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From: Hans Vasquez-G. <hav...@uc...> - 2021-02-01 23:01:11
|
Thank you Colin. I am trying to workout firewall restrictions with campus IT, so right now my JBrowse instance isn't publicly available. A couple of additional questions have come up with collaborating on this project. Is there a way to share the current view via a link that is urlencoded? I was going to share a link with a user, but noticed the share option requires a session parameter. Also, is there a way to add tracks via a urlencoded link like jbrowse1? I was able to write a php script that takes blast results to dynamically display BLAST hits on a given reference on JBrowse1. I would like to port this functionality to JBrowse2. Thank you, -Hans On Wed, Jan 27, 2021 at 4:00 PM Colin <col...@gm...> wrote: > No worries:) > > We would be happy to check out the BAM file also if it is causing issue > with JBrowse 2 > > If there is a public web link or jbrowse instance available we can try to > download from there > > Can also use a samtools view to get a slice of the region and send that > through any file service to mine or garrett's email > > -Colin > > On Wed, Jan 27, 2021 at 3:11 PM Hans Vasquez-Gross < > hav...@uc...> wrote: > >> Hi Colin, >> >> Thank you for your email. Converting the BAM to CRAM has definitely sped >> up the loading. I'll do more tests and see if I notice it failing to load, >> but so far it hasn't in my limited testing. >> >> Best, >> -Hans >> >> On Wed, Jan 27, 2021 at 10:39 AM Colin <col...@gm...> wrote: >> >>> Note also that CRAM will in many cases also be faster than BAM, so if >>> possible I would suggest using CRAM just in case you want to make your own >>> usage of the app faster >>> >>> Possibly a worthwhile datapoint to add when doing benchmark >>> >>> -Colin >>> >>> On Wed, Jan 27, 2021 at 11:35 AM Colin <col...@gm...> wrote: >>> >>>> >>>> Echoing what Garrett said. Generally a package-lock.json will be >>>> created if you use "npm install" instead of "yarn". >>>> >>>> >>>> Also regarding JBrowse 2 being slower than JBrowse 1, this is a real >>>> issue that you might see, and something we are aware of >>>> >>>> Here are some factors that can make JBrowse 2 slower >>>> >>>> 1) JBrowse 2 uses webworkers, and each track gets a dedicated >>>> webworker, so each track needs to initialize a large (~3mb) webworker >>>> bundle before a track is loaded >>>> 2) JBrowse 2 serializes the BAM/CRAM data from the webworker back to >>>> the main thread, which may increase the time to render >>>> 3) If you are not using Chrome in JBrowse 2, it also has to serialize >>>> drawing commands back to the main thread, which may increase the time to >>>> render. Therefore, Chrome will generally be faster when using JBrowse 2. >>>> Chrome can do the drawing on the webworker and we take advantage of that. >>>> 4) If you are using the embedded mode component, it will not use a >>>> webworker at all, and will still do step (2) and therefore will be slower >>>> also. >>>> >>>> >>>> All these things will make JBrowse 2 slower than JBrowse 1. JBrowse 2 >>>> ideally benefits from offloading heavy computations to the webworker, so >>>> the overall experience is hopefully that it feels smoother, but there is a >>>> tradeoff there. >>>> >>>> Anyways, all that said, there are real reasons, as listed above, that >>>> JBrowse 2 can be a bit slower, and we should indeed make a measured attempt >>>> to benchmark >>>> >>>> We would be happy to collaborate on this if you want. I have myself >>>> done some cursory comparisons here >>>> https://github.com/GMOD/jbrowse-components/issues/969 >>>> >>>> >>>> -Colin >>>> >>>> On Tue, Jan 26, 2021 at 5:45 PM Garrett Stevens < >>>> ste...@gm...> wrote: >>>> >>>>> Hi Hans, >>>>> >>>>> I don't think that error is due to JBrowse 2, the two projects are >>>>> isolated. I'm guessing that you're cloning the GitHub repos and installing >>>>> from there? package-lock.json is a file that NPM uses to make sure the same >>>>> versions of dependencies are always installed, but we don't use that in >>>>> JBrowse 1 or 2 (we use a similar yarn.lock file instead), so I'm not sure >>>>> where that file is being detected. If you let us know the commands you used >>>>> to get to that point, it might help us figure out what is wrong. >>>>> >>>>> Best, >>>>> Garrett >>>>> >>>>> On Tue, Jan 26, 2021 at 4:25 PM Hans Vasquez-Gross via Gmod-ajax < >>>>> gmo...@li...> wrote: >>>>> >>>>>> Hello JBrowse team, >>>>>> >>>>>> I recently tried to install both jbrowse1 and jbrowse2 on the same >>>>>> machine. It seems as though there are competing node/npm requirements. >>>>>> >>>>>> I already have jbrowse2 setup on a new machine, but it feels slower >>>>>> loading BAM files, so I was going to install jbrowse1 as well, to compare >>>>>> the load times. However, when I went to install jbrowse1, it fails during >>>>>> the nodejs installation because there are files locked. >>>>>> >>>>>> "Node v15.5.1 installed at >>>>>> /home/hvasquezgross/.nvm/versions/node/v15.5.1/bin/node with npm 7.3.0 >>>>>> yarn install v1.22.4 >>>>>> warning package-lock.json found. Your project contains lock files >>>>>> generated by tools other than Yarn. It is advised not to mix package >>>>>> managers in order to avoid resolution inc >>>>>> onsistencies caused by unsynchronized lock files. To clear this >>>>>> warning, remove package-lock.json." >>>>>> >>>>>> >>>>>> Is this due to the jbrowse2 installation? >>>>>> >>>>>> Thank you, >>>>>> -Hans >>>>>> _______________________________________________ >>>>>> Gmod-ajax mailing list >>>>>> Gmo...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>>> >>>>> _______________________________________________ >>>>> Gmod-ajax mailing list >>>>> Gmo...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>> >>>> >> >> -- >> Hans Vasquez-Gross >> <http://dubcovskylab.ucdavis.edu/lab-member/hans-vasquez-gross> >> PhD Candidate >> Dubcovsky Website - http://dubcovskylab.ucdavis.edu/ >> Department of Plant Science >> University of California at Davis >> Email: hav...@uc... >> Skype: hansvg.ucd >> > -- Hans Vasquez-Gross <http://dubcovskylab.ucdavis.edu/lab-member/hans-vasquez-gross> PhD Candidate Dubcovsky Website - http://dubcovskylab.ucdavis.edu/ Department of Plant Science University of California at Davis Email: hav...@uc... Skype: hansvg.ucd |
|
From: Colin <col...@gm...> - 2021-01-28 00:01:08
|
No worries:) We would be happy to check out the BAM file also if it is causing issue with JBrowse 2 If there is a public web link or jbrowse instance available we can try to download from there Can also use a samtools view to get a slice of the region and send that through any file service to mine or garrett's email -Colin On Wed, Jan 27, 2021 at 3:11 PM Hans Vasquez-Gross < hav...@uc...> wrote: > Hi Colin, > > Thank you for your email. Converting the BAM to CRAM has definitely sped > up the loading. I'll do more tests and see if I notice it failing to load, > but so far it hasn't in my limited testing. > > Best, > -Hans > > On Wed, Jan 27, 2021 at 10:39 AM Colin <col...@gm...> wrote: > >> Note also that CRAM will in many cases also be faster than BAM, so if >> possible I would suggest using CRAM just in case you want to make your own >> usage of the app faster >> >> Possibly a worthwhile datapoint to add when doing benchmark >> >> -Colin >> >> On Wed, Jan 27, 2021 at 11:35 AM Colin <col...@gm...> wrote: >> >>> >>> Echoing what Garrett said. Generally a package-lock.json will be created >>> if you use "npm install" instead of "yarn". >>> >>> >>> Also regarding JBrowse 2 being slower than JBrowse 1, this is a real >>> issue that you might see, and something we are aware of >>> >>> Here are some factors that can make JBrowse 2 slower >>> >>> 1) JBrowse 2 uses webworkers, and each track gets a dedicated webworker, >>> so each track needs to initialize a large (~3mb) webworker bundle before a >>> track is loaded >>> 2) JBrowse 2 serializes the BAM/CRAM data from the webworker back to the >>> main thread, which may increase the time to render >>> 3) If you are not using Chrome in JBrowse 2, it also has to serialize >>> drawing commands back to the main thread, which may increase the time to >>> render. Therefore, Chrome will generally be faster when using JBrowse 2. >>> Chrome can do the drawing on the webworker and we take advantage of that. >>> 4) If you are using the embedded mode component, it will not use a >>> webworker at all, and will still do step (2) and therefore will be slower >>> also. >>> >>> >>> All these things will make JBrowse 2 slower than JBrowse 1. JBrowse 2 >>> ideally benefits from offloading heavy computations to the webworker, so >>> the overall experience is hopefully that it feels smoother, but there is a >>> tradeoff there. >>> >>> Anyways, all that said, there are real reasons, as listed above, that >>> JBrowse 2 can be a bit slower, and we should indeed make a measured attempt >>> to benchmark >>> >>> We would be happy to collaborate on this if you want. I have myself done >>> some cursory comparisons here >>> https://github.com/GMOD/jbrowse-components/issues/969 >>> >>> >>> -Colin >>> >>> On Tue, Jan 26, 2021 at 5:45 PM Garrett Stevens < >>> ste...