.35-11.el6.x86_64 already installed and latest version > Package zlib-devel-1.2.3-29.el6.x86_64 already installed and latest version > Package perl-ExtUtils-MakeMaker-6.55-144.el6.x86_64 already installed and > latest version > Nothing to do > [root@localhost JBrowse-1.14.2]# > > Still this error occurs. > > > -- > > ONKAR NATH > Senior Research Fellow > National Institute of Plant Genome Research > Aruna Asaf Ali Marg, New Delhi- 110067 > Email- onk...@gm... > Mob: +91-9136065766 > skype id: onkarnath89 > > > On Sun, Jun 17, 2018 at 5:54 AM, Colin <col...@gm...> wrote: > >> It is recommended to install zlib and some basic dependencies for your >> linux setup >> >> A command you can run is here >> >> http://gmod.org/wiki/JBrowse_Configuration_Guide#Making_a_New_JBrowse >> >> >> sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev >> build-essential >> >> >> -Colin >> >> On Sat, Jun 16, 2018 at 7:38 AM Onkar Nath <onk...@gm...> wrote: >> >>> Dear JBrowse team, >>> I want to imbed JBrowse into my html page. So I tried installing it on >>> my system. But I am getting an error of zlib.h. I have tried the >>> instructions available on your wikipage and some others by google search. >>> But none has worked. Kindly Consider the related log file. >>> Any support will be helpful. >>> Waiting eagerly for your reply. >>> >>> Regards >>> -- >>> >>> ONKAR NATH >>> Senior Research Fellow >>> National Institute of Plant Genome Research >>> Aruna Asaf Ali Marg, New Delhi- 110067 >>> Email- onk...@gm... >>> Mob: +91-9136065766 >>> skype id: onkarnath89 >>> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> Gmod-ajax mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>> >> > |
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From: Onkar N. <onk...@gm...> - 2018-06-18 05:01:29
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I had Ran this command and found all these installed yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker Details: [root@localhost JBrowse-1.14.2]# yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker Loaded plugins: fastestmirror, refresh-packagekit, security Setting up Install Process Loading mirror speeds from cached hostfile * base: mirror.dhakacom.com * epel: ftp.riken.jp * extras: mirror.dhakacom.com * updates: mirror.dhakacom.com Package 2:libpng-devel-1.2.49-2.el6_7.x86_64 already installed and latest version Package gd-devel-2.0.35-11.el6.x86_64 already installed and latest version Package zlib-devel-1.2.3-29.el6.x86_64 already installed and latest version Package perl-ExtUtils-MakeMaker-6.55-144.el6.x86_64 already installed and latest version Nothing to do [root@localhost JBrowse-1.14.2]# Still this error occurs. -- ONKAR NATH Senior Research Fellow National Institute of Plant Genome Research Aruna Asaf Ali Marg, New Delhi- 110067 Email- onk...@gm... Mob: +91-9136065766 skype id: onkarnath89 On Sun, Jun 17, 2018 at 5:54 AM, Colin <col...@gm...> wrote: > It is recommended to install zlib and some basic dependencies for your > linux setup > > A command you can run is here > > http://gmod.org/wiki/JBrowse_Configuration_Guide#Making_a_New_JBrowse > > > sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev > build-essential > > > -Colin > > On Sat, Jun 16, 2018 at 7:38 AM Onkar Nath <onk...@gm...> wrote: > >> Dear JBrowse team, >> I want to imbed JBrowse into my html page. So I tried installing it on my >> system. But I am getting an error of zlib.h. I have tried the instructions >> available on your wikipage and some others by google search. But none has >> worked. Kindly Consider the related log file. >> Any support will be helpful. >> Waiting eagerly for your reply. >> >> Regards >> -- >> >> ONKAR NATH >> Senior Research Fellow >> National Institute of Plant Genome Research >> Aruna Asaf Ali Marg, New Delhi- 110067 >> Email- onk...@gm... >> Mob: +91-9136065766 >> skype id: onkarnath89 >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot______ >> _________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > |
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From: Michal Č. <mis...@gm...> - 2018-06-17 12:59:09
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Dear JBrowse team, I am experiencing difficulties with biodb-to-json.pl configuration file. I would like to use feature - subfeature relationship and using various glyphs the visualization looks okey, but i am not able to see labels, or name tags over the sub-features, i would like them to behave like ordinary features. If i use only ordinary features they are drawn under each other. I would like them to be in one row with sub-features of different color. I would love to have visualization like Volvox CanvasFeatures - Protein-coding gene, but with named sub-features. Can you recommend me how to achieve it ? Any tip would be helpful. Thanks for your help. Regards Michal Červeňanský. |
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From: Colin <col...@gm...> - 2018-06-17 00:24:55
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It is recommended to install zlib and some basic dependencies for your linux setup A command you can run is here http://gmod.org/wiki/JBrowse_Configuration_Guide#Making_a_New_JBrowse sudo apt-get install zlib1g-dev libpng-dev libgd2-noxpm-dev build-essential -Colin On Sat, Jun 16, 2018 at 7:38 AM Onkar Nath <onk...@gm...> wrote: > Dear JBrowse team, > I want to imbed JBrowse into my html page. So I tried installing it on my > system. But I am getting an error of zlib.h. I have tried the instructions > available on your wikipage and some others by google search. But none has > worked. Kindly Consider the related log file. > Any support will be helpful. > Waiting eagerly for your reply. > > Regards > -- > > ONKAR NATH > Senior Research Fellow > National Institute of Plant Genome Research > Aruna Asaf Ali Marg, New Delhi- 110067 > Email- onk...@gm... > Mob: +91-9136065766 > skype id: onkarnath89 > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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