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From: Anubhav R. <anu...@gm...> - 2018-09-21 10:18:17
|
volvox example data is not opening in browser though i have successfully installed and run setup.sh file .i have also installed lampp web server.please help.SCREENSHOT and SET.LOG are ATTACHED. -- Anubhav Roy Ph.D. (Bioinformatics) IASRI, Pusa, New delhi - 110012 |
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From: Nicolas D. <nic...@um...> - 2018-09-14 10:35:13
|
Thanks Colin! Yup, I'd be in sort of things :-) I was not sure how linked the two (the docs and GitHub) were because of the different URLs, so I went for the "safest" way. Thanks for the quick fix. Have a nice WE, Nico --------------------------------------------------------------- Nicolas Delhomme, PhD UPSC bioinformatics facility Manager Umeå Plant Science Center, Swedish University for Agricultural Sciences (SLU) and Umeå University Tel: +46 90 786 5478 Email: nic...@um... SLU - Umeå universitet Umeå S-901 87 Sweden www.slu.se/framtidiskogen --------------------------------------------------------------- > On 13 Sep 2018, at 19:35, Colin <col...@gm...> wrote: > > Thanks Nicolas :) > > I went ahead and fixed those. Note that the documentation for the website can now be fixed via pull requests to the GMOD/jbrowse repository on github if you're into that sort of thing too. It's just encoded in markdown files > > In any case, thanks for reporting > > -Colin > > On Thu, Sep 13, 2018 at 11:17 AM Nicolas Delhomme <nic...@um...> wrote: > Hej! > > The pages https://jbrowse.org/docs/canvas_features.html and https://jbrowse.org/docs/html_features.html have a broken link: flatfile-to-json.pl that links to "https://jbrowse.org/docs/flatfile-to-json.pl" instead of "https://jbrowse.org/docs/flatfile-to-json.pl.html". Also there is a space missing in front of the link. > > Best, > > --------------------------------------------------------------- > Nicolas Delhomme, PhD > > UPSC bioinformatics facility Manager > Umeå Plant Science Center, > Swedish University for Agricultural > Sciences (SLU) and Umeå University > > Tel: +46 90 786 5478 > Email: nic...@um... > SLU - Umeå universitet > Umeå S-901 87 Sweden > www.slu.se/framtidiskogen > --------------------------------------------------------------- > > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
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From: Colin <col...@gm...> - 2018-09-13 17:36:05
|
Thanks Nicolas :) I went ahead and fixed those. Note that the documentation for the website can now be fixed via pull requests to the GMOD/jbrowse repository on github if you're into that sort of thing too. It's just encoded in markdown files In any case, thanks for reporting -Colin On Thu, Sep 13, 2018 at 11:17 AM Nicolas Delhomme <nic...@um...> wrote: > Hej! > > The pages https://jbrowse.org/docs/canvas_features.html and > https://jbrowse.org/docs/html_features.html have a broken link: > flatfile-to-json.pl that links to " > https://jbrowse.org/docs/flatfile-to-json.pl" instead of " > https://jbrowse.org/docs/flatfile-to-json.pl.html". Also there is a space > missing in front of the link. > > Best, > > --------------------------------------------------------------- > Nicolas Delhomme, PhD > > UPSC bioinformatics facility Manager > Umeå Plant Science Center, > Swedish University for Agricultural > Sciences (SLU) and Umeå University > > Tel: +46 90 786 5478 > Email: nic...@um... > SLU - Umeå universitet > Umeå S-901 87 Sweden > www.slu.se/framtidiskogen > --------------------------------------------------------------- > > > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Nicolas D. <nic...@um...> - 2018-09-13 15:01:12
|
Hej! The pages https://jbrowse.org/docs/canvas_features.html and https://jbrowse.org/docs/html_features.html have a broken link: flatfile-to-json.pl that links to "https://jbrowse.org/docs/flatfile-to-json.pl" instead of "https://jbrowse.org/docs/flatfile-to-json.pl.html". Also there is a space missing in front of the link. Best, --------------------------------------------------------------- Nicolas Delhomme, PhD UPSC bioinformatics facility Manager Umeå Plant Science Center, Swedish University for Agricultural Sciences (SLU) and Umeå University Tel: +46 90 786 5478 Email: nic...@um... SLU - Umeå universitet Umeå S-901 87 Sweden www.slu.se/framtidiskogen --------------------------------------------------------------- |
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From: Colin <col...@gm...> - 2018-09-05 19:10:55
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Hi Vaneet, I added this github issue to track it https://github.com/GMOD/jbrowse/issues/1203 -Colin On Wed, Sep 5, 2018 at 1:10 PM Vaneet Lotay <van...@uc...> wrote: > Hey guys, > > > > Just want to reiterate that having a custom sort function both for sorting > categories and the tracks in the categories would be very useful and > beneficial for me too. I hope it’s on the list of features to add for > future JBrowse releases. > > > > Thanks, > > > Vaneet > > > > *Vaneet Lotay* > > *Xenbase Bioinformatician* > > *716 ICT Building - University of Calgary* > > *2500 University Drive NW* > > *Calgary AB T2N 1N4* > > *CANADA* > > > > *From:* Colin [mailto:col...@gm...] > *Sent:* Tuesday, August 14, 2018 1:46 PM > *To:* Ben Bimber <bb...@gm...> > *Cc:* gmo...@li... > *Subject:* Re: [Gmod-ajax] Control Ordering of Categories in Left-hand > Panel? > > > > There is no way to provide a custom sort function currently but you can > specify "trackSelector.sortHierarchical=false" and then the sorting will be > basically in whichever order the tracks are loaded as. If that does not > satisfy the issue, as in maybe you do need a custom sorter besides "no > sorting", feel free to make a github issue > > > > In jbrowse.conf that might look like > > > > [trackSelector] > > sortHierarchical=false > > > > > > Or in trackList.json > > > > "trackSelector": { > > "sortHierarchical": false > > } > > > > -Colin > > > > On Tue, Aug 14, 2018 at 3:36 PM Ben Bimber <bb...@gm...> wrote: > > Hello, > > > > In a jbrowse session, you provide a list of tracks, and these tracks can > have a category. The left-hand panel shows available tracks, with tracks > grouped by category. It seems to sort categories alphabetically. is it > possible to manually provide a sort order for categories in one of the JSON > contig files? I didnt see anything like this in the examples: > http://gmod.org/wiki/JBrowse_Configuration_Guide. > > > > Thanks for any help, > > Ben > > > ------------------------------------------------------------------------------ > 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: Vaneet L. <van...@uc...> - 2018-09-05 17:10:32
|
Hey guys,
Just want to reiterate that having a custom sort function both for sorting categories and the tracks in the categories would be very useful and beneficial for me too. I hope it’s on the list of features to add for future JBrowse releases.
Thanks,
Vaneet
Vaneet Lotay
Xenbase Bioinformatician
716 ICT Building - University of Calgary
2500 University Drive NW
Calgary AB T2N 1N4
CANADA
From: Colin [mailto:col...@gm...]
Sent: Tuesday, August 14, 2018 1:46 PM
To: Ben Bimber <bb...@gm...>
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] Control Ordering of Categories in Left-hand Panel?
There is no way to provide a custom sort function currently but you can specify "trackSelector.sortHierarchical=false" and then the sorting will be basically in whichever order the tracks are loaded as. If that does not satisfy the issue, as in maybe you do need a custom sorter besides "no sorting", feel free to make a github issue
In jbrowse.conf that might look like
[trackSelector]
sortHierarchical=false
Or in trackList.json
"trackSelector": {
"sortHierarchical": false
}
-Colin
On Tue, Aug 14, 2018 at 3:36 PM Ben Bimber <bb...@gm...<mailto:bb...@gm...>> wrote:
Hello,
In a jbrowse session, you provide a list of tracks, and these tracks can have a category. The left-hand panel shows available tracks, with tracks grouped by category. It seems to sort categories alphabetically. is it possible to manually provide a sort order for categories in one of the JSON contig files? I didnt see anything like this in the examples: http://gmod.org/wiki/JBrowse_Configuration_Guide.