@gm...> wrote: >>> >>>> Hi Hans, >>>> >>>> I don't think that error is due to JBrowse 2, the two projects are >>>> isolated. I'm guessing that you're cloning the GitHub repos and installing >>>> from there? package-lock.json is a file that NPM uses to make sure the same >>>> versions of dependencies are always installed, but we don't use that in >>>> JBrowse 1 or 2 (we use a similar yarn.lock file instead), so I'm not sure >>>> where that file is being detected. If you let us know the commands you used >>>> to get to that point, it might help us figure out what is wrong. >>>> >>>> Best, >>>> Garrett >>>> >>>> On Tue, Jan 26, 2021 at 4:25 PM Hans Vasquez-Gross via Gmod-ajax < >>>> gmo...@li...> wrote: >>>> >>>>> Hello JBrowse team, >>>>> >>>>> I recently tried to install both jbrowse1 and jbrowse2 on the same >>>>> machine. It seems as though there are competing node/npm requirements. >>>>> >>>>> I already have jbrowse2 setup on a new machine, but it feels slower >>>>> loading BAM files, so I was going to install jbrowse1 as well, to compare >>>>> the load times. However, when I went to install jbrowse1, it fails during >>>>> the nodejs installation because there are files locked. >>>>> >>>>> "Node v15.5.1 installed at >>>>> /home/hvasquezgross/.nvm/versions/node/v15.5.1/bin/node with npm 7.3.0 >>>>> yarn install v1.22.4 >>>>> warning package-lock.json found. Your project contains lock files >>>>> generated by tools other than Yarn. It is advised not to mix package >>>>> managers in order to avoid resolution inc >>>>> onsistencies caused by unsynchronized lock files. To clear this >>>>> warning, remove package-lock.json." >>>>> >>>>> >>>>> Is this due to the jbrowse2 installation? >>>>> >>>>> Thank you, >>>>> -Hans >>>>> _______________________________________________ >>>>> Gmod-ajax mailing list >>>>> Gmo...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>>> >>>> _______________________________________________ >>>> Gmod-ajax mailing list >>>> Gmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>> >>> > > -- > Hans Vasquez-Gross > <http://dubcovskylab.ucdavis.edu/lab-member/hans-vasquez-gross> > PhD Candidate > Dubcovsky Website - http://dubcovskylab.ucdavis.edu/ > Department of Plant Science > University of California at Davis > Email: hav...@uc... > Skype: hansvg.ucd > |
|
From: Hans Vasquez-G. <hav...@uc...> - 2021-01-27 22:12:10
|
Hi Colin, Thank you for your email. Converting the BAM to CRAM has definitely sped up the loading. I'll do more tests and see if I notice it failing to load, but so far it hasn't in my limited testing. Best, -Hans On Wed, Jan 27, 2021 at 10:39 AM Colin <col...@gm...> wrote: > Note also that CRAM will in many cases also be faster than BAM, so if > possible I would suggest using CRAM just in case you want to make your own > usage of the app faster > > Possibly a worthwhile datapoint to add when doing benchmark > > -Colin > > On Wed, Jan 27, 2021 at 11:35 AM Colin <col...@gm...> wrote: > >> >> Echoing what Garrett said. Generally a package-lock.json will be created >> if you use "npm install" instead of "yarn". >> >> >> Also regarding JBrowse 2 being slower than JBrowse 1, this is a real >> issue that you might see, and something we are aware of >> >> Here are some factors that can make JBrowse 2 slower >> >> 1) JBrowse 2 uses webworkers, and each track gets a dedicated webworker, >> so each track needs to initialize a large (~3mb) webworker bundle before a >> track is loaded >> 2) JBrowse 2 serializes the BAM/CRAM data from the webworker back to the >> main thread, which may increase the time to render >> 3) If you are not using Chrome in JBrowse 2, it also has to serialize >> drawing commands back to the main thread, which may increase the time to >> render. Therefore, Chrome will generally be faster when using JBrowse 2. >> Chrome can do the drawing on the webworker and we take advantage of that. >> 4) If you are using the embedded mode component, it will not use a >> webworker at all, and will still do step (2) and therefore will be slower >> also. >> >> >> All these things will make JBrowse 2 slower than JBrowse 1. JBrowse 2 >> ideally benefits from offloading heavy computations to the webworker, so >> the overall experience is hopefully that it feels smoother, but there is a >> tradeoff there. >> >> Anyways, all that said, there are real reasons, as listed above, that >> JBrowse 2 can be a bit slower, and we should indeed make a measured attempt >> to benchmark >> >> We would be happy to collaborate on this if you want. I have myself done >> some cursory comparisons here >> https://github.com/GMOD/jbrowse-components/issues/969 >> >> >> -Colin >> >> On Tue, Jan 26, 2021 at 5:45 PM Garrett Stevens < >> ste...@gm...> wrote: >> >>> Hi Hans, >>> >>> I don't think that error is due to JBrowse 2, the two projects are >>> isolated. I'm guessing that you're cloning the GitHub repos and installing >>> from there? package-lock.json is a file that NPM uses to make sure the same >>> versions of dependencies are always installed, but we don't use that in >>> JBrowse 1 or 2 (we use a similar yarn.lock file instead), so I'm not sure >>> where that file is being detected. If you let us know the commands you used >>> to get to that point, it might help us figure out what is wrong. >>> >>> Best, >>> Garrett >>> >>> On Tue, Jan 26, 2021 at 4:25 PM Hans Vasquez-Gross via Gmod-ajax < >>> gmo...@li...> wrote: >>> >>>> Hello JBrowse team, >>>> >>>> I recently tried to install both jbrowse1 and jbrowse2 on the same >>>> machine. It seems as though there are competing node/npm requirements. >>>> >>>> I already have jbrowse2 setup on a new machine, but it feels slower >>>> loading BAM files, so I was going to install jbrowse1 as well, to compare >>>> the load times. However, when I went to install jbrowse1, it fails during >>>> the nodejs installation because there are files locked. >>>> >>>> "Node v15.5.1 installed at >>>> /home/hvasquezgross/.nvm/versions/node/v15.5.1/bin/node with npm 7.3.0 >>>> yarn install v1.22.4 >>>> warning package-lock.json found. Your project contains lock files >>>> generated by tools other than Yarn. It is advised not to mix package >>>> managers in order to avoid resolution inc >>>> onsistencies caused by unsynchronized lock files. To clear this >>>> warning, remove package-lock.json." >>>> >>>> >>>> Is this due to the jbrowse2 installation? >>>> >>>> Thank you, >>>> -Hans >>>> _______________________________________________ >>>> Gmod-ajax mailing list >>>> Gmo...@li... >>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>>> >>> _______________________________________________ >>> Gmod-ajax mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>> >> -- Hans Vasquez-Gross <http://dubcovskylab.ucdavis.edu/lab-member/hans-vasquez-gross> PhD Candidate Dubcovsky Website - http://dubcovskylab.ucdavis.edu/ Department of Plant Science University of California at Davis Email: hav...@uc... Skype: hansvg.ucd |
|
From: Colin <col...@gm...> - 2021-01-27 18:40:11
|
Note also that CRAM will in many cases also be faster than BAM, so if possible I would suggest using CRAM just in case you want to make your own usage of the app faster Possibly a worthwhile datapoint to add when doing benchmark -Colin On Wed, Jan 27, 2021 at 11:35 AM Colin <col...@gm...> wrote: > > Echoing what Garrett said. Generally a package-lock.json will be created > if you use "npm install" instead of "yarn". > > > Also regarding JBrowse 2 being slower than JBrowse 1, this is a real issue > that you might see, and something we are aware of > > Here are some factors that can make JBrowse 2 slower > > 1) JBrowse 2 uses webworkers, and each track gets a dedicated webworker, > so each track needs to initialize a large (~3mb) webworker bundle before a > track is loaded > 2) JBrowse 2 serializes the BAM/CRAM data from the webworker back to the > main thread, which may increase the time to render > 3) If you are not using Chrome in JBrowse 2, it also has to serialize > drawing commands back to the main thread, which may increase the time to > render. Therefore, Chrome will generally be faster when using JBrowse 2. > Chrome can do the drawing on the webworker and we take advantage of that. > 4) If you are using the embedded mode component, it will not use a > webworker at all, and will still do step (2) and therefore will be slower > also. > > > All these things will make JBrowse 2 slower than JBrowse 1. JBrowse 2 > ideally benefits from offloading heavy computations to the webworker, so > the overall experience is hopefully that it feels smoother, but there is a > tradeoff there. > > Anyways, all that said, there are real reasons, as listed above, that > JBrowse 2 can be a bit slower, and we should indeed make a measured attempt > to benchmark > > We would be happy to collaborate on this if you want. I have myself done > some cursory comparisons here > https://github.com/GMOD/jbrowse-components/issues/969 > > > -Colin > > On Tue, Jan 26, 2021 at 5:45 PM Garrett Stevens < > ste...@gm...> wrote: > >> Hi Hans, >> >> I don't think that error is due to JBrowse 2, the two projects are >> isolated. I'm guessing that you're cloning the GitHub repos and installing >> from there? package-lock.json is a file that NPM uses to make sure the same >> versions of dependencies are always installed, but we don't use that in >> JBrowse 1 or 2 (we use a similar yarn.lock file instead), so I'm not sure >> where that file is being detected. If you let us know the commands you used >> to get to that point, it might help us figure out what is wrong. >> >> Best, >> Garrett >> >> On Tue, Jan 26, 2021 at 4:25 PM Hans Vasquez-Gross via Gmod-ajax < >> gmo...@li...> wrote: >> >>> Hello JBrowse team, >>> >>> I recently tried to install both jbrowse1 and jbrowse2 on the same >>> machine. It seems as though there are competing node/npm requirements. >>> >>> I already have jbrowse2 setup on a new machine, but it feels slower >>> loading BAM files, so I was going to install jbrowse1 as well, to compare >>> the load times. However, when I went to install jbrowse1, it fails during >>> the nodejs installation because there are files locked. >>> >>> "Node v15.5.1 installed at >>> /home/hvasquezgross/.nvm/versions/node/v15.5.1/bin/node with npm 7.3.0 >>> yarn install v1.22.4 >>> warning package-lock.json found. Your project contains lock files >>> generated by tools other than Yarn. It is advised not to mix package >>> managers in order to avoid resolution inc >>> onsistencies caused by unsynchronized lock files. To clear this warning, >>> remove package-lock.json." >>> >>> >>> Is this due to the jbrowse2 installation? >>> >>> Thank you, >>> -Hans >>> _______________________________________________ >>> Gmod-ajax mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>> >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > |
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From: Colin <col...@gm...> - 2021-01-27 18:36:05
|
Echoing what Garrett said. Generally a package-lock.json will be created if you use "npm install" instead of "yarn". Also regarding JBrowse 2 being slower than JBrowse 1, this is a real issue that you might see, and something we are aware of Here are some factors that can make JBrowse 2 slower 1) JBrowse 2 uses webworkers, and each track gets a dedicated webworker, so each track needs to initialize a large (~3mb) webworker bundle before a track is loaded 2) JBrowse 2 serializes the BAM/CRAM data from the webworker back to the main thread, which may increase the time to render 3) If you are not using Chrome in JBrowse 2, it also has to serialize drawing commands back to the main thread, which may increase the time to render. Therefore, Chrome will generally be faster when using JBrowse 2. Chrome can do the drawing on the webworker and we take advantage of that. 4) If you are using the embedded mode component, it will not use a webworker at all, and will still do step (2) and therefore will be slower also. All these things will make JBrowse 2 slower than JBrowse 1. JBrowse 2 ideally benefits from offloading heavy computations to the webworker, so the overall experience is hopefully that it feels smoother, but there is a tradeoff there. Anyways, all that said, there are real reasons, as listed above, that JBrowse 2 can be a bit slower, and we should indeed make a measured attempt to benchmark We would be happy to collaborate on this if you want. I have myself done some cursory comparisons here https://github.com/GMOD/jbrowse-components/issues/969 -Colin On Tue, Jan 26, 2021 at 5:45 PM Garrett Stevens <ste...@gm...> wrote: > Hi Hans, > > I don't think that error is due to JBrowse 2, the two projects are > isolated. I'm guessing that you're cloning the GitHub repos and installing > from there? package-lock.json is a file that NPM uses to make sure the same > versions of dependencies are always installed, but we don't use that in > JBrowse 1 or 2 (we use a similar yarn.lock file instead), so I'm not sure > where that file is being detected. If you let us know the commands you used > to get to that point, it might help us figure out what is wrong. > > Best, > Garrett > > On Tue, Jan 26, 2021 at 4:25 PM Hans Vasquez-Gross via Gmod-ajax < > gmo...@li...> wrote: > >> Hello JBrowse team, >> >> I recently tried to install both jbrowse1 and jbrowse2 on the same >> machine. It seems as though there are competing node/npm requirements. >> >> I already have jbrowse2 setup on a new machine, but it feels slower >> loading BAM files, so I was going to install jbrowse1 as well, to compare >> the load times. However, when I went to install jbrowse1, it fails during >> the nodejs installation because there are files locked. >> >> "Node v15.5.1 installed at >> /home/hvasquezgross/.nvm/versions/node/v15.5.1/bin/node with npm 7.3.0 >> yarn install v1.22.4 >> warning package-lock.json found. Your project contains lock files >> generated by tools other than Yarn. It is advised not to mix package >> managers in order to avoid resolution inc >> onsistencies caused by unsynchronized lock files. To clear this warning, >> remove package-lock.json." >> >> >> Is this due to the jbrowse2 installation? >> >> Thank you, >> -Hans >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Hans Vasquez-G. <hav...@uc...> - 2021-01-27 18:03:42
|
Hi Garrett,
Thank you for the help. It takes about 2 minutes before it times out, not 5
minutes. Here is another screenshot of it partially loading data then
failing.
[image: Screen Shot 2021-01-27 at 9.56.48 AM.png]
I'm using a BAM file with BAI index in the JBrowse configuration. Below is
an excerpt from the config.json file for one of these tracks.
{
"type": "AlignmentsTrack",
"trackId": "C1M_S3Aligned.sortedByCoord.out",
"name": "C1M_S3_mapping",
"assemblyNames": [
"VectorBase-50_AstephensiSDA-500_Genome"
],
"adapter": {
"type": "BamAdapter",
"bamLocation": {
"uri": "C1M_S3Aligned.sortedByCoord.out.bam"
},
"index": {
"location": {
"uri": "C1M_S3Aligned.sortedByCoord.out.bam.bai"
},
"indexType": "BAI"
},
"sequenceAdapter": {
"type": "IndexedFastaAdapter",
"fastaLocation": {
"uri": "VectorBase-50_AstephensiSDA-500_Genome.fasta"
},
"faiLocation": {
"uri": "VectorBase-50_AstephensiSDA-500_Genome.fasta.fai"
}
}
}
},
The reference genome is db49 from vectorbase for SDA-500 here
<https://vectorbase.org/vectorbase/app/downloads/release-49/AstephensiSDA-500/fasta/data/>.
Would you like me to send you this BAM file? How would you like me to
transfer it?
Thank you for your help debugging this problem.
All the best,
-Hans
On Wed, Jan 27, 2021 at 9:28 AM Garrett Stevens <ste...@gm...>
wrote:
> Hi Hans,
>
> How long does the track load for before you get the timeout error?
> Generally if it takes longer than 5 minutes, JBrowse 2 assumes something
> went wrong and stops the process. Perhaps this timeout could be extended or
> configurable in future releases if necessary. If you're able to share the
> alignments BAM/CRAM file, we could also try it out and see if we see
> anything unusual happening.
>
> Best,
> Garrett
>
> On Tue, Jan 26, 2021 at 5:50 PM Hans Vasquez-Gross <
> hav...@uc...> wrote:
>
>> Hi Garrett,
>>
>> Thank you for the reply. This error occurs when I run the ./setup.sh from
>> JBrowse1. If this isn't related, I will debug this on my end for the
>> JBrowse1 installation.
>>
>> However, do you have any suggestions on how to speed up rendering BAM
>> files in JBrowse2? Mine typically fail to render on JBrowse2, but I didn't
>> have the problem with JBrowse1 at my old lab.
>>
>> [image: Screen Shot 2021-01-26 at 4.47.37 PM.png]
>>
>> [image: Screen Shot 2021-01-26 at 4.48.15 PM.png]
>>
>> Thank you,
>> -Hans
>>
>>
>> On Tue, Jan 26, 2021 at 4:38 PM Garrett Stevens <
>> ste...@gm...> wrote:
>>
>>> Hi Hans,
>>>
>>> I don't think that error is due to JBrowse 2, the two projects are
>>> isolated. I'm guessing that you're cloning the GitHub repos and installing
>>> from there? package-lock.json is a file that NPM uses to make sure the same
>>> versions of dependencies are always installed, but we don't use that in
>>> JBrowse 1 or 2 (we use a similar yarn.lock file instead), so I'm not sure
>>> where that file is being detected. If you let us know the commands you used
>>> to get to that point, it might help us figure out what is wrong.