Thanks for any help,
Ben
------------------------------------------------------------------------------
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
|
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From: Nathan D. <nat...@lb...> - 2018-09-05 16:29:14
|
> On Sep 5, 2018, at 8:53 AM, Sofia Robb <so...@so...> wrote: > > The add tracks works, but the data isn't in the track selector. We love the track selector! Hmm . . I would follow up with the JBrowse team (and cc me) directly on that. You should be able to see the track selector as well, depending on how its configured. > > The two different jbrowse/trackList with same data is the way we handling this now. Though we use apache authentication. I need to check out auth0 and passport. Can they use drupal user and password info? I haven’t done it, but I think so. https://www.npmjs.com/package/passport-drupal <https://www.npmjs.com/package/passport-drupal> Nathan > > > On Wed, Sep 5, 2018 at 7:38 AM, Nathan Dunn <nat...@lb... <mailto:nat...@lb...>> wrote: > > I think the easiest way to keep them “private” would be make them available and unlinked and then bring them in via a URL. > > You should be able to use a combination of addStores and addTracks (+1 on the new documentation BTW): > > http://jbrowse.org/docs/url_strings.html#addtracks <http://jbrowse.org/docs/url_strings.html#addtracks> > > Not exactly HIPPA compliant, but you can you an external web application to inject those URLs as I know that some groups have done. > > > That being said, if you are embedding JBrowse within a website and you need true security, I would advocate using something like auth0 or passport (https://www.npmjs.com/package/passport <https://www.npmjs.com/package/passport>) and them maybe maintaining two instances of the same JBrowse (same data, but different trackList.json available). > > Nathan > > >> On Sep 4, 2018, at 11:55 PM, SAPET, Frederic <fre...@bi... <mailto:fre...@bi...>> wrote: >> >> Hello all, >> >> Just like Sofia, our needs are the same here. >> >> Fred >> >> De : Sofia Robb [mailto:so...@so... <mailto:so...@so...>] >> Envoyé : mardi 4 septembre 2018 20:02 >> À : Hulse-Kemp, Amanda - ARS <Ama...@ar... <mailto:Ama...@ar...>> >> Cc : gmo...@li... <mailto:gmo...@li...> >> Objet : Re: [Gmod-ajax] Jbrowse Authentication >> >> Hello Rob and Colin and All. >> >> Just wanted to through in my two cents. >> >> User Authentication in JBrowse is definitely something we are interested in. We would LOVE to be able to keep some tracks private, such as on going research, while the rest are open to the world. Right now I have to set up two separate JBrowse installations to get what we need, and it is sometimes kinda a pain to remember to do what I need to do in both. >> >> Thanks, >> Sofia >> >> >> >> On Tue, Sep 4, 2018 at 7:59 AM, Hulse-Kemp, Amanda - ARS <Ama...@ar... <mailto:Ama...@ar...>> wrote: >> On our side it would seem beneficial, as there is a lot of “polishing” work to be done on Jbrowse before you want it officially public outside of the research group. It would be ideal where something could start as accessible in private files and then move over to anonymous access. I am thinking in terms of large amounts of projects and something to allow this to be done relatively easy, without too much intervention of IT permissions etc. as many of the scientists handling it would not be able to work through those hurdles. >> >> It appears there is a possibility through Apollo, however that is an extra step and I have found is not exactly possible through CyVerse hosting and must be on a private server – unless someone has experience with doing this?? >> >> Best, >> Amanda >> >> From: Colin <col...@gm... <mailto:col...@gm...>> >> Sent: Friday, August 31, 2018 6:33 PM >> To: Nathan Dunn <nat...@lb... <mailto:nat...@lb...>> >> Cc: Robert Buels <rb...@gm... <mailto:rb...@gm...>>; Hulse-Kemp, Amanda - ARS <Ama...@AR... <mailto:Ama...@AR...>>; gmo...@li... <mailto:gmo...@li...> >> Subject: Re: [Gmod-ajax] Jbrowse Authentication >> >> Is it specifically desirable to access data remotely hosted in CyVerse? >> >> I know araport has written about this to some extent but I haven't extensively looked into it >> >> https://github.com/Arabidopsis-Information-Portal/CyverseRemoteTracks <https://github.com/Arabidopsis-Information-Portal/CyverseRemoteTracks> >> >> It does say that it is made to allow anonymous which I assume means public access, but it would be very cool if it could be extended to access private files too >> >> -Colin >> >> On Fri, Aug 31, 2018 at 6:05 PM Nathan Dunn <nat...@lb... <mailto:nat...@lb...>> wrote: >> >> I’d advocate wrapping your JBrowse page in an client-side app that uses GitHub or Google+ for authentication. >> >> If you’re really lazy (like me), I would use something like auth0 to manage allowable users. Its typically not a ton of code: https://auth0.com/docs/quickstart/spa/vanillajs <https://auth0.com/docs/quickstart/spa/vanillajs> >> >> Something like this (or just simply a GitHub authenticator) would make a great JBrowse plugin. >> >> Nathan >> >> >> >> On Aug 31, 2018, at 2:01 PM, Robert Buels <rb...@gm... <mailto:rb...@gm...>> wrote: >> >> Ccing gmod-ajax list, since he JBrowse community probably has better feedback on authentication than I do. >> >> Most people who password protect JBrowse installations use the standard HTTP Basic authentication, configured at the level of the web server. This works fine with JBrowse, and no additional configuration is needed, as long as he JBrowse main page (jbowse/index.html) is configured to be authenticated under the same scheme as the other data resources. >> >> There hasn’t been a lot of demand for additional authentication features, but the dev team is certainly open to discussing adding some. >> >> Hope this helps! >> >> Rob >> >> On Fri, Aug 31, 2018 at 8:32 AM Hulse-Kemp, Amanda - ARS <Ama...@ar... <mailto:Ama...@ar...>> wrote: >> Hello Robert, >> >> I am working with GOnRamp group as a way to launch Jbrowse instances for USDA associated genome publications with data hosting in Cyverse. I have developed a test version of my genome and currently have it implemented, however I’d really like to be able to password protect the URL. I see a number of discussions on password protection, and wanted to contact you to discuss where you were with that? >> >> Best, >> Amanda >> >> Amanda Hulse-Kemp, Ph.D. >> Computational Biologist >> USDA-ARS, Genomics and Bioinformatics Research Unit >> 1244 Williams Hall | North Carolina State University | Raleigh | NC | 27695 >> ama...@ar... <mailto:ama...@ar...> >> 919-515-7599 >> >> >> >> >> >> This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org <http://slashdot.org/>! http://sdm.link/slashdot_______________________________________________ <http://sdm.link/slashdot_______________________________________________> >> Gmod-ajax mailing list >> Gmo...@li... <mailto:Gmo...@li...> >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax <https://lists.sourceforge.net/lists/listinfo/gmod-ajax> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org <http://slashdot.org/>! http://sdm.link/slashdot <http://sdm.link/slashdot>_______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... <mailto:Gmo...@li...> >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax <https://lists.sourceforge.net/lists/listinfo/gmod-ajax> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org <http://slashdot.org/>! http://sdm.link/slashdot <http://sdm.link/slashdot> >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... <mailto:Gmo...@li...> >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax <https://lists.sourceforge.net/lists/listinfo/gmod-ajax> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org <http://slashdot.org/>! http://sdm.link/slashdot_______________________________________________ <http://sdm.link/slashdot_______________________________________________> >> Gmod-ajax mailing list >> Gmo...@li... <mailto:Gmo...@li...> >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax <https://lists.sourceforge.net/lists/listinfo/gmod-ajax> > |
|
From: Sofia R. <so...@so...> - 2018-09-05 15:53:54
|
The add tracks works, but the data isn't in the track selector. We love the track selector! The two different jbrowse/trackList with same data is the way we handling this now. Though we use apache authentication. I need to check out auth0 and passport. Can they use drupal user and password info? On Wed, Sep 5, 2018 at 7:38 AM, Nathan Dunn <nat...@lb...> wrote: > > I think the easiest way to keep them “private” would be make them > available and unlinked and then bring them in via a URL. > > You should be able to use a combination of addStores and addTracks (+1 on > the new documentation BTW): > > http://jbrowse.org/docs/url_strings.html#addtracks > > Not exactly HIPPA compliant, but you can you an external web application > to inject those URLs as I know that some groups have done. > > > That being said, if you are embedding JBrowse within a website and you > need true security, I would advocate using something like auth0 or passport > (https://www.npmjs.com/package/passport) and them maybe maintaining two > instances of the same JBrowse (same data, but different trackList.json > available). > > Nathan > > > On Sep 4, 2018, at 11:55 PM, SAPET, Frederic <fre...@bi...> > wrote: > > Hello all, > > Just like Sofia, our needs are the same here. > > Fred > > *De :* Sofia Robb [mailto:so...@so... <so...@so...>] > *Envoyé :* mardi 4 septembre 2018 20:02 > *À :* Hulse-Kemp, Amanda - ARS <Ama...@ar...> > *Cc :* gmo...@li... > *Objet :* Re: [Gmod-ajax] Jbrowse Authentication > > Hello Rob and Colin and All. > > Just wanted to through in my two cents. > > User Authentication in JBrowse is definitely something we are interested > in. We would LOVE to be able to keep some tracks private, such as on going > research, while the rest are open to the world. Right now I have to set up > two separate JBrowse installations to get what we need, and it is sometimes > kinda a pain to remember to do what I need to do in both. > > Thanks, > Sofia > > > > On Tue, Sep 4, 2018 at 7:59 AM, Hulse-Kemp, Amanda - ARS < > Ama...@ar...> wrote: > > On our side it would seem beneficial, as there is a lot of “polishing” > work to be done on Jbrowse before you want it officially public outside of > the research group. It would be ideal where something could start as > accessible in private files and then move over to anonymous access. I am > thinking in terms of large amounts of projects and something to allow this > to be done relatively easy, without too much intervention of IT permissions > etc. as many of the scientists handling it would not be able to work > through those hurdles. > > It appears there is a possibility through Apollo, however that is an extra > step and I have found is not exactly possible through CyVerse hosting and > must be on a private server – unless someone has experience with doing > this?? > > Best, > Amanda > > *From:* Colin <col...@gm...> > *Sent:* Friday, August 31, 2018 6:33 PM > *To:* Nathan Dunn <nat...@lb...> > *Cc:* Robert Buels <rb...@gm...>; Hulse-Kemp, Amanda - ARS < > Ama...@AR...>; gmo...@li... > *Subject:* Re: [Gmod-ajax] Jbrowse Authentication > > Is it specifically desirable to access data remotely hosted in CyVerse? > > I know araport has written about this to some extent but I haven't > extensively looked into it > > https://github.com/Arabidopsis-Information-Portal/CyverseRemoteTracks > > It does say that it is made to allow anonymous which I assume means public > access, but it would be very cool if it could be extended to access private > files too > > -Colin > > On Fri, Aug 31, 2018 at 6:05 PM Nathan Dunn <nat...@lb...> wrote: > > > I’d advocate wrapping your JBrowse page in an client-side app that uses > GitHub or Google+ for authentication. > > If you’re really lazy (like me), I would use something like auth0 to > manage allowable users. Its typically not a ton of code: > https://auth0.com/docs/quickstart/spa/vanillajs > > Something like this (or just simply a GitHub authenticator) would make a > great JBrowse plugin. > > Nathan > > > > > On Aug 31, 2018, at 2:01 PM, Robert Buels <rb...@gm...> wrote: > > Ccing gmod-ajax list, since he JBrowse community probably has better > feedback on authentication than I do. > > Most people who password protect JBrowse installations use the standard > HTTP Basic authentication, configured at the level of the web server. This > works fine with JBrowse, and no additional configuration is needed, as long > as he JBrowse main page (jbowse/index.html) is configured to be > authenticated under the same scheme as the other data resources. > > There hasn’t been a lot of demand for additional authentication features, > but the dev team is certainly open to discussing adding some. > > Hope this helps! > > Rob > > On Fri, Aug 31, 2018 at 8:32 AM Hulse-Kemp, Amanda - ARS < > Ama...@ar...> wrote: > > Hello Robert, > > I am working with GOnRamp group as a way to launch Jbrowse instances for > USDA associated genome publications with data hosting in Cyverse. I have > developed a test version of my genome and currently have it implemented, > however I’d really like to be able to password protect the URL. I see a > number of discussions on password protection, and wanted to contact you to > discuss where you were with that? > > Best, > Amanda > > Amanda Hulse-Kemp, Ph.D. > Computational Biologist > USDA-ARS, Genomics and Bioinformatics Research Unit > 1244 Williams Hall | North Carolina State University | Raleigh | NC | 27695 > ama...@ar... > 919-515-7599 > > > > > > This electronic message contains information generated by the USDA solely > for the intended recipients. Any unauthorized interception of this message > or the use or disclosure of the information it contains may violate the law > and subject the violator to civil or criminal penalties. If you believe you > have received this message in error, please notify the sender and delete > the email immediately. > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org <http://slashdot.org/>! http:// > sdm.link/slashdot_______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org <http://slashdot.org/>! http:// > sdm.link/slashdot_______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org <http://slashdot.org/>! http:// > sdm.link/slashdot > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org <http://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: Nathan D. <nat...@lb...> - 2018-09-05 13:38:21
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I think the easiest way to keep them “private” would be make them available and unlinked and then bring them in via a URL. You should be able to use a combination of addStores and addTracks (+1 on the new documentation BTW): http://jbrowse.org/docs/url_strings.html#addtracks <http://jbrowse.org/docs/url_strings.html#addtracks> Not exactly HIPPA compliant, but you can you an external web application to inject those URLs as I know that some groups have done. That being said, if you are embedding JBrowse within a website and you need true security, I would advocate using something like auth0 or passport (https://www.npmjs.com/package/passport <https://www.npmjs.com/package/passport>) and them maybe maintaining two instances of the same JBrowse (same data, but different trackList.json available). Nathan > On Sep 4, 2018, at 11:55 PM, SAPET, Frederic <fre...@bi...> wrote: > > Hello all, > > Just like Sofia, our needs are the same here. > > Fred > > De : Sofia Robb [mailto:so...@so... <mailto:so...@so...>] > Envoyé : mardi 4 septembre 2018 20:02 > À : Hulse-Kemp, Amanda - ARS <Ama...@ar... <mailto:Ama...@ar...>> > Cc : gmo...@li... <mailto:gmo...@li...> > Objet : Re: [Gmod-ajax] Jbrowse Authentication > > Hello Rob and Colin and All. > > Just wanted to through in my two cents. > > User Authentication in JBrowse is definitely something we are interested in. We would LOVE to be able to keep some tracks private, such as on going research, while the rest are open to the world. Right now I have to set up two separate JBrowse installations to get what we need, and it is sometimes kinda a pain to remember to do what I need to do in both. > > Thanks, > Sofia > > > > On Tue, Sep 4, 2018 at 7:59 AM, Hulse-Kemp, Amanda - ARS <Ama...@ar... <mailto:Ama...@ar...>> wrote: > On our side it would seem beneficial, as there is a lot of “polishing” work to be done on Jbrowse before you want it officially public outside of the research group. It would be ideal where something could start as accessible in private files and then move over to anonymous access. I am thinking in terms of large amounts of projects and something to allow this to be done relatively easy, without too much intervention of IT permissions etc. as many of the scientists handling it would not be able to work through those hurdles. > > It appears there is a possibility through Apollo, however that is an extra step and I have found is not exactly possible through CyVerse hosting and must be on a private server – unless someone has experience with doing this?? > > Best, > Amanda > > From: Colin <col...@gm... <mailto:col...@gm...>> > Sent: Friday, August 31, 2018 6:33 PM > To: Nathan Dunn <nat...@lb... <mailto:nat...@lb...>> > Cc: Robert Buels <rb...@gm... <mailto:rb...@gm...>>; Hulse-Kemp, Amanda - ARS <Ama...@AR... <mailto:Ama...@AR...>>; gmo...@li... <mailto:gmo...@li...> > Subject: Re: [Gmod-ajax] Jbrowse Authentication > > Is it specifically desirable to access data remotely hosted in CyVerse? > > I know araport has written about this to some extent but I haven't extensively looked into it > > https://github.com/Arabidopsis-Information-Portal/CyverseRemoteTracks <https://github.com/Arabidopsis-Information-Portal/CyverseRemoteTracks> > > It does say that it is made to allow anonymous which I assume means public access, but it would be very cool if it could be extended to access private files too > > -Colin > > On Fri, Aug 31, 2018 at 6:05 PM Nathan Dunn <nat...@lb... <mailto:nat...@lb...>> wrote: > > I’d advocate wrapping your JBrowse page in an client-side app that uses GitHub or Google+ for authentication. > > If you’re really lazy (like me), I would use something like auth0 to manage allowable users. Its typically not a ton of code: https://auth0.com/docs/quickstart/spa/vanillajs <https://auth0.com/docs/quickstart/spa/vanillajs> > > Something like this (or just simply a GitHub authenticator) would make a great JBrowse plugin. > > Nathan > > > > On Aug 31, 2018, at 2:01 PM, Robert Buels <rb...@gm... <mailto:rb...@gm...>> wrote: > > Ccing gmod-ajax list, since he JBrowse community probably has better feedback on authentication than I do. > > Most people who password protect JBrowse installations use the standard HTTP Basic authentication, configured at the level of the web server. This works fine with JBrowse, and no additional configuration is needed, as long as he JBrowse main page (jbowse/index.html) is configured to be authenticated under the same scheme as the other data resources. > > There hasn’t been a lot of demand for additional authentication features, but the dev team is certainly open to discussing adding some. > > Hope this helps! > > Rob > > On Fri, Aug 31, 2018 at 8:32 AM Hulse-Kemp, Amanda - ARS <Ama...@ar... <mailto:Ama...@ar...>> wrote: > Hello Robert, > > I am working with GOnRamp group as a way to launch Jbrowse instances for USDA associated genome publications with data hosting in Cyverse. I have developed a test version of my genome and currently have it implemented, however I’d really like to be able to password protect the URL. I see a number of discussions on password protection, and wanted to contact you to discuss where you were with that? > > Best, > Amanda > > Amanda Hulse-Kemp, Ph.D. > Computational Biologist > USDA-ARS, Genomics and Bioinformatics Research Unit > 1244 Williams Hall | North Carolina State University | Raleigh | NC | 27695 > ama...@ar... <mailto:ama...@ar...> > 919-515-7599 > > > > > > This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org <http://slashdot.org/>! http://sdm.link/slashdot_______________________________________________ <http://sdm.link/slashdot_______________________________________________> > Gmod-ajax mailing list > Gmo...@li... <mailto:Gmo...@li...> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax <https://lists.sourceforge.net/lists/listinfo/gmod-ajax> > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org <http://slashdot.org/>! http://sdm.link/slashdot <http://sdm.link/slashdot>_______________________________________________ > Gmod-ajax mailing list > Gmo...@li... <mailto:Gmo...@li...> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax <https://lists.sourceforge.net/lists/listinfo/gmod-ajax> > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org <http://slashdot.org/>! http://sdm.link/slashdot <http://sdm.link/slashdot> > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... <mailto:Gmo...@li...> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax <https://lists.sourceforge.net/lists/listinfo/gmod-ajax> > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org <http://slashdot.org/>! http://sdm.link/slashdot_______________________________________________ <http://sdm.link/slashdot_______________________________________________> > Gmod-ajax mailing list > Gmo...@li... <mailto:Gmo...@li...> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax <https://lists.sourceforge.net/lists/listinfo/gmod-ajax> |
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From: SAPET, F. <fre...@bi...> - 2018-09-05 12:31:17