>>>
>>> Best,
>>> Garrett
>>>
>>> On Tue, Jan 26, 2021 at 4:25 PM Hans Vasquez-Gross via Gmod-ajax <
>>> gmo...@li...> wrote:
>>>
>>>> Hello JBrowse team,
>>>>
>>>> I recently tried to install both jbrowse1 and jbrowse2 on the same
>>>> machine. It seems as though there are competing node/npm requirements.
>>>>
>>>> I already have jbrowse2 setup on a new machine, but it feels slower
>>>> loading BAM files, so I was going to install jbrowse1 as well, to compare
>>>> the load times. However, when I went to install jbrowse1, it fails during
>>>> the nodejs installation because there are files locked.
>>>>
>>>> "Node v15.5.1 installed at
>>>> /home/hvasquezgross/.nvm/versions/node/v15.5.1/bin/node with npm 7.3.0
>>>> yarn install v1.22.4
>>>> warning package-lock.json found. Your project contains lock files
>>>> generated by tools other than Yarn. It is advised not to mix package
>>>> managers in order to avoid resolution inc
>>>> onsistencies caused by unsynchronized lock files. To clear this
>>>> warning, remove package-lock.json."
>>>>
>>>>
>>>> Is this due to the jbrowse2 installation?
>>>>
>>>> Thank you,
>>>> -Hans
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>
>>
>>
|
|
From: Garrett S. <ste...@gm...> - 2021-01-27 17:29:02
|
Hi Hans, How long does the track load for before you get the timeout error? Generally if it takes longer than 5 minutes, JBrowse 2 assumes something went wrong and stops the process. Perhaps this timeout could be extended or configurable in future releases if necessary. If you're able to share the alignments BAM/CRAM file, we could also try it out and see if we see anything unusual happening. Best, Garrett On Tue, Jan 26, 2021 at 5:50 PM Hans Vasquez-Gross < hav...@uc...> wrote: > Hi Garrett, > > Thank you for the reply. This error occurs when I run the ./setup.sh from > JBrowse1. If this isn't related, I will debug this on my end for the > JBrowse1 installation. > > However, do you have any suggestions on how to speed up rendering BAM > files in JBrowse2? Mine typically fail to render on JBrowse2, but I didn't > have the problem with JBrowse1 at my old lab. > > [image: Screen Shot 2021-01-26 at 4.47.37 PM.png] > > [image: Screen Shot 2021-01-26 at 4.48.15 PM.png] > > Thank you, > -Hans > > > On Tue, Jan 26, 2021 at 4:38 PM Garrett Stevens < > ste...@gm...> wrote: > >> Hi Hans, >> >> I don't think that error is due to JBrowse 2, the two projects are >> isolated. I'm guessing that you're cloning the GitHub repos and installing >> from there? package-lock.json is a file that NPM uses to make sure the same >> versions of dependencies are always installed, but we don't use that in >> JBrowse 1 or 2 (we use a similar yarn.lock file instead), so I'm not sure >> where that file is being detected. If you let us know the commands you used >> to get to that point, it might help us figure out what is wrong. >> >> Best, >> Garrett >> >> On Tue, Jan 26, 2021 at 4:25 PM Hans Vasquez-Gross via Gmod-ajax < >> gmo...@li...> wrote: >> >>> Hello JBrowse team, >>> >>> I recently tried to install both jbrowse1 and jbrowse2 on the same >>> machine. It seems as though there are competing node/npm requirements. >>> >>> I already have jbrowse2 setup on a new machine, but it feels slower >>> loading BAM files, so I was going to install jbrowse1 as well, to compare >>> the load times. However, when I went to install jbrowse1, it fails during >>> the nodejs installation because there are files locked. >>> >>> "Node v15.5.1 installed at >>> /home/hvasquezgross/.nvm/versions/node/v15.5.1/bin/node with npm 7.3.0 >>> yarn install v1.22.4 >>> warning package-lock.json found. Your project contains lock files >>> generated by tools other than Yarn. It is advised not to mix package >>> managers in order to avoid resolution inc >>> onsistencies caused by unsynchronized lock files. To clear this warning, >>> remove package-lock.json." >>> >>> >>> Is this due to the jbrowse2 installation? >>> >>> Thank you, >>> -Hans >>> _______________________________________________ >>> Gmod-ajax mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>> >> > > |
|
From: Hans Vasquez-G. <hav...@uc...> - 2021-01-27 01:16:18
|
Hi Garrett, Thank you for the reply. This error occurs when I run the ./setup.sh from JBrowse1. If this isn't related, I will debug this on my end for the JBrowse1 installation. However, do you have any suggestions on how to speed up rendering BAM files in JBrowse2? Mine typically fail to render on JBrowse2, but I didn't have the problem with JBrowse1 at my old lab. [image: Screen Shot 2021-01-26 at 4.47.37 PM.png] [image: Screen Shot 2021-01-26 at 4.48.15 PM.png] Thank you, -Hans On Tue, Jan 26, 2021 at 4:38 PM Garrett Stevens <ste...@gm...> wrote: > Hi Hans, > > I don't think that error is due to JBrowse 2, the two projects are > isolated. I'm guessing that you're cloning the GitHub repos and installing > from there? package-lock.json is a file that NPM uses to make sure the same > versions of dependencies are always installed, but we don't use that in > JBrowse 1 or 2 (we use a similar yarn.lock file instead), so I'm not sure > where that file is being detected. If you let us know the commands you used > to get to that point, it might help us figure out what is wrong. > > Best, > Garrett > > On Tue, Jan 26, 2021 at 4:25 PM Hans Vasquez-Gross via Gmod-ajax < > gmo...@li...> wrote: > >> Hello JBrowse team, >> >> I recently tried to install both jbrowse1 and jbrowse2 on the same >> machine. It seems as though there are competing node/npm requirements. >> >> I already have jbrowse2 setup on a new machine, but it feels slower >> loading BAM files, so I was going to install jbrowse1 as well, to compare >> the load times. However, when I went to install jbrowse1, it fails during >> the nodejs installation because there are files locked. >> >> "Node v15.5.1 installed at >> /home/hvasquezgross/.nvm/versions/node/v15.5.1/bin/node with npm 7.3.0 >> yarn install v1.22.4 >> warning package-lock.json found. Your project contains lock files >> generated by tools other than Yarn. It is advised not to mix package >> managers in order to avoid resolution inc >> onsistencies caused by unsynchronized lock files. To clear this warning, >> remove package-lock.json." >> >> >> Is this due to the jbrowse2 installation? >> >> Thank you, >> -Hans >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > |
|
From: Garrett S. <ste...@gm...> - 2021-01-27 00:44:58
|
Hi Hans, I don't think that error is due to JBrowse 2, the two projects are isolated. I'm guessing that you're cloning the GitHub repos and installing from there? package-lock.json is a file that NPM uses to make sure the same versions of dependencies are always installed, but we don't use that in JBrowse 1 or 2 (we use a similar yarn.lock file instead), so I'm not sure where that file is being detected. If you let us know the commands you used to get to that point, it might help us figure out what is wrong. Best, Garrett On Tue, Jan 26, 2021 at 4:25 PM Hans Vasquez-Gross via Gmod-ajax < gmo...@li...> wrote: > Hello JBrowse team, > > I recently tried to install both jbrowse1 and jbrowse2 on the same > machine. It seems as though there are competing node/npm requirements. > > I already have jbrowse2 setup on a new machine, but it feels slower > loading BAM files, so I was going to install jbrowse1 as well, to compare > the load times. However, when I went to install jbrowse1, it fails during > the nodejs installation because there are files locked. > > "Node v15.5.1 installed at > /home/hvasquezgross/.nvm/versions/node/v15.5.1/bin/node with npm 7.3.0 > yarn install v1.22.4 > warning package-lock.json found. Your project contains lock files > generated by tools other than Yarn. It is advised not to mix package > managers in order to avoid resolution inc > onsistencies caused by unsynchronized lock files. To clear this warning, > remove package-lock.json." > > > Is this due to the jbrowse2 installation? > > Thank you, > -Hans > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
|
From: Hans Vasquez-G. <hav...@uc...> - 2021-01-26 23:25:22
|
Hello JBrowse team, I recently tried to install both jbrowse1 and jbrowse2 on the same machine. It seems as though there are competing node/npm requirements. I already have jbrowse2 setup on a new machine, but it feels slower loading BAM files, so I was going to install jbrowse1 as well, to compare the load times. However, when I went to install jbrowse1, it fails during the nodejs installation because there are files locked. "Node v15.5.1 installed at /home/hvasquezgross/.nvm/versions/node/v15.5.1/bin/node with npm 7.3.0 yarn install v1.22.4 warning package-lock.json found. Your project contains lock files generated by tools other than Yarn. It is advised not to mix package managers in order to avoid resolution inc onsistencies caused by unsynchronized lock files. To clear this warning, remove package-lock.json." Is this due to the jbrowse2 installation? Thank you, -Hans |