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Hello all, Just like Sofia, our needs are the same here. Fred De : Sofia Robb [mailto:so...@so...] Envoyé : mardi 4 septembre 2018 20:02 À : Hulse-Kemp, Amanda - ARS <Ama...@ar...> Cc : gmo...@li... Objet : Re: [Gmod-ajax] Jbrowse Authentication Hello Rob and Colin and All. Just wanted to through in my two cents. User Authentication in JBrowse is definitely something we are interested in. We would LOVE to be able to keep some tracks private, such as on going research, while the rest are open to the world. Right now I have to set up two separate JBrowse installations to get what we need, and it is sometimes kinda a pain to remember to do what I need to do in both. Thanks, Sofia On Tue, Sep 4, 2018 at 7:59 AM, Hulse-Kemp, Amanda - ARS <Ama...@ar...<mailto:Ama...@ar...>> wrote: On our side it would seem beneficial, as there is a lot of “polishing” work to be done on Jbrowse before you want it officially public outside of the research group. It would be ideal where something could start as accessible in private files and then move over to anonymous access. I am thinking in terms of large amounts of projects and something to allow this to be done relatively easy, without too much intervention of IT permissions etc. as many of the scientists handling it would not be able to work through those hurdles. It appears there is a possibility through Apollo, however that is an extra step and I have found is not exactly possible through CyVerse hosting and must be on a private server – unless someone has experience with doing this?? Best, Amanda From: Colin <col...@gm...<mailto:col...@gm...>> Sent: Friday, August 31, 2018 6:33 PM To: Nathan Dunn <nat...@lb...<mailto:nat...@lb...>> Cc: Robert Buels <rb...@gm...<mailto:rb...@gm...>>; Hulse-Kemp, Amanda - ARS <Ama...@AR...<mailto:Ama...@AR...>>; gmo...@li...<mailto:gmo...@li...> Subject: Re: [Gmod-ajax] Jbrowse Authentication Is it specifically desirable to access data remotely hosted in CyVerse? I know araport has written about this to some extent but I haven't extensively looked into it https://github.com/Arabidopsis-Information-Portal/CyverseRemoteTracks It does say that it is made to allow anonymous which I assume means public access, but it would be very cool if it could be extended to access private files too -Colin On Fri, Aug 31, 2018 at 6:05 PM Nathan Dunn <nat...@lb...<mailto:nat...@lb...>> wrote: I’d advocate wrapping your JBrowse page in an client-side app that uses GitHub or Google+ for authentication. If you’re really lazy (like me), I would use something like auth0 to manage allowable users. Its typically not a ton of code: https://auth0.com/docs/quickstart/spa/vanillajs Something like this (or just simply a GitHub authenticator) would make a great JBrowse plugin. Nathan On Aug 31, 2018, at 2:01 PM, Robert Buels <rb...@gm...<mailto:rb...@gm...>> wrote: Ccing gmod-ajax list, since he JBrowse community probably has better feedback on authentication than I do. Most people who password protect JBrowse installations use the standard HTTP Basic authentication, configured at the level of the web server. This works fine with JBrowse, and no additional configuration is needed, as long as he JBrowse main page (jbowse/index.html) is configured to be authenticated under the same scheme as the other data resources. There hasn’t been a lot of demand for additional authentication features, but the dev team is certainly open to discussing adding some. Hope this helps! Rob On Fri, Aug 31, 2018 at 8:32 AM Hulse-Kemp, Amanda - ARS <Ama...@ar...<mailto:Ama...@ar...>> wrote: Hello Robert, I am working with GOnRamp group as a way to launch Jbrowse instances for USDA associated genome publications with data hosting in Cyverse. I have developed a test version of my genome and currently have it implemented, however I’d really like to be able to password protect the URL. I see a number of discussions on password protection, and wanted to contact you to discuss where you were with that? Best, Amanda Amanda Hulse-Kemp, Ph.D. Computational Biologist USDA-ARS, Genomics and Bioinformatics Research Unit 1244 Williams Hall | North Carolina State University | Raleigh | NC | 27695 ama...@ar...<mailto:ama...@ar...> 919-515-7599 This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org<http://Slashdot.org>! http://sdm.link/slashdot_______________________________________________ Gmod-ajax mailing list Gmo...@li...<mailto:Gmo...@li...> https://lists.sourceforge.net/lists/listinfo/gmod-ajax ------------------------------------------------------------------------------ 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 ------------------------------------------------------------------------------ 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 |
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From: Sofia R. <so...@so...> - 2018-09-04 18:02:06
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Hello Rob and Colin and All. Just wanted to through in my two cents. User Authentication in JBrowse is definitely something we are interested in. We would LOVE to be able to keep some tracks private, such as on going research, while the rest are open to the world. Right now I have to set up two separate JBrowse installations to get what we need, and it is sometimes kinda a pain to remember to do what I need to do in both. Thanks, Sofia On Tue, Sep 4, 2018 at 7:59 AM, Hulse-Kemp, Amanda - ARS < Ama...@ar...> wrote: > On our side it would seem beneficial, as there is a lot of “polishing” > work to be done on Jbrowse before you want it officially public outside of > the research group. It would be ideal where something could start as > accessible in private files and then move over to anonymous access. I am > thinking in terms of large amounts of projects and something to allow this > to be done relatively easy, without too much intervention of IT permissions > etc. as many of the scientists handling it would not be able to work > through those hurdles. > > > > It appears there is a possibility through Apollo, however that is an extra > step and I have found is not exactly possible through CyVerse hosting and > must be on a private server – unless someone has experience with doing > this?? > > > > Best, > > Amanda > > > > *From:* Colin <col...@gm...> > *Sent:* Friday, August 31, 2018 6:33 PM > *To:* Nathan Dunn <nat...@lb...> > *Cc:* Robert Buels <rb...@gm...>; Hulse-Kemp, Amanda - ARS < > Ama...@AR...>; gmo...@li... > *Subject:* Re: [Gmod-ajax] Jbrowse Authentication > > > > Is it specifically desirable to access data remotely hosted in CyVerse? > > > > I know araport has written about this to some extent but I haven't > extensively looked into it > > > > https://github.com/Arabidopsis-Information-Portal/CyverseRemoteTracks > > > > It does say that it is made to allow anonymous which I assume means public > access, but it would be very cool if it could be extended to access private > files too > > > > -Colin > > > > On Fri, Aug 31, 2018 at 6:05 PM Nathan Dunn <nat...@lb...> wrote: > > > > I’d advocate wrapping your JBrowse page in an client-side app that uses > GitHub or Google+ for authentication. > > > > If you’re really lazy (like me), I would use something like auth0 to > manage allowable users. Its typically not a ton of code: > https://auth0.com/docs/quickstart/spa/vanillajs > > > > Something like this (or just simply a GitHub authenticator) would make a > great JBrowse plugin. > > > > Nathan > > > > > > On Aug 31, 2018, at 2:01 PM, Robert Buels <rb...@gm...> wrote: > > > > Ccing gmod-ajax list, since he JBrowse community probably has better > feedback on authentication than I do. > > > > Most people who password protect JBrowse installations use the standard > HTTP Basic authentication, configured at the level of the web server. This > works fine with JBrowse, and no additional configuration is needed, as long > as he JBrowse main page (jbowse/index.html) is configured to be > authenticated under the same scheme as the other data resources. > > > > There hasn’t been a lot of demand for additional authentication features, > but the dev team is certainly open to discussing adding some. > > > > Hope this helps! > > > > Rob > > > > On Fri, Aug 31, 2018 at 8:32 AM Hulse-Kemp, Amanda - ARS < > Ama...@ar...> wrote: > > Hello Robert, > > > > I am working with GOnRamp group as a way to launch Jbrowse instances for > USDA associated genome publications with data hosting in Cyverse. I have > developed a test version of my genome and currently have it implemented, > however I’d really like to be able to password protect the URL. I see a > number of discussions on password protection, and wanted to contact you to > discuss where you were with that? > > > > Best, > > Amanda > > > > Amanda Hulse-Kemp, Ph.D. > > Computational Biologist > > USDA-ARS, Genomics and Bioinformatics Research Unit > > 1244 Williams Hall | North Carolina State University | Raleigh | NC | 27695 > > ama...@ar... > > 919-515-7599 > > > > > > > > This electronic message contains information generated by the USDA solely > for the intended recipients. Any unauthorized interception of this message > or the use or disclosure of the information it contains may violate the law > and subject the violator to civil or criminal penalties. If you believe you > have received this message in error, please notify the sender and delete > the email immediately. > > ------------------------------------------------------------ > ------------------ > 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 > > > > ------------------------------------------------------------ > ------------------ > 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 > > > ------------------------------------------------------------ > ------------------ > 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: Hulse-Kemp, A. - A. <Ama...@AR...> - 2018-09-04 13:59:20
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On our side it would seem beneficial, as there is a lot of “polishing” work to be done on Jbrowse before you want it officially public outside of the research group. It would be ideal where something could start as accessible in private files and then move over to anonymous access. I am thinking in terms of large amounts of projects and something to allow this to be done relatively easy, without too much intervention of IT permissions etc. as many of the scientists handling it would not be able to work through those hurdles. It appears there is a possibility through Apollo, however that is an extra step and I have found is not exactly possible through CyVerse hosting and must be on a private server – unless someone has experience with doing this?? Best, Amanda From: Colin <col...@gm...> Sent: Friday, August 31, 2018 6:33 PM To: Nathan Dunn <nat...@lb...> Cc: Robert Buels <rb...@gm...>; Hulse-Kemp, Amanda - ARS <Ama...@AR...>; gmo...@li... Subject: Re: [Gmod-ajax] Jbrowse Authentication Is it specifically desirable to access data remotely hosted in CyVerse? I know araport has written about this to some extent but I haven't extensively looked into it https://github.com/Arabidopsis-Information-Portal/CyverseRemoteTracks It does say that it is made to allow anonymous which I assume means public access, but it would be very cool if it could be extended to access private files too -Colin On Fri, Aug 31, 2018 at 6:05 PM Nathan Dunn <nat...@lb...<mailto:nat...@lb...>> wrote: I’d advocate wrapping your JBrowse page in an client-side app that uses GitHub or Google+ for authentication. If you’re really lazy (like me), I would use something like auth0 to manage allowable users. Its typically not a ton of code: https://auth0.com/docs/quickstart/spa/vanillajs Something like this (or just simply a GitHub authenticator) would make a great JBrowse plugin. Nathan On Aug 31, 2018, at 2:01 PM, Robert Buels <rb...@gm...<mailto:rb...@gm...>> wrote: Ccing gmod-ajax list, since he JBrowse community probably has better feedback on authentication than I do. Most people who password protect JBrowse installations use the standard HTTP Basic authentication, configured at the level of the web server. This works fine with JBrowse, and no additional configuration is needed, as long as he JBrowse main page (jbowse/index.html) is configured to be authenticated under the same scheme as the other data resources. There hasn’t been a lot of demand for additional authentication features, but the dev team is certainly open to discussing adding some. Hope this helps! Rob On Fri, Aug 31, 2018 at 8:32 AM Hulse-Kemp, Amanda - ARS <Ama...@ar...<mailto:Ama...@ar...>> wrote: Hello Robert, I am working with GOnRamp group as a way to launch Jbrowse instances for USDA associated genome publications with data hosting in Cyverse. I have developed a test version of my genome and currently have it implemented, however I’d really like to be able to password protect the URL. I see a number of discussions on password protection, and wanted to contact you to discuss where you were with that? Best, Amanda Amanda Hulse-Kemp, Ph.D. Computational Biologist USDA-ARS, Genomics and Bioinformatics Research Unit 1244 Williams Hall | North Carolina State University | Raleigh | NC | 27695 ama...@ar...<mailto:ama...@ar...> 919-515-7599 This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org<http://Slashdot.org>! http://sdm.link/slashdot_______________________________________________ Gmod-ajax mailing list Gmo...@li...<mailto:Gmo...@li...> https://lists.sourceforge.net/lists/listinfo/gmod-ajax ------------------------------------------------------------------------------ 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 |
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From: Colin <col...@gm...> - 2018-08-31 22:33:10
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Is it specifically desirable to access data remotely hosted in CyVerse? I know araport has written about this to some extent but I haven't extensively looked into it https://github.com/Arabidopsis-Information-Portal/CyverseRemoteTracks It does say that it is made to allow anonymous which I assume means public access, but it would be very cool if it could be extended to access private files too -Colin On Fri, Aug 31, 2018 at 6:05 PM Nathan Dunn <nat...@lb...> wrote: > > I’d advocate wrapping your JBrowse page in an client-side app that uses > GitHub or Google+ for authentication. > > If you’re really lazy (like me), I would use something like auth0 to > manage allowable users. Its typically not a ton of code: > https://auth0.com/docs/quickstart/spa/vanillajs > > Something like this (or just simply a GitHub authenticator) would make a > great JBrowse plugin. > > Nathan > > > On Aug 31, 2018, at 2:01 PM, Robert Buels <rb...@gm...> wrote: > > Ccing gmod-ajax list, since he JBrowse community probably has better > feedback on authentication than I do. > > Most people who password protect JBrowse installations use the standard > HTTP Basic authentication, configured at the level of the web server. This > works fine with JBrowse, and no additional configuration is needed, as long > as he JBrowse main page (jbowse/index.html) is configured to be > authenticated under the same scheme as the other data resources. > > There hasn’t been a lot of demand for additional authentication features, > but the dev team is certainly open to discussing adding some. > > Hope this helps! > > Rob > > On Fri, Aug 31, 2018 at 8:32 AM Hulse-Kemp, Amanda - ARS < > Ama...@ar...> wrote: > >> Hello Robert, >> >> >> >> I am working with GOnRamp group as a way to launch Jbrowse instances for >> USDA associated genome publications with data hosting in Cyverse. I have >> developed a test version of my genome and currently have it implemented, >> however I’d really like to be able to password protect the URL. I see a >> number of discussions on password protection, and wanted to contact you to >> discuss where you were with that? >> >> >> >> Best, >> >> Amanda >> >> >> >> Amanda Hulse-Kemp, Ph.D. >> >> Computational Biologist >> >> USDA-ARS, Genomics and Bioinformatics Research Unit >> >> 1244 Williams Hall | North Carolina State University | Raleigh | NC | >> 27695 >> >> ama...@ar... >> >> 919-515-7599 >> >> >> >> >> >> >> This electronic message contains information generated by the USDA solely >> for the intended recipients. Any unauthorized interception of this message >> or the use or disclosure of the information it contains may violate the law >> and subject the violator to civil or criminal penalties. If you believe you >> have received this message in error, please notify the sender and delete >> the email immediately. >> > > ------------------------------------------------------------------------------ > 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 > > > > ------------------------------------------------------------------------------ > 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: Nathan D. <nat...@lb...> - 2018-08-31 22:05:20
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I’d advocate wrapping your JBrowse page in an client-side app that uses GitHub or Google+ for authentication. If you’re really lazy (like me), I would use something like auth0 to manage allowable users. Its typically not a ton of code: https://auth0.com/docs/quickstart/spa/vanillajs <https://auth0.com/docs/quickstart/spa/vanillajs> Something like this (or just simply a GitHub authenticator) would make a great JBrowse plugin. Nathan > On Aug 31, 2018, at 2:01 PM, Robert Buels <rb...@gm...> wrote: > > Ccing gmod-ajax list, since he JBrowse community probably has better feedback on authentication than I do. > > Most people who password protect JBrowse installations use the standard HTTP Basic authentication, configured at the level of the web server. This works fine with JBrowse, and no additional configuration is needed, as long as he JBrowse main page (jbowse/index.html) is configured to be authenticated under the same scheme as the other data resources. > > There hasn’t been a lot of demand for additional authentication features, but the dev team is certainly open to discussing adding some. > > Hope this helps! > > Rob > > On Fri, Aug 31, 2018 at 8:32 AM Hulse-Kemp, Amanda - ARS <Ama...@ar... <mailto:Ama...@ar...>> wrote: > Hello Robert, > > > > I am working with GOnRamp group as a way to launch Jbrowse instances for USDA associated genome publications with data hosting in Cyverse. I have developed a test version of my genome and currently have it implemented, however I’d really like to be able to password protect the URL. I see a number of discussions on password protection, and wanted to contact you to discuss where you were with that? > > > > Best, > > Amanda > > > > Amanda Hulse-Kemp, Ph.D. > > Computational Biologist > > USDA-ARS, Genomics and Bioinformatics Research Unit > > 1244 Williams Hall | North Carolina State University | Raleigh | NC | 27695 > > ama...@ar... <mailto:ama...@ar...> > 919-515-7599 > > > > > > > > This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. > ------------------------------------------------------------------------------ > 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: Robert B. <rb...@gm...> - 2018-08-31 21:01:58
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Ccing gmod-ajax list, since he JBrowse community probably has better feedback on authentication than I do. Most people who password protect JBrowse installations use the standard HTTP Basic authentication, configured at the level of the web server. This works fine with JBrowse, and no additional configuration is needed, as long as he JBrowse main page (jbowse/index.html) is configured to be authenticated under the same scheme as the other data resources. There hasn’t been a lot of demand for additional authentication features, but the dev team is certainly open to discussing adding some. Hope this helps! Rob On Fri, Aug 31, 2018 at 8:32 AM Hulse-Kemp, Amanda - ARS < Ama...@ar...> wrote: > Hello Robert, > > > > I am working with GOnRamp group as a way to launch Jbrowse instances for > USDA associated genome publications with data hosting in Cyverse. I have > developed a test version of my genome and currently have it implemented, > however I’d really like to be able to password protect the URL. I see a > number of discussions on password protection, and wanted to contact you to > discuss where you were with that? > > > > Best, > > Amanda > > > > Amanda Hulse-Kemp, Ph.D. > > Computational Biologist > > USDA-ARS, Genomics and Bioinformatics Research Unit > > 1244 Williams Hall | North Carolina State University | Raleigh | NC | 27695 > > ama...@ar... > > 919-515-7599 > > > > > > > This electronic message contains information generated by the USDA solely > for the intended recipients. Any unauthorized interception of this message > or the use or disclosure of the information it contains may violate the law > and subject the violator to civil or criminal penalties. If you believe you > have received this message in error, please notify the sender and delete > the email immediately. > |
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From: Sridhar A. M. <sma...@wv...> - 2018-08-30 19:39:03
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You are right that there is some issue about the subfolder. I checked all the folllowing urls https://localhost/jbrowse/data/json/pepperCM155/tracks.conf <https://localhost/jbrowse/data/json/pepperCM155/tracks.conf> https://localhost/jbrowse/data/json/pepperCM155 <https://localhost/jbrowse/data/json/pepperCM155/tracks.conf> https://localhost/jbrowse/data/json <https://localhost/jbrowse/data/json> https://localhost/jbrowse/data <https://localhost/jbrowse/data> All of them give “Forbidden You don’t have permission to access… “ on the webbrowser. And in apache logs I get, “client denied by server configuration /var/www/html/jbrowse/data/“, etc However, I can browse all the below, without any error. https://localhost/jbrowse/sample_data/json/v <https://localhost/jbrowse/sample_data/json/v>olvox/tracks.conf https://localhost/jbrowse/sample_data/json/v <https://localhost/jbrowse/sample_data/json/v>olvox https://localhost/jbrowse/sample_data/json <https://localhost/jbrowse/sample_data/json/v> https://localhost/jbrowse/sample_data <https://localhost/jbrowse/sample_data> If the issue is due to my global apache settings, I think I should not be able to browse even the sample_data subdirectories. Could it be due to the way the data directory is created by the reference_sequence/gff creation perl scripts and the corresponding permissions written to any config files read by jbrowse? I am also going to ask about this issue in an apache specific forum. With Kind Regards, Sridhar > On Aug 30, 2018, at 3:00 PM, Colin <col...@gm...> wrote: > > If you are able to access the jbrowse index.html (e.g. you see it on the web browser enough to get that error about tracks.conf) but you are not able to access the subfolder or files in that subfolder for your data then it seems to me that there is something about that subfolder that is causing the issue > > It is a little outside the realm of jbrowse to debug such an issue with apache but I think your configuration should work if you can get apache to cooperate. You can probably visit your url https://localhost/jbrowse/data/json/pepperCM155/tracks.conf <https://localhost/jbrowse/data/json/pepperCM155/tracks.conf> and see the error literally and then try and change config to make it work > > -Colin > > On Thu, Aug 30, 2018 at 2:38 PM Sridhar Acharya Malkaram <sma...@wv... <mailto:sma...@wv...