|
From: Ke J. <bio...@gm...> - 2020-12-21 17:25:14
|
Sounds great! Thanks! On Mon, Dec 21, 2020 at 10:56 AM Robert Buels <rb...@gm...> wrote: > Hi Ke! > > JBrowse 1 is in maintenance mode, but it will still be maintained and > bug-fixed as much as we can. > > That said, it’s a good idea to plan to switch to JBrowse 2 at some point. > I’d encourage you to try it out, we would like to hear what you like and > don’t like about it! It’s new, probably still has some rough edges, but can > really do a lot! > > Rob > > On Mon, Dec 21, 2020 at 7:13 AM Ke Jiang <bio...@gm...> wrote: > >> Hi, >> >> With the first release of JBrowse2, I have a question about the original >> JBrowse: is it still actively developed or under maintenance mode? We >> really like our established JBrowse setup, especially the collection of >> plugins. But we also would like to future proof our genome browsers, so are >> considering the switch to JBrowse2. What are the thoughts of the >> developers? Would you recommend the switch at this time? >> >> Thanks! >> >> Ke >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > |
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From: Robert B. <rb...@gm...> - 2020-12-21 16:56:30
|
Hi Ke! JBrowse 1 is in maintenance mode, but it will still be maintained and bug-fixed as much as we can. That said, it’s a good idea to plan to switch to JBrowse 2 at some point. I’d encourage you to try it out, we would like to hear what you like and don’t like about it! It’s new, probably still has some rough edges, but can really do a lot! Rob On Mon, Dec 21, 2020 at 7:13 AM Ke Jiang <bio...@gm...> wrote: > Hi, > > With the first release of JBrowse2, I have a question about the original > JBrowse: is it still actively developed or under maintenance mode? We > really like our established JBrowse setup, especially the collection of > plugins. But we also would like to future proof our genome browsers, so are > considering the switch to JBrowse2. What are the thoughts of the > developers? Would you recommend the switch at this time? > > Thanks! > > Ke > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Ke J. <bio...@gm...> - 2020-12-21 15:13:01
|
Hi, With the first release of JBrowse2, I have a question about the original JBrowse: is it still actively developed or under maintenance mode? We really like our established JBrowse setup, especially the collection of plugins. But we also would like to future proof our genome browsers, so are considering the switch to JBrowse2. What are the thoughts of the developers? Would you recommend the switch at this time? Thanks! Ke |
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From: Nathan D. <nat...@lb...> - 2020-12-18 04:08:10
|
Apollo 2.6.2 released https://github.com/GMOD/Apollo/releases/tag/2.6.2 Features Add option to suppress calculation of non-canonical splice site 2509 <https://github.com/GMOD/Apollo/issues/2509>. Added the ability to sync the gene and transcript name with the click of a button 2519 <https://github.com/GMOD/Apollo/issues/2519>. Added organism and species to menus 2537 <https://github.com/GMOD/Apollo/pull/2537>. Added UUID lookup and link 2539 <https://github.com/GMOD/Apollo/pull/2539/>. Added status filter for recent annotations 2543 <https://github.com/GMOD/Apollo/pull/2543/>. Add feature name loc to loadLink 2544 <https://github.com/GMOD/Apollo/issues/2544>. loc loadLink now supports UUID and ID popup provides link 2549 <https://github.com/GMOD/Apollo/issues/2549>. Bug Fixes BLAT search should send annotation creation results to the proper reference sequence 2514 <https://github.com/GMOD/Apollo/issues/2514>. Properly handle Shine_Dalgarno sequences when added as part of gene model 2515 <https://github.com/GMOD/Apollo/issues/2515>. Now able to resize terminators by dragging 2521 <https://github.com/GMOD/Apollo/issues/2521>. Added missing GO annotations 2535 <https://github.com/GMOD/Apollo/pull/2535>. findAllOrganism webserver failed when user is not an admin and no session is present 2540 <https://github.com/GMOD/Apollo/issues/2540>. Provide minor UI and bug fixes 2548 <https://github.com/GMOD/Apollo/pull/2548>. Infrastructure Changes Upgrade to JBrowse 1.16.10 <https://github.com/GMOD/jbrowse/releases/tag/1.16.10-release> Full change long for all versions can be found here: https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md <https://github.com/GMOD/Apollo/blob/develop/ChangeLog.md> Docker builds are on quay.io and docker hub: https://quay.io/repository/gmod/apollo?tab=builds <https://quay.io/repository/gmod/apollo?tab=builds> https://hub.docker.com/r/gmod/apollo <https://hub.docker.com/r/gmod/apollo> Please review the documentation pages for more details: http://genomearchitect.readthedocs.io/en/latest/ <http://genomearchitect.readthedocs.io/en/latest/> Note: You can find a guide upgrading existing Apollo installations here: https://genomearchitect.readthedocs.io/en/latest/Migration.html <https://genomearchitect.readthedocs.io/en/latest/Migration.html> Report issues if found. Active mailing list (ap...@lb... <mailto:ap...@lb...>) and google group <https://groups.google.com/a/lbl.gov/g/apollo>. |
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From: Nathan D. <nat...@lb...> - 2020-12-11 01:05:42
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There are a few options (at least for Apollo): 1 - if you configure BLAT binaries, you can just use those directly: https://hgdownload.soe.ucsc.edu/admin/exe/ <https://hgdownload.soe.ucsc.edu/admin/exe/> https://genomearchitect.readthedocs.io/en/latest/Configure.html?highlight=blast#search-tools <https://genomearchitect.readthedocs.io/en/latest/Configure.html?highlight=blast#search-tools> This should work for either blat or blast (https://blast.ncbi.nlm.nih.gov/Blast.cgi <https://blast.ncbi.nlm.nih.gov/Blast.cgi> ) . This is provided by default with Docker. 2 - The i5k workspace is here: https://github.com/NAL-i5K 3 - https://github.com/GMOD/jblast-jbconnect-hook <https://github.com/GMOD/jblast-jbconnect-hook> ? (For JBrowse) maintained by Eric Yao. 4 - I believe the galaxy.eu <http://galaxy.eu/> server has one: https://annotation.usegalaxy.eu/ <https://annotation.usegalaxy.eu/> 5 - https://i5k.nal.usda.gov/webapp/blast/ <https://i5k.nal.usda.gov/webapp/blast/> (this is probably pretty specialized) I’m sure there are other ones. Nathan > On Dec 10, 2020, at 3:57 PM, Michał T. Lorenc <m.t...@gm...> wrote: > > Hi, > I found this BLAST server (https://solgenomics.net/tools/blast/ <https://solgenomics.net/tools/blast/>) which is able to highlight matching protein sequence. Unfortunately, this one is not open source and not available for download. By any change, do any one know a Blast server which can be downloaded, highlight maching protein sequence and allows to jump to Jbrowse/Apollo? > > > <image.png> > > > <image.png> > > <image.png> > Thank you in advance, > > Michal |
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From: Michał T. L. <m.t...@gm...> - 2020-12-10 23:58:22
|
Hi, I found this BLAST server (https://solgenomics.net/tools/blast/) which is able to highlight matching protein sequence. Unfortunately, this one is not open source and not available for download. By any change, do any one know a Blast server which can be downloaded, highlight maching protein sequence and allows to jump to Jbrowse/Apollo? [image: image.png] [image: image.png] [image: image.png] Thank you in advance, Michal |
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From: Adams, S. <Sal...@wa...> - 2020-12-10 13:59:36
|