>> wrote: > Thanks Colin, > > I’ll just tried newest 1.15.3 version. But I still get this error message. > Just to check, I tried to connect from localhost, but it still gives the error. > Some setting is probably preventing the web browser access. > Apache is running under username ‘apache’ and group ‘apache’, and the jbrowse directories and files are owned by 'apache’. So, it is puzzling why this happens. > > >> error] [client 10.1.1.254] client denied by server configuration: /var/www/html/jbrowse/data/json/pepperCM155/tracks.conf, referer: https://10.1.1.2/jbrowse/?data=data/json/pepperCM155 <https://10.1.1.2/jbrowse/?data=data/json/pepperCM155> > >> error] [client 127.0.0.1] client denied by server configuration: /var/www/html/jbrowse/data/json/pepperCM155/tracks.conf, referer: https://localhost/jbrowse/?data=data/json/pepperCM155 <https://localhost/jbrowse/?data=data/json/pepperCM155>With Kind Regards, > > Sridhar > > > >> On Aug 30, 2018, at 1:56 PM, Colin <col...@gm... <mailto:col...@gm...>> wrote: >> >> I think your config is probably fine, I have tested similar things. However, note that the latest JBrowse 1.15.3 release (available since yesterday) provides a possible fix for the 401 errors and I would upgrade (see http://jbrowse.org/blog/2018/08/29/jbrowse-1-15-3.html <http://jbrowse.org/blog/2018/08/29/jbrowse-1-15-3.html>) >> >> The 403 errors might suggest some actual permission problem on your data directory. You should try and view your apache error log to debug these >> >> >> -Colin >> >> >> On Thu, Aug 30, 2018 at 1:20 PM Sridhar Acharya Malkaram <sma...@wv... <mailto:sma...@wv...>> wrote: >> Hi I am trying to get Jbrowse configured with a genome and gene tracks, but am facing some problems that I couldn’t figureout after going through all guides/documentation. Any help is appreciated. >> >> I have installed jbrowse under the web_root directory (/var/www/html/jbrowse). The installation went fine without any errors. >> >> Then I used the script prepare-refseqs.pl <http://prepare-refseqs.pl/> to upload a fasta indexed genome sequence, under “data/json/pepperCM155" directory, relative to jbrowse installation. >> Also used the script flatfile-to-json.pl <http://flatfile-to-json.pl/> to upload a tabix indexed gff under the same directory. >> >> in the main jbrowse.conf the following was added >> >> [datasets.pepperCM155] >> url = ?data=data/json/pepperCM155 >> name = pepperCM155 >> >> Added the following in data/json/pepperCM155/tracks.conf >> >> [GENERAL] >> dataset_id=pepperCM155 >> refSeqs=seq/pepper.fa.fai >> >> [tracks.refseq] >> urlTemplate=seq/pepper.fa >> storeClass=JBrowse/Store/SeqFeature/IndexedFasta >> type=Sequence >> >> [tracks.genes] >> urlTemplate=pepper.gff3.gz >> storeClass=JBrowse/Store/SeqFeature/GFF3Tabix >> type=CanvasFeatures >> >> >> Upon viewing in browser I get the general “Congratulations, JBrowse is on the web!” page, with an error message, >> “RequestError: Unable to load https://10.1.1.2/jbrowse/data/json/pepperCM155/trackList.json?v=0.21140536806861931 <https://10.1.1.2/jbrowse/data/json/pepperCM155/trackList.json?v=0.21140536806861931> status:403 >> >> I see the following under apache ssl_error_log. >> [error] [client 10.1.1.254] client denied by server configuration: /var/www/html/jbrowse/data/json/pepperCM155/tracks.conf, referer: https://10.1.1.2/jbrowse/?data=data/json/pepperCM155 <https://10.1.1.2/jbrowse/?data=data/json/pepperCM155> >> >> I am not sure what is the problem. >> >> I have proper ownership and permissions for the jbrowse directory and all underneath it. I have the following set in apache configurations files. >> >> Alias /jbrowse “/var/www/html/jbrowse” >> SetEnv JBROWSE_ROOT “/var/www/html/jbrowse" >> <Directory “/var/www/html/jbrowse”> >> SSLRequireSSL >> AllowOverride FileInfo Options AuthConfig >> Order deny, allow >> Deny from all >> Allow from 127.0.0.1 >> Allow from 10.1.1. >> AuthType Basic >> AuthName “Genome Browser” >> AuthBasicProvider external >> AuthExternal pwauth >> require valid-user >> </Directory> >> >> —— >> I could display the volvox test data. The reference sequence is displayed fine, but all the tracks are giving errors. For example, >> Error: HTTP 401 when fetching https:://10.1.1.2/jbrowse/sample_data/raw/volvox/volvox.subsubparts.gff3 <http://10.1.1.2/jbrowse/sample_data/raw/volvox/volvox.subsubparts.gff3> bytes 0-262143 >> >> >> With Kind Regards, >> >> Sridhar >> >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org <http://slashdot.org/>! http://sdm.link/slashdot <http://sdm.link/slashdot>_______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... <mailto:Gmo...@li...> >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax <https://lists.sourceforge.net/lists/listinfo/gmod-ajax> > |
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From: Colin <col...@gm...> - 2018-08-30 19:01:13
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If you are able to access the jbrowse index.html (e.g. you see it on the web browser enough to get that error about tracks.conf) but you are not able to access the subfolder or files in that subfolder for your data then it seems to me that there is something about that subfolder that is causing the issue It is a little outside the realm of jbrowse to debug such an issue with apache but I think your configuration should work if you can get apache to cooperate. You can probably visit your url https://localhost/jbrowse/data/json/pepperCM155/tracks.conf and see the error literally and then try and change config to make it work -Colin On Thu, Aug 30, 2018 at 2:38 PM Sridhar Acharya Malkaram < sma...@wv...> wrote: > Thanks Colin, > > I’ll just tried newest 1.15.3 version. But I still get this error > message. > Just to check, I tried to connect from localhost, but it still gives the > error. > Some setting is probably preventing the web browser access. > Apache is running under username ‘apache’ and group ‘apache’, and the > jbrowse directories and files are owned by 'apache’. So, it is puzzling why > this happens. > > > error] [client 10.1.1.254] client denied by server configuration: >> /var/www/html/jbrowse/data/json/pepperCM155/tracks.conf, referer: >> https://10.1.1.2/jbrowse/?data=data/json/pepperCM155 >> > > error] [client 127.0.0.1] client denied by server configuration: >> /var/www/html/jbrowse/data/json/pepperCM155/tracks.conf, referer: >> https://localhost/jbrowse/?data=data/json/pepperCM155 >> > With Kind Regards, > > Sridhar > > > > On Aug 30, 2018, at 1:56 PM, Colin <col...@gm...> wrote: > > I think your config is probably fine, I have tested similar things. > However, note that the latest JBrowse 1.15.3 release (available since > yesterday) provides a possible fix for the 401 errors and I would upgrade > (see http://jbrowse.org/blog/2018/08/29/jbrowse-1-15-3.html) > > The 403 errors might suggest some actual permission problem on your data > directory. You should try and view your apache error log to debug these > > > -Colin > > > On Thu, Aug 30, 2018 at 1:20 PM Sridhar Acharya Malkaram < > sma...@wv...> wrote: > >> Hi I am trying to get Jbrowse configured with a genome and gene tracks, >> but am facing some problems that I couldn’t figureout after going through >> all guides/documentation. Any help is appreciated. >> >> I have installed jbrowse under the web_root directory >> (/var/www/html/jbrowse). The installation went fine without any errors. >> >> Then I used the script prepare-refseqs.pl to upload a fasta indexed >> genome sequence, under “data/json/pepperCM155" directory, relative to >> jbrowse installation. >> Also used the script flatfile-to-json.pl to upload a tabix indexed gff >> under the same directory. >> >> in the main jbrowse.conf the following was added >> >> *[datasets.pepperCM155]* >> *url = ?data=data/json/pepperCM155* >> *name = pepperCM155* >> >> Added the following in data/json/pepperCM155/tracks.conf >> >> *[GENERAL]* >> *dataset_id=pepperCM155* >> *refSeqs=seq/pepper.fa.fai* >> >> *[tracks.refseq]* >> *urlTemplate=seq/pepper.fa* >> *storeClass=JBrowse/Store/SeqFeature/IndexedFasta* >> *type=Sequence* >> >> *[tracks.genes]* >> *urlTemplate=pepper.gff3.gz* >> *storeClass=JBrowse/Store/SeqFeature/GFF3Tabix* >> *type=CanvasFeatures* >> >> >> Upon viewing in browser I get the general “Congratulations, JBrowse is on >> the web!” page, with an error message, >> “RequestError: Unable to load >> https://10.1.1.2/jbrowse/data/json/pepperCM155/trackList.json?v=0.21140536806861931 >> status:403 >> >> I see the following under apache ssl_error_log. >> [error] [client 10.1.1.254] client denied by server configuration: >> /var/www/html/jbrowse/data/json/pepperCM155/tracks.conf, referer: >> https://10.1.1.2/jbrowse/?data=data/json/pepperCM155 >> >> I am not sure what is the problem. >> >> I have proper ownership and permissions for the jbrowse directory and all >> underneath it. I have the following set in apache configurations files. >> >> *Alias /jbrowse “/var/www/html/jbrowse”* >> *SetEnv JBROWSE_ROOT “/var/www/html/jbrowse"* >> *<Directory “/var/www/html/jbrowse”>* >> * SSLRequireSSL* >> * AllowOverride FileInfo Options AuthConfig* >> * Order deny, allow* >> * Deny from all* >> * Allow from 127.0.0.1* >> * Allow from 10.1.1.* >> * AuthType Basic* >> * AuthName “Genome Browser”* >> * AuthBasicProvider external* >> * AuthExternal pwauth* >> * require valid-user* >> *</Directory>* >> >> —— >> I could display the volvox test data. The reference sequence is displayed >> fine, but all the tracks are giving errors. For example, >> Error: HTTP 401 when fetching https::// >> 10.1.1.2/jbrowse/sample_data/raw/volvox/volvox.subsubparts.gff3 bytes >> 0-262143 >> >> >> With Kind Regards, >> >> Sridhar >> >> >> >> >> ------------------------------------------------------------------------------ >> 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: Sridhar A. M. <sma...@wv...> - 2018-08-30 18:39:05