Dear Colin, Thanks for getting back to me so quick. I must admit to being rather smitten with JBrowse2. We work with only recently described nematodes and I think this will be a great way of sharing our data with collaborators etc. I am going to check out your suggestions now. Thanks again Sally ________________________________ From: Colin <col...@gm...> Sent: 09 December 2020 23:04 To: Adams, Sally <Sal...@wa...> Cc: gmo...@li... <gmo...@li...> Subject: Re: [Gmod-ajax] Jbrowse2 chunksize error on upload of gff3 file. Hi there, Really glad to hear interest in JBrowse 2 :) In general these chunkSizeLimits are a pain and we are working to solve them References https://github.com/GMOD/tabix-js/issues/120 https://github.com/GMOD/tabix-js/pull/117 These could help with this issue In general, these error messages may also happen if you are zoomed too far out. We are trying to put a heuristic that says "Zoom in to see features" or something like this also in jbrowse 2, but this is not available Reference for that issue https://github.com/GMOD/jbrowse-components/pull/1394 If you zoom in and hit the "Reload" button, the "chunkSizeLimit" error might go away -Colin On Wed, Dec 9, 2020 at 5:27 PM Adams, Sally <Sal...@wa...<mailto:Sal...@wa...>> wrote: Hi there, I am in the process of annotating my Genome using Maker2 and would like to use Jbrowse2 to visually inspect the annotation. I have been following the method outlined at https://jbrowse.org/jb2/docs/combined/ JBrowse 2 combined guide | JBrowse<https://jbrowse.org/jb2/docs/combined/> This document is a collection of all our documentation. It includes our quick start guide, user guide, configuration guide, CLI guide, developer guide, and FAQ. You can browse the other documents individually, but this page is to help simple ctrl+f searching and easy browsing. You can also download a pdf version of these same docs located at https://jbrowse.org/jb2/jbrowse2.pdf jbrowse.org<http://jbrowse.org> I downloaded using the CLI and have successfully uploaded both the genome and a vcf file. It looks great. However, I am having trouble with the gff3 file. I have followed the sorting, compression and tabix indexing steps but I keep getting the error that the chunk size is too large (mine is nearly 4 million and my chunk size is set at 2 million). I know in Jbrowse you can reset the chunk size but I am really unsure where I might be able to set this in the config files for Jbrowse2. I know my gff file is pretty big as it contains the annotated repeats as well as predicted genes. Am I asking for too much? Thanks ever so much Sally _______________________________________________ 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...> - 2020-12-09 23:04:39
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Hi there, Really glad to hear interest in JBrowse 2 :) In general these chunkSizeLimits are a pain and we are working to solve them References https://github.com/GMOD/tabix-js/issues/120 https://github.com/GMOD/tabix-js/pull/117 These could help with this issue In general, these error messages may also happen if you are zoomed too far out. We are trying to put a heuristic that says "Zoom in to see features" or something like this also in jbrowse 2, but this is not available Reference for that issue https://github.com/GMOD/jbrowse-components/pull/1394 If you zoom in and hit the "Reload" button, the "chunkSizeLimit" error might go away -Colin On Wed, Dec 9, 2020 at 5:27 PM Adams, Sally <Sal...@wa...> wrote: > Hi there, > > I am in the process of annotating my Genome using Maker2 and would like to > use Jbrowse2 to visually inspect the annotation. I have been following the > method outlined at https://jbrowse.org/jb2/docs/combined/ > JBrowse 2 combined guide | JBrowse > <https://jbrowse.org/jb2/docs/combined/> > This document is a collection of all our documentation. It includes our > quick start guide, user guide, configuration guide, CLI guide, developer > guide, and FAQ. You can browse the other documents individually, but this > page is to help simple ctrl+f searching and easy browsing. You can also > download a pdf version of these same docs located at > https://jbrowse.org/jb2/jbrowse2.pdf > jbrowse.org > I downloaded using the CLI and have successfully uploaded both the genome > and a vcf file. It looks great. However, I am having trouble with the gff3 > file. I have followed the sorting, compression and tabix indexing steps but > I keep getting the error that the chunk size is too large (mine is nearly 4 > million and my chunk size is set at 2 million). I know in Jbrowse you can > reset the chunk size but I am really unsure where I might be able to set > this in the config files for Jbrowse2. I know my gff file is pretty big as > it contains the annotated repeats as well as predicted genes. Am I asking > for too much? > > Thanks ever so much > > Sally > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Adams, S. <Sal...@wa...> - 2020-12-09 21:50:00
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Hi there, I am in the process of annotating my Genome using Maker2 and would like to use Jbrowse2 to visually inspect the annotation. I have been following the method outlined at https://jbrowse.org/jb2/docs/combined/ JBrowse 2 combined guide | JBrowse<https://jbrowse.org/jb2/docs/combined/> This document is a collection of all our documentation. It includes our quick start guide, user guide, configuration guide, CLI guide, developer guide, and FAQ. You can browse the other documents individually, but this page is to help simple ctrl+f searching and easy browsing. You can also download a pdf version of these same docs located at https://jbrowse.org/jb2/jbrowse2.pdf jbrowse.org I downloaded using the CLI and have successfully uploaded both the genome and a vcf file. It looks great. However, I am having trouble with the gff3 file. I have followed the sorting, compression and tabix indexing steps but I keep getting the error that the chunk size is too large (mine is nearly 4 million and my chunk size is set at 2 million). I know in Jbrowse you can reset the chunk size but I am really unsure where I might be able to set this in the config files for Jbrowse2. I know my gff file is pretty big as it contains the annotated repeats as well as predicted genes. Am I asking for too much? Thanks ever so much Sally |
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From: Scott C. <sc...@sc...> - 2020-12-05 01:44:28
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The last week has seen a few updates to the SARS-CoV-2 browser at http://covid19.jbrowse.org/ : 1. We added the "Crowd-sourced data" track from the UCSC Genome Browser. For more information on this data, see https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=964789411_Dx02mdF71mqfaL8arKFW3ATS0Va0&c=NC_045512v2&g=publicAnnots 2. Several improvements to the "Mature peptides" track that came about due to improvements for the SARS-CoV-2 browser at the Alliance for Genome Resources (see https://www.alliancegenome.org/jbrowse/?data=data%2FSARS-CoV-2) 3. References to the NextStrain variant tracks were removed because the VCF files are no longer available. The docker container is available on Docker Hub at https://hub.docker.com/r/gmod/sars-cov-2-jbrowse and the GitHub repo for the Dockerfile and JBrowse configuration is at https://github.com/GMOD/sars-cov-2-jbrowse Happy Browsing, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |
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From: Nathan D. <nat...@lb...> - 2020-11-30 17:53:03
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Oh, this makes sense. > If I create a new Jbrowse installation with the 1.16.9 files in Apollo 2.6.1, it works fine. Any ideas? Many thanks! Apollo 2.5+ needs a requires version of JBrowse. I think 1.15+. My suggestion, use Apollo 2.6.X with JBrowse 1.16.X. By default it should be using 1.16 internally, so not sure how the data format would be changing. Other than potential CSS differences, there shouldn’t be any actual differences in data files. I would upgrade all of your JBrowses to 1.16.X if possible anyway as there have been numerous bug fixes and enhancements. Good luck, Nathan > On Nov 30, 2020, at 9:16 AM, Surya Saha <ss...@co...> wrote: > > Hi Nathan, > > Thank you for taking time during the break! > > We tried both apache2 and nginx as described in the instructions but the websocket handshaking problem between the proxy and tomcat is still there. We also tried tomcat9. I can file an issue if that will be useful. > > So it's on plain HTTP for the moment which is not great but a working solution. There is an issue with the JBrowse. The old Apollo 2.0.5 was working with a mix of Jbrowse 1.12 and 1.11 data files. > > Now I see this error for a bunch of the genomes > "TypeError: Cannot read property 'name' of undefined at Object.renderDatasetSelect (http://apollo.sgn.cornell.edu/apollo/6175841221635210385384582466/jbrowse/dist/1.bundle.js:1:31154 <http://apollo.sgn.cornell.edu/apollo/6175841221635210385384582466/jbrowse/dist/1.bundle.js:1:31154>) > <image.png> > > I have added the console error to the gist > https://gist.github.com/suryasaha/238d0522a274c5d90dc160e663c208f9#gistcomment-3545098 <https://gist.github.com/suryasaha/238d0522a274c5d90dc160e663c208f9#gistcomment-3545098> > > If I create a new Jbrowse installation with the 1.16.9 files in Apollo 2.6.1, it works fine. Any ideas? Many thanks! > > Cheers, > Surya > > > > > On Fri, Nov 27, 2020 at 1:03 PM Nathan Dunn <nat...@lb... <mailto:nat...@lb...