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Thanks Colin, I’ll just tried newest 1.15.3 version. But I still get this error message. Just to check, I tried to connect from localhost, but it still gives the error. Some setting is probably preventing the web browser access. Apache is running under username ‘apache’ and group ‘apache’, and the jbrowse directories and files are owned by 'apache’. So, it is puzzling why this happens. > error] [client 10.1.1.254] client denied by server configuration: /var/www/html/jbrowse/data/json/pepperCM155/tracks.conf, referer: https://10.1.1.2/jbrowse/?data=data/json/pepperCM155 <https://10.1.1.2/jbrowse/?data=data/json/pepperCM155> > error] [client 127.0.0.1] client denied by server configuration: /var/www/html/jbrowse/data/json/pepperCM155/tracks.conf, referer: https://localhost/jbrowse/?data=data/json/pepperCM155 <https://localhost/jbrowse/?data=data/json/pepperCM155>With Kind Regards, Sridhar > On Aug 30, 2018, at 1:56 PM, Colin <col...@gm...> wrote: > > I think your config is probably fine, I have tested similar things. However, note that the latest JBrowse 1.15.3 release (available since yesterday) provides a possible fix for the 401 errors and I would upgrade (see http://jbrowse.org/blog/2018/08/29/jbrowse-1-15-3.html <http://jbrowse.org/blog/2018/08/29/jbrowse-1-15-3.html>) > > The 403 errors might suggest some actual permission problem on your data directory. You should try and view your apache error log to debug these > > > -Colin > > > On Thu, Aug 30, 2018 at 1:20 PM Sridhar Acharya Malkaram <sma...@wv... <mailto:sma...@wv...>> wrote: > Hi I am trying to get Jbrowse configured with a genome and gene tracks, but am facing some problems that I couldn’t figureout after going through all guides/documentation. Any help is appreciated. > > I have installed jbrowse under the web_root directory (/var/www/html/jbrowse). The installation went fine without any errors. > > Then I used the script prepare-refseqs.pl <http://prepare-refseqs.pl/> to upload a fasta indexed genome sequence, under “data/json/pepperCM155" directory, relative to jbrowse installation. > Also used the script flatfile-to-json.pl <http://flatfile-to-json.pl/> to upload a tabix indexed gff under the same directory. > > in the main jbrowse.conf the following was added > > [datasets.pepperCM155] > url = ?data=data/json/pepperCM155 > name = pepperCM155 > > Added the following in data/json/pepperCM155/tracks.conf > > [GENERAL] > dataset_id=pepperCM155 > refSeqs=seq/pepper.fa.fai > > [tracks.refseq] > urlTemplate=seq/pepper.fa > storeClass=JBrowse/Store/SeqFeature/IndexedFasta > type=Sequence > > [tracks.genes] > urlTemplate=pepper.gff3.gz > storeClass=JBrowse/Store/SeqFeature/GFF3Tabix > type=CanvasFeatures > > > Upon viewing in browser I get the general “Congratulations, JBrowse is on the web!” page, with an error message, > “RequestError: Unable to load https://10.1.1.2/jbrowse/data/json/pepperCM155/trackList.json?v=0.21140536806861931 <https://10.1.1.2/jbrowse/data/json/pepperCM155/trackList.json?v=0.21140536806861931> status:403 > > I see the following under apache ssl_error_log. > [error] [client 10.1.1.254] client denied by server configuration: /var/www/html/jbrowse/data/json/pepperCM155/tracks.conf, referer: https://10.1.1.2/jbrowse/?data=data/json/pepperCM155 <https://10.1.1.2/jbrowse/?data=data/json/pepperCM155> > > I am not sure what is the problem. > > I have proper ownership and permissions for the jbrowse directory and all underneath it. I have the following set in apache configurations files. > > Alias /jbrowse “/var/www/html/jbrowse” > SetEnv JBROWSE_ROOT “/var/www/html/jbrowse" > <Directory “/var/www/html/jbrowse”> > SSLRequireSSL > AllowOverride FileInfo Options AuthConfig > Order deny, allow > Deny from all > Allow from 127.0.0.1 > Allow from 10.1.1. > AuthType Basic > AuthName “Genome Browser” > AuthBasicProvider external > AuthExternal pwauth > require valid-user > </Directory> > > —— > I could display the volvox test data. The reference sequence is displayed fine, but all the tracks are giving errors. For example, > Error: HTTP 401 when fetching https:://10.1.1.2/jbrowse/sample_data/raw/volvox/volvox.subsubparts.gff3 <http://10.1.1.2/jbrowse/sample_data/raw/volvox/volvox.subsubparts.gff3> bytes 0-262143 > > > With Kind Regards, > > Sridhar > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot <http://sdm.link/slashdot>_______________________________________________ > Gmod-ajax mailing list > Gmo...@li... <mailto:Gmo...@li...> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax <https://lists.sourceforge.net/lists/listinfo/gmod-ajax> |
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From: Colin <col...@gm...> - 2018-08-30 17:56:44
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I think your config is probably fine, I have tested similar things. However, note that the latest JBrowse 1.15.3 release (available since yesterday) provides a possible fix for the 401 errors and I would upgrade (see http://jbrowse.org/blog/2018/08/29/jbrowse-1-15-3.html) The 403 errors might suggest some actual permission problem on your data directory. You should try and view your apache error log to debug these -Colin On Thu, Aug 30, 2018 at 1:20 PM Sridhar Acharya Malkaram < sma...@wv...> wrote: > Hi I am trying to get Jbrowse configured with a genome and gene tracks, > but am facing some problems that I couldn’t figureout after going through > all guides/documentation. Any help is appreciated. > > I have installed jbrowse under the web_root directory > (/var/www/html/jbrowse). The installation went fine without any errors. > > Then I used the script prepare-refseqs.pl to upload a fasta indexed > genome sequence, under “data/json/pepperCM155" directory, relative to > jbrowse installation. > Also used the script flatfile-to-json.pl to upload a tabix indexed gff > under the same directory. > > in the main jbrowse.conf the following was added > > *[datasets.pepperCM155]* > *url = ?data=data/json/pepperCM155* > *name = pepperCM155* > > Added the following in data/json/pepperCM155/tracks.conf > > *[GENERAL]* > *dataset_id=pepperCM155* > *refSeqs=seq/pepper.fa.fai* > > *[tracks.refseq]* > *urlTemplate=seq/pepper.fa* > *storeClass=JBrowse/Store/SeqFeature/IndexedFasta* > *type=Sequence* > > *[tracks.genes]* > *urlTemplate=pepper.gff3.gz* > *storeClass=JBrowse/Store/SeqFeature/GFF3Tabix* > *type=CanvasFeatures* > > > Upon viewing in browser I get the general “Congratulations, JBrowse is on > the web!” page, with an error message, > “RequestError: Unable to load > https://10.1.1.2/jbrowse/data/json/pepperCM155/trackList.json?v=0.21140536806861931 > status:403 > > I see the following under apache ssl_error_log. > [error] [client 10.1.1.254] client denied by server configuration: > /var/www/html/jbrowse/data/json/pepperCM155/tracks.conf, referer: > https://10.1.1.2/jbrowse/?data=data/json/pepperCM155 > > I am not sure what is the problem. > > I have proper ownership and permissions for the jbrowse directory and all > underneath it. I have the following set in apache configurations files. > > *Alias /jbrowse “/var/www/html/jbrowse”* > *SetEnv JBROWSE_ROOT “/var/www/html/jbrowse"* > *<Directory “/var/www/html/jbrowse”>* > * SSLRequireSSL* > * AllowOverride FileInfo Options AuthConfig* > * Order deny, allow* > * Deny from all* > * Allow from 127.0.0.1* > * Allow from 10.1.1.* > * AuthType Basic* > * AuthName “Genome Browser”* > * AuthBasicProvider external* > * AuthExternal pwauth* > * require valid-user* > *</Directory>* > > —— > I could display the volvox test data. The reference sequence is displayed > fine, but all the tracks are giving errors. For example, > Error: HTTP 401 when fetching https::// > 10.1.1.2/jbrowse/sample_data/raw/volvox/volvox.subsubparts.gff3 bytes > 0-262143 > > > With Kind Regards, > > Sridhar > > > > > ------------------------------------------------------------------------------ > 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: Sridhar A. M. <sma...@wv...> - 2018-08-30 17:20:25
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Hi I am trying to get Jbrowse configured with a genome and gene tracks, but am facing some problems that I couldn’t figureout after going through all guides/documentation. Any help is appreciated. I have installed jbrowse under the web_root directory (/var/www/html/jbrowse). The installation went fine without any errors. Then I used the script prepare-refseqs.pl to upload a fasta indexed genome sequence, under “data/json/pepperCM155" directory, relative to jbrowse installation. Also used the script flatfile-to-json.pl to upload a tabix indexed gff under the same directory. in the main jbrowse.conf the following was added [datasets.pepperCM155] url = ?data=data/json/pepperCM155 name = pepperCM155 Added the following in data/json/pepperCM155/tracks.conf [GENERAL] dataset_id=pepperCM155 refSeqs=seq/pepper.fa.fai [tracks.refseq] urlTemplate=seq/pepper.fa storeClass=JBrowse/Store/SeqFeature/IndexedFasta type=Sequence [tracks.genes] urlTemplate=pepper.gff3.gz storeClass=JBrowse/Store/SeqFeature/GFF3Tabix type=CanvasFeatures Upon viewing in browser I get the general “Congratulations, JBrowse is on the web!” page, with an error message, “RequestError: Unable to load https://10.1.1.2/jbrowse/data/json/pepperCM155/trackList.json?v=0.21140536806861931 <https://10.1.1.2/jbrowse/data/json/pepperCM155/trackList.json?v=0.21140536806861931> status:403 I see the following under apache ssl_error_log. [error] [client 10.1.1.254] client denied by server configuration: /var/www/html/jbrowse/data/json/pepperCM155/tracks.conf, referer: https://10.1.1.2/jbrowse/?data=data/json/pepperCM155 <https://10.1.1.2/jbrowse/?data=data/json/pepperCM155> I am not sure what is the problem. I have proper ownership and permissions for the jbrowse directory and all underneath it. I have the following set in apache configurations files. Alias /jbrowse “/var/www/html/jbrowse” SetEnv JBROWSE_ROOT “/var/www/html/jbrowse" <Directory “/var/www/html/jbrowse”> SSLRequireSSL AllowOverride FileInfo Options AuthConfig Order deny, allow Deny from all Allow from 127.0.0.1 Allow from 10.1.1. AuthType Basic AuthName “Genome Browser” AuthBasicProvider external AuthExternal pwauth require valid-user </Directory> —— I could display the volvox test data. The reference sequence is displayed fine, but all the tracks are giving errors. For example, Error: HTTP 401 when fetching https:://10.1.1.2/jbrowse/sample_data/raw/volvox/volvox.subsubparts.gff3 bytes 0-262143 With Kind Regards, Sridhar |
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From: Colin <col...@gm...> - 2018-08-29 23:13:17
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Hi all, JBrowse 1.15.3 has been released! This contains a fix for an issue where typing a reference sequence name in the search bar did not navigate to it properly. It also contains a cool feature where "ultra minimal configs" can be specified by simply specifying a track label and urlTemplate Enjoy browsing! - JBrowse-1.15.3.zip <https://github.com/GMOD/jbrowse/releases/download/1.15.3-release/JBrowse-1.15.3.zip> - minified release - JBrowse-1.15.3-dev.zip <https://github.com/GMOD/jbrowse/archive/1.15.3-release.zip> - use this if you modify jbrowse source code or use plugins - JBrowse-1.15.3-desktop-win32-x64.zip <https://github.com/GMOD/jbrowse/releases/download/1.15.3-release/JBrowse-1.15.3-desktop-win32-x64.zip> - JBrowse-1.15.3-desktop-linux-x64.zip <https://github.com/GMOD/jbrowse/releases/download/1.15.3-release/JBrowse-1.15.3-desktop-linux-x64.zip> - JBrowse-1.15.3-desktop-darwin-x64.zip <https://github.com/GMOD/jbrowse/releases/download/1.15.3-release/JBrowse-1.15.3-desktop-darwin-x64.zip> <http://localhost:3000/blog#minor-improvements>Minor improvements - Add ability to automatically deduce the storeClass and trackType of files based on the file extension of urlTemplate. This allows very minimal configs where only track label and urlTemplate can be specified. (issue #1189 <https://github.com/gmod/jbrowse/pull/1189>, @cmdcolin <https://github.com/cmdcolin>) <http://localhost:3000/blog#bug-fixes>Bug fixes - Fixed an issue with servers that use HTTP Basic Authentication on certain browsers, notably some Chromium, Firefox 60 and earlier, and Safari. Thanks to Keiran Raine for reporting and @cmdcolin <https://github.com/cmdcolin> for debugging. (issue #1186 <https://github.com/gmod/jbrowse/issues/1186>, @rbuels <https://github.com/rbuels>) - Fix issue where searching for reference sequence names would not be navigate to the typed in reference sequence (issue #1193 <https://github.com/gmod/jbrowse/issues/1193>, @cmdcolin <https://github.com/cmdcolin>) |
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From: Colin <col...@gm...> - 2018-08-21 18:23:12