>> wrote: > > > Oh, thanks for the logs. > > > spring-websocket.js:1213 WebSocket connection to 'wss://apollo.sgn.cornell.edu/apollo-2.6.1/stomp/733/yuxp71f5/websocketfailed <http://apollo.sgn.cornell.edu/apollo-2.6.1/stomp/733/yuxp71f5/websocketfailed>: Error during WebSocket handshake: Unexpected response code: 403 > > SockJS.websocket @ spring-websocket.js:1213 > > /apollo-2.6.1/stomp/733/nva3rn3i/xhr_streaming:1 Failed to load resource: the server responded with a status of 403 () > > /apollo-2.6.1/stomp/733/om6nby3l/xhr:1 Failed to load resource: the server responded with a status of 403 () > > > I think its a problem with the web socket proxy. If you are accessing Apollo through a proxy, the proxy changed slightly between 2.0 and 2.6. More info can be found here. > > https://genomearchitect.readthedocs.io/en/latest/Configure.html?highlight=nginx#apache-nginx-configuration <https://genomearchitect.readthedocs.io/en/latest/Configure.html?highlight=nginx#apache-nginx-configuration> > > If you connect directly to tomcat it **should** work as desired and then you can update directly. > > Nathan > > > > On Nov 27, 2020, at 4:26 AM, Surya Saha <ss...@co... <mailto:ss...@co...>> wrote: > > > > Hi Nathan et al, > > > > I have upgraded an installation from v2.0.5 to v2.6.1 and moved the postgresql db to a different server. No issues building the .WAR file. I have downloaded https://github.com/GMOD/Apollo/archive/2.6.1.tar.gz <https://github.com/GMOD/Apollo/archive/2.6.1.tar.gz> and followed > > standard instructions https://genomearchitect.readthedocs.io/en/latest/Setup.html <https://genomearchitect.readthedocs.io/en/latest/Setup.html> > > My current config is > > Apollo Version: 2.6.1 > > Grails version: 2.5.5 > > Groovy version: 2.4.4 > > JVM version: 1.8.0_272 > > Servlet Container Version: Apache Tomcat/8.5.54 (Debian) > > JBrowse config: 1.16.9-release > > > > I can add a new organism and tracks but cannot create new user annotations. > > I see an access error in the tomcat log even though the directory is owned by tomcat8. I also see 403 errors in the console so maybe it's a permission issue in apache2/tomcat8? Apollo can connect to postgresql as I see all the old users, user annotations and organisms. The messages are in this gist > > https://gist.github.com/suryasaha/238d0522a274c5d90dc160e663c208f9 <https://gist.github.com/suryasaha/238d0522a274c5d90dc160e663c208f9> > > Any suggestions? I am happy to provide a test login if that helps. > > > > Belated Happy Thanksgiving to all! > > > > Cheers, > > Surya > > > > -- > > > > Surya Saha > > Sol Genomics Network > > Boyce Thompson Institute, Ithaca, NY, USA > > https://citrusgreening.org/ <https://citrusgreening.org/> > > https://orcid.org/0000-0002-1160-1413 <https://orcid.org/0000-0002-1160-1413> > > http://www.linkedin.com/in/suryasaha <http://www.linkedin.com/in/suryasaha> > > https://twitter.com/SahaSurya <https://twitter.com/SahaSurya> > > -- > To unsubscribe from this group and stop receiving emails from it, send an email to apo...@lb... <mailto:apollo%2Bu...@lb...>. > > > > -- > > Surya Saha > Sol Genomics Network > Boyce Thompson Institute, Ithaca, NY, USA > https://citrusgreening.org/ <https://citrusgreening.org/> > https://orcid.org/0000-0002-1160-1413 <https://orcid.org/0000-0002-1160-1413> > http://www.linkedin.com/in/suryasaha <http://www.linkedin.com/in/suryasaha> > https://twitter.com/SahaSurya <https://twitter.com/SahaSurya> |
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From: Michał T. L. <m.t...@gm...> - 2020-11-30 00:31:23
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Cool, thanks! It works. On Sat, Nov 28, 2020 at 4:39 AM Colin <col...@gm...> wrote: > This documentation page could help > > https://jbrowse.org/docs/mouse_configs.html#customizing-left-click-behavior-1 > > > Could also use > > "onClick" : { > "label": "search at NCBI", > "action": "newWindow", > "url": "http://www.ncbi.nlm.nih.gov/gquery/?term={name}" > } > > Which should open it up in a new window > > > -Colin > > On Fri, Nov 27, 2020 at 12:01 AM Michał T. Lorenc <m.t...@gm...> > wrote: > >> Hi, >> How Is it possible to allow the user a left-click on a gene which will >> trigger to open for example this URL *https://www.ncbi.nlm.nih.gov/protein/ >> <https://www.ncbi.nlm.nih.gov/protein/>XP_019258550.1/*? If not what >> other alternatives exist? >> >> >> The data is stored in this GFF3: >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> *##gff-version 3##sequence-region chr01_pilon_pilon 1 >> 141847987chr01_pilon_pilon transdecoder gene 410672 411597 . >> + . ID=gene.5.0;chr01_pilon_pilon transdecoder >> mRNA 410672 411597 . + . >> ID=gene.5.0.0.p1;Name=XP_019258550.1;Note=uncharacterized protein >> LOC109236786 isoform X2;Parent=gene.5.0chr01_pilon_pilon transdecoder >> exon 410672 410798 . + . >> ID=gene.5.0.0.p1.exon1;Parent=gene.5.0.0.p1chr01_pilon_pilon >> transdecoder exon 410939 411205 . + . >> ID=gene.5.0.0.p1.exon2;Parent=gene.5.0.0.p1chr01_pilon_pilon >> transdecoder exon 411326 411597 . + . >> ID=gene.5.0.0.p1.exon3;Parent=gene.5.0.0.p1chr01_pilon_pilon >> transdecoder CDS 411087 411205 . + 0 >> ID=cds.gene.5.0.0.p1;Parent=gene.5.0.0.p1chr01_pilon_pilon >> transdecoder CDS 411326 411596 . + 1 >> ID=cds.gene.5.0.0.p1;Parent=gene.5.0.0.p1chr01_pilon_pilon >> transdecoder five_prime_UTR 410672 410798 . + . >> ID=gene.5.0.0.p1.utr5p1;Parent=gene.5.0.0.p1chr01_pilon_pilon >> transdecoder five_prime_UTR 410939 411086 . + . >> ID=gene.5.0.0.p1.utr5p2;Parent=gene.5.0.0.p1chr01_pilon_pilon >> transdecoder three_prime_UTR 411597 411597 . + . >> ID=nbis_NEW-three_prime_utr-1647;Parent=gene.5.0.0.p1chr01_pilon_pilon >> AUGUSTUS gene 548726 549814 0.05 - . >> ID=chr01.g50chr01_pilon_pilon AUGUSTUS mRNA 548726 549814 >> 0.05 - . ID=chr01.g50.t1;Name=*XP_009763891.1;*Note=probable >> peroxygenase 4%2C partial;Parent=chr01.g50* >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> *chr01_pilon_pilon AUGUSTUS TSS 549814 549814 . >> - . ID=tss-50;Parent=chr01.g50.t1chr01_pilon_pilon >> AUGUSTUS exon 548726 549025 0.75 - . >> ID=nbis_NEW-exon-508444;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS >> exon 549117 549231 0.75 - . >> ID=nbis_NEW-exon-508445;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS >> exon 549446 549814 0.75 - . >> ID=nbis_NEW-exon-508446;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS >> CDS 548872 549025 0.75 - 1 >> ID=chr01.g50.t1.cds;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS >> CDS 549117 549231 0.87 - 2 >> ID=IDmodified-cds-835457;Parent=chr01.g50.t1chr01_pilon_pilon >> AUGUSTUS CDS 549446 549491 0.87 - 0 >> ID=IDmodified-cds-835458;Parent=chr01.g50.t1chr01_pilon_pilon >> AUGUSTUS five_prime_utr 549492 549814 0.37 - . >> ID=five_prime_utr-58;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS >> intron 549026 549116 0.88 - . >> ID=intron-212;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS >> intron 549232 549445 0.87 - . >> ID=intron-213;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS >> start_codon 549489 549491 . - 0 >> ID=start_codon-50;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS >> stop_codon 548872 548874 . - 0 >> ID=stop_codon-50;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS >> three_prime_utr 548726 548871 0.17 - . >> ID=three_prime_utr-52;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS >> transcription_end_site 548726 548726 . - . >> ID=transcription_end_site-50;Parent=chr01.g50.t1* >> ... >> >> Thank you in advance, >> >> Mic >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> > |
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From: Colin <col...@gm...> - 2020-11-27 18:39:52
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This documentation page could help https://jbrowse.org/docs/mouse_configs.html#customizing-left-click-behavior-1 Could also use "onClick" : { "label": "search at NCBI", "action": "newWindow", "url": "http://www.ncbi.nlm.nih.gov/gquery/?term={name}" } Which should open it up in a new window -Colin On Fri, Nov 27, 2020 at 12:01 AM Michał T. Lorenc <m.t...@gm...> wrote: > Hi, > How Is it possible to allow the user a left-click on a gene which will > trigger to open for example this URL *https://www.ncbi.nlm.nih.gov/protein/ > <https://www.ncbi.nlm.nih.gov/protein/>XP_019258550.1/*? If not what > other alternatives exist? > > > The data is stored in this GFF3: > > > > > > > > > > > > > > > *##gff-version 3##sequence-region chr01_pilon_pilon 1 > 141847987chr01_pilon_pilon transdecoder gene 410672 411597 . > + . ID=gene.5.0;chr01_pilon_pilon transdecoder > mRNA 410672 411597 . + . > ID=gene.5.0.0.p1;Name=XP_019258550.1;Note=uncharacterized protein > LOC109236786 isoform X2;Parent=gene.5.0chr01_pilon_pilon transdecoder > exon 410672 410798 . + . > ID=gene.5.0.0.p1.exon1;Parent=gene.5.0.0.p1chr01_pilon_pilon > transdecoder exon 410939 411205 . + . > ID=gene.5.0.0.p1.exon2;Parent=gene.5.0.0.p1chr01_pilon_pilon > transdecoder exon 411326 411597 . + . > ID=gene.5.0.0.p1.exon3;Parent=gene.5.0.0.p1chr01_pilon_pilon > transdecoder CDS 411087 411205 . + 0 > ID=cds.gene.5.0.0.p1;Parent=gene.5.0.0.p1chr01_pilon_pilon > transdecoder CDS 411326 411596 . + 1 > ID=cds.gene.5.0.0.p1;Parent=gene.5.0.0.p1chr01_pilon_pilon > transdecoder five_prime_UTR 410672 410798 . + . > ID=gene.5.0.0.p1.utr5p1;Parent=gene.5.0.0.p1chr01_pilon_pilon > transdecoder five_prime_UTR 410939 411086 . + . > ID=gene.5.0.0.p1.utr5p2;Parent=gene.5.0.0.p1chr01_pilon_pilon > transdecoder three_prime_UTR 411597 411597 . + . > ID=nbis_NEW-three_prime_utr-1647;Parent=gene.5.0.0.p1chr01_pilon_pilon > AUGUSTUS gene 548726 549814 0.05 - . > ID=chr01.g50chr01_pilon_pilon AUGUSTUS mRNA 548726 549814 > 0.05 - . ID=chr01.g50.t1;Name=*XP_009763891.1;*Note=probable > peroxygenase 4%2C partial;Parent=chr01.g50* > > > > > > > > > > > > > > > *chr01_pilon_pilon AUGUSTUS TSS 549814 549814 . - > . ID=tss-50;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS > exon 548726 549025 0.75 - . > ID=nbis_NEW-exon-508444;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS > exon 549117 549231 0.75 - . > ID=nbis_NEW-exon-508445;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS > exon 549446 549814 0.75 - . > ID=nbis_NEW-exon-508446;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS > CDS 548872 549025 0.75 - 1 > ID=chr01.g50.t1.cds;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS > CDS 549117 549231 0.87 - 2 > ID=IDmodified-cds-835457;Parent=chr01.g50.t1chr01_pilon_pilon > AUGUSTUS CDS 549446 549491 0.87 - 0 > ID=IDmodified-cds-835458;Parent=chr01.g50.t1chr01_pilon_pilon > AUGUSTUS five_prime_utr 549492 549814 0.37 - . > ID=five_prime_utr-58;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS > intron 549026 549116 0.88 - . > ID=intron-212;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS > intron 549232 549445 0.87 - . > ID=intron-213;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS > start_codon 549489 549491 . - 0 > ID=start_codon-50;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS > stop_codon 548872 548874 . - 0 > ID=stop_codon-50;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS > three_prime_utr 548726 548871 0.17 - . > ID=three_prime_utr-52;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS > transcription_end_site 548726 548726 . - . > ID=transcription_end_site-50;Parent=chr01.g50.t1* > ... > > Thank you in advance, > > Mic > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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From: Michał T. L. <m.t...@gm...> - 2020-11-27 05:00:40
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Hi, How Is it possible to allow the user a left-click on a gene which will trigger to open for example this URL *https://www.ncbi.nlm.nih.gov/protein/ <https://www.ncbi.nlm.nih.gov/protein/>XP_019258550.1/*? If not what other alternatives exist? The data is stored in this GFF3: *##gff-version 3##sequence-region chr01_pilon_pilon 1 141847987chr01_pilon_pilon transdecoder gene 410672 411597 . + . ID=gene.5.0;chr01_pilon_pilon transdecoder mRNA 410672 411597 . + . ID=gene.5.0.0.p1;Name=XP_019258550.1;Note=uncharacterized protein LOC109236786 isoform X2;Parent=gene.5.0chr01_pilon_pilon transdecoder exon 410672 410798 . + . ID=gene.5.0.0.p1.exon1;Parent=gene.5.0.0.p1chr01_pilon_pilon transdecoder exon 410939 411205 . + . ID=gene.5.0.0.p1.exon2;Parent=gene.5.0.0.p1chr01_pilon_pilon transdecoder exon 411326 411597 . + . ID=gene.5.0.0.p1.exon3;Parent=gene.5.0.0.p1chr01_pilon_pilon transdecoder CDS 411087 411205 . + 0 ID=cds.gene.5.0.0.p1;Parent=gene.5.0.0.p1chr01_pilon_pilon transdecoder CDS 411326 411596 . + 1 ID=cds.gene.5.0.0.p1;Parent=gene.5.0.0.p1chr01_pilon_pilon transdecoder five_prime_UTR 410672 410798 . + . ID=gene.5.0.0.p1.utr5p1;Parent=gene.5.0.0.p1chr01_pilon_pilon transdecoder five_prime_UTR 410939 411086 . + . ID=gene.5.0.0.p1.utr5p2;Parent=gene.5.0.0.p1chr01_pilon_pilon transdecoder three_prime_UTR 411597 411597 . + . ID=nbis_NEW-three_prime_utr-1647;Parent=gene.5.0.0.p1chr01_pilon_pilon AUGUSTUS gene 548726 549814 0.05 - . ID=chr01.g50chr01_pilon_pilon AUGUSTUS mRNA 548726 549814 0.05 - . ID=chr01.g50.t1;Name=*XP_009763891.1;*Note=probable peroxygenase 4%2C partial;Parent=chr01.g50* *chr01_pilon_pilon AUGUSTUS TSS 549814 549814 . - . ID=tss-50;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS exon 548726 549025 0.75 - . ID=nbis_NEW-exon-508444;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS exon 549117 549231 0.75 - . ID=nbis_NEW-exon-508445;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS exon 549446 549814 0.75 - . ID=nbis_NEW-exon-508446;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS CDS 548872 549025 0.75 - 1 ID=chr01.g50.t1.cds;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS CDS 549117 549231 0.87 - 2 ID=IDmodified-cds-835457;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS CDS 549446 549491 0.87 - 0 ID=IDmodified-cds-835458;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS five_prime_utr 549492 549814 0.37 - . ID=five_prime_utr-58;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS intron 549026 549116 0.88 - . ID=intron-212;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS intron 549232 549445 0.87 - . ID=intron-213;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS start_codon 549489 549491 . - 0 ID=start_codon-50;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS stop_codon 548872 548874 . - 0 ID=stop_codon-50;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS three_prime_utr 548726 548871 0.17 - . ID=three_prime_utr-52;Parent=chr01.g50.t1chr01_pilon_pilon AUGUSTUS transcription_end_site 548726 548726 . - . ID=transcription_end_site-50;Parent=chr01.g50.t1* ... Thank you in advance, Mic |
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From: Ben B. <bb...@gm...> - 2020-11-20 23:52:50
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Just a thought: since the core configuration of the genome/assembly would it be useful to define that in one JSON file, and reference the URL to that file from other config.json files? For example, we might have grch38.json, mmul10.json and grch37.json. In the primary config.json, you then have assembly = https://..../grch38.json? This would allow multiple instances to share genomes nicely? At least in the way we use it (in JBrowse 1), we have a 'base genome' instance, which generally has the assembly and a core set of tracks (like NCBI/Ensembl gene builds). Users then create "sessions" based on that genome, which in our code clones the resources of that base genome and appends their custom tracks. Our code does this by copying/merging the JSON file, but it would be nice if there was more direct layering/merging, like what Colin seems to be implying. This might be what Colin is describing with "the include system" ,but perhaps a config.json could also specify a "baseConfig: https://.../defaultGRCH38.json', which might be a JSON file describing the assembly and default tracks? -Ben On Tue, Nov 17, 2020 at 9:31 AM Ke Jiang <bio...@gm...> wrote: > Sounds good! These are very valuable comments. Thanks! > > On Tue, Nov 17, 2020 at 11:03 AM Colin <col...@gm...> wrote: > >> In general we do allow and encourage putting multiple genome assemblies >> in a single config.json.for jbrowse 2. Then each track specifies which >> assembly each track belongs to (or for synteny tracks, which assemblies >> [plural] it belongs to) >> >> >> >> In Jbrowse 2 we allow ?config= so you could have multiple unrelated >> configs but we have not made the "include" system of jbrowse 1 that lets >> you merge multiple configs though. >> >> If this is seems important to separate things out, let us know but single >> config.json containing multiple assemblies is the current concept :) >> >> -Colin >> >> On Mon, Nov 16, 2020, 10:28 AM Ke Jiang <bio...@gm...> wrote: >> >>> Hi, >>> >>> I've been playing with JBrowse2 first release for a few days. In >>> JBorwse (1), I've been using a strategy to separate configuration and data >>> for multiple genomes by creating config.json for each genome (and pointing >>> data to the corresponding genomic data). It worked pretty well as it >>> reduced chances of messing up other genomes while making changes to one >>> genome. I noticed for JBrowse2, there is a master config.json sitting in >>> the JBrowe2 folder and we lay out multiple genomes and assemblies in it. Is >>> this the way to manage multiple genomes in JBrowse2 now? Because JBrowse2 >>> has to consider the multiple genome view for synteny, so everything has to >>> be in one single config.json? Or more generally, what is the general idea >>> (or best practices?) of handling multiple organisms in JBrowse2? >>> >>> Thanks again for the development of JBrowse 2! It is truly exciting to >>> see it! >>> >>> Ke >>> _______________________________________________ >>> Gmod-ajax mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >>> >> _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > |
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