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Hi Vaneet, The new 1.15.2 now recommends downloading the source code from GitHub release page if you need to rebuild or use plugins, the "-dev" release was removed as it doesn't add anything compared to the source distribution Try the source code download from https://github.com/GMOD/jbrowse/releases/tag/1.15.2-release and I think it will work for you The source code download will have the css directory also. The compiled releases use scss to compile the css into a "module" so the css directory is unneeded. -Colin On Tue, Aug 21, 2018 at 1:27 PM Vaneet Lotay <van...@uc...> wrote: > Hey Colin, > > > > Having trouble installing this new release of JBrowse. I ran setup.sh > script and then ran the npm command (‘npm run build’) as usual but it > returned with errors. I’ve attached the npm log file. > > > > Also I could not find the ‘css’ directory in this release, where is that > located? Have those files been reorganized somehow. > > > > Thanks, > > > > Vaneet > > > > *Vaneet Lotay* > > *Xenbase Bioinformatician* > > *716 ICT Building - University of Calgary* > > *2500 University Drive NW* > > *Calgary AB T2N 1N4* > > *CANADA* > > > > *From:* Colin [mailto:col...@gm...] > *Sent:* Thursday, August 16, 2018 4:12 PM > *To:* gmo...@li... > *Subject:* [Gmod-ajax] JBrowse 1.15.2 released > > > > Hi all, > > > > JBrowse 1.15.2 has been released! This contains a couple nice features > including estimating feature density directly from the index file of BAM, > VCF, and other tabix formats. We also updated the website with a new > blogging and documentation platform! Please try it out and give us feedback. > > Enjoy browsing! > > · JBrowse-1.15.2.zip > <https://github.com/GMOD/jbrowse/releases/download/1.15.2-release/JBrowse-1.15.2.zip> - > 4.34 MB > > · JBrowse-1.15.2-desktop-win32-x64.zip > <https://github.com/GMOD/jbrowse/releases/download/1.15.2-release/JBrowse-1.15.2-desktop-win32-x64.zip> - > 69M > > · JBrowse-1.15.2-desktop-linux-x64.zip > <https://github.com/GMOD/jbrowse/releases/download/1.15.2-release/JBrowse-1.15.2-desktop-linux-x64.zip> - > 67M > > · JBrowse-1.15.2-desktop-darwin-x64.zip > <https://github.com/GMOD/jbrowse/releases/download/1.15.2-release/JBrowse-1.15.2-desktop-darwin-x64.zip> - > 68M > Minor improvements > > · Created "index stats estimation" which overrides the older > "global stats estimation" that randomly samples genomic regions of BAM, > VCF, etc to find feature density. This allows initial track load to be > faster automatically. (issue #1092 > <https://github.com/gmod/jbrowse/issues/1092>, issue #1167 > <https://github.com/gmod/jbrowse/pull/1167>, @cmdcolin > <https://github.com/cmdcolin>) > > · Removed the "full" or "dev" releases from the build. If you > need a "dev" release, you can simply download the JBrowse "source code" > link from the GitHub releases page, or use a git clone of the JBrowse > repository. This will behave the same as the "dev" release. (issue #1160 > <https://github.com/gmod/jbrowse/issues/1160>, issue #1170 > <https://github.com/gmod/jbrowse/pull/1170>, @cmdcolin > <https://github.com/cmdcolin>) > > · JBrowse now uses a new binary-file caching and fetching backend > based on the http-range-fetcher > <https://www.npmjs.com/package/http-range-fetcher> andtenacious-fetch > <https://www.npmjs.com/package/tenacious-fetch> npm modules. Users may > see slightly higher performance when viewing indexed binary formats such as > BAM, CRAM, 2bit, etc. (issue #1155 > <https://github.com/gmod/jbrowse/issues/1155>, issue #1175 > <https://github.com/gmod/jbrowse/issues/1175>, issue #1165 > <https://github.com/gmod/jbrowse/pull/1165>, @rbuels > <https://github.com/rbuels>) > > · Updated the main jbrowse.org website to use the docusaurus > platform. The main docs for the website are now moved from the GMOD.org > server to jbrowse.org. You can find the latest documentation in the > header bar. We hope you will enjoy this upgrade! There is also a new quick > start guide based on setting up JBrowse with indexed file formats. (issue > #1153 <https://github.com/gmod/jbrowse/issues/1153>, issue #1137 > <https://github.com/gmod/jbrowse/issues/1137>, issue #1173 > <https://github.com/gmod/jbrowse/pull/1173>, @cmdcolin > <https://github.com/cmdcolin>) > Bug fixes > > · Added a more robust HTML processing in Util.js. Thanks to > @hkmoon <https://github.com/hkmoon> for the idea and implementation. (issue > #1169 <https://github.com/gmod/jbrowse/pull/1169>, @hkmoon > <https://github.com/hkmoon>) > > · Remove utils/jb_run.js from the minified release (issue #1161 > <https://github.com/gmod/jbrowse/issues/1161>, issue #1160 > <https://github.com/gmod/jbrowse/issues/1160>, @cmdcolin > <https://github.com/cmdcolin>) > > · Fixes issue where navigating away from genome browser and > returning would not remember the location. Thanks to Vaneet Lotay for > reporting. (issue #1168 <https://github.com/gmod/jbrowse/issues/1168>, > @cmdcolin <https://github.com/cmdcolin>) > > · Fixes off-by-one in the display of the size of the genomic > region being viewed. Thanks to @sammyjava <https://github.com/sammyjava>for > the bug report! (issue #1176 <https://github.com/gmod/jbrowse/issues/1176> > , @cmdcolin <https://github.com/cmdcolin>) > |
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From: Vaneet L. <van...@uc...> - 2018-08-21 17:27:36
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Hey Colin, Having trouble installing this new release of JBrowse. I ran setup.sh script and then ran the npm command (‘npm run build’) as usual but it returned with errors. I’ve attached the npm log file. Also I could not find the ‘css’ directory in this release, where is that located? Have those files been reorganized somehow. Thanks, Vaneet Vaneet Lotay Xenbase Bioinformatician 716 ICT Building - University of Calgary 2500 University Drive NW Calgary AB T2N 1N4 CANADA From: Colin [mailto:col...@gm...] Sent: Thursday, August 16, 2018 4:12 PM To: gmo...@li... Subject: [Gmod-ajax] JBrowse 1.15.2 released Hi all, JBrowse 1.15.2 has been released! This contains a couple nice features including estimating feature density directly from the index file of BAM, VCF, and other tabix formats. We also updated the website with a new blogging and documentation platform! Please try it out and give us feedback. Enjoy browsing! · JBrowse-1.15.2.zip<https://github.com/GMOD/jbrowse/releases/download/1.15.2-release/JBrowse-1.15.2.zip> - 4.34 MB · JBrowse-1.15.2-desktop-win32-x64.zip<https://github.com/GMOD/jbrowse/releases/download/1.15.2-release/JBrowse-1.15.2-desktop-win32-x64.zip> - 69M · JBrowse-1.15.2-desktop-linux-x64.zip<https://github.com/GMOD/jbrowse/releases/download/1.15.2-release/JBrowse-1.15.2-desktop-linux-x64.zip> - 67M · JBrowse-1.15.2-desktop-darwin-x64.zip<https://github.com/GMOD/jbrowse/releases/download/1.15.2-release/JBrowse-1.15.2-desktop-darwin-x64.zip> - 68M Minor improvements · Created "index stats estimation" which overrides the older "global stats estimation" that randomly samples genomic regions of BAM, VCF, etc to find feature density. This allows initial track load to be faster automatically. (issue #1092<https://github.com/gmod/jbrowse/issues/1092>, issue #1167<https://github.com/gmod/jbrowse/pull/1167>, @cmdcolin<https://github.com/cmdcolin>) · Removed the "full" or "dev" releases from the build. If you need a "dev" release, you can simply download the JBrowse "source code" link from the GitHub releases page, or use a git clone of the JBrowse repository. This will behave the same as the "dev" release. (issue #1160<https://github.com/gmod/jbrowse/issues/1160>, issue #1170<https://github.com/gmod/jbrowse/pull/1170>, @cmdcolin<https://github.com/cmdcolin>) · JBrowse now uses a new binary-file caching and fetching backend based on the http-range-fetcher<https://www.npmjs.com/package/http-range-fetcher> andtenacious-fetch<https://www.npmjs.com/package/tenacious-fetch> npm modules. Users may see slightly higher performance when viewing indexed binary formats such as BAM, CRAM, 2bit, etc. (issue #1155<https://github.com/gmod/jbrowse/issues/1155>, issue #1175<https://github.com/gmod/jbrowse/issues/1175>, issue #1165<https://github.com/gmod/jbrowse/pull/1165>, @rbuels<https://github.com/rbuels>) · Updated the main jbrowse.org<http://jbrowse.org> website to use the docusaurus platform. The main docs for the website are now moved from the GMOD.org server to jbrowse.org<http://jbrowse.org>. You can find the latest documentation in the header bar. We hope you will enjoy this upgrade! There is also a new quick start guide based on setting up JBrowse with indexed file formats. (issue #1153<https://github.com/gmod/jbrowse/issues/1153>, issue #1137<https://github.com/gmod/jbrowse/issues/1137>, issue #1173<https://github.com/gmod/jbrowse/pull/1173>, @cmdcolin<https://github.com/cmdcolin>) Bug fixes · Added a more robust HTML processing in Util.js. Thanks to @hkmoon<https://github.com/hkmoon> for the idea and implementation. (issue #1169<https://github.com/gmod/jbrowse/pull/1169>, @hkmoon<https://github.com/hkmoon>) · Remove utils/jb_run.js from the minified release (issue #1161<https://github.com/gmod/jbrowse/issues/1161>, issue #1160<https://github.com/gmod/jbrowse/issues/1160>, @cmdcolin<https://github.com/cmdcolin>) · Fixes issue where navigating away from genome browser and returning would not remember the location. Thanks to Vaneet Lotay for reporting. (issue #1168<https://github.com/gmod/jbrowse/issues/1168>, @cmdcolin<https://github.com/cmdcolin>) · Fixes off-by-one in the display of the size of the genomic region being viewed. Thanks to @sammyjava<https://github.com/sammyjava>for the bug report! (issue #1176<https://github.com/gmod/jbrowse/issues/1176>, @cmdcolin<https://github.com/cmdcolin>) |
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From: Colin <col...@gm...> - 2018-08-18 20:03:46
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It should be fine but note that you will need to actually edit the
trackList.json to get this (e.g. I don't think it works to put this in the
"Edit config" as that ignores callbacks)
Other than this I think the config you posted works ok
-Colin
On Sat, Aug 18, 2018, 3:33 PM Vaughn, Justin - ARS <
Jus...@ar...> wrote:
> Such as:
>
> "color": "function(feature) {return feature.get('col')}”
>
> For example input like this:
>
> ##gff-version 3
> Chr1 MSU7 mRNA 10 80 . + . Name=hooka;ID=1;col=‘green'
> Chr1 MSU7 five_prime_UTR 10 30 . + . Name=1.1;Parent=1
> Chr1 MSU7 CDS 31 60 . + 0 Name=1.2;Parent=1
> Chr1 MSU7 three_prime_UTR 61 80 . + . Name=1.3;Parent=1
>
> Thanks, Justin
>
>
>
>
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> the email immediately.
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> _______________________________________________
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> Gmo...@li...
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From: Vaughn, J. - A. <Jus...@AR...> - 2018-08-17 17:04:57
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Such as:
"color": "function(feature) {return feature.get('col')}”
For example input like this:
##gff-version 3
Chr1 MSU7 mRNA 10 80 . + . Name=hooka;ID=1;col=‘green'
Chr1 MSU7 five_prime_UTR 10 30 . + . Name=1.1;Parent=1
Chr1 MSU7 CDS 31 60 . + 0 Name=1.2;Parent=1
Chr1 MSU7 three_prime_UTR 61 80 . + . Name=1.3;Parent=1
Thanks, Justin
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