gmod-ajax — JBrowse list

Re: [Gmod-ajax] jbrowse_help

[Scott C. <sc...@sc...>]

Hi anubhav,

Can you tell us what you did to prepare the GFF data, and what the track configuration looks like?  If this site is available somewhere on the web that we can get to, that would probably help too. 

Also, I know you are fairly new to jbrowse; let me suggest that you might want to look at jbrowse 1, as it is more mature (I know I just steered you away from GBrowse because it’s “too mature”). It all depends on what you want the browser for. 

Scott

> On Mar 18, 2021, at 10:29 AM, anubhav roy <anu...@gm...> wrote:
> 
> 
> I have loaded Rice gff3 file but in GUI no genes or transcripts or any information is shown.why?
> I want genes in my gff3 file to be shown in GUI. kindly help.
> screenshot is Attached.
> <jbrowse.png>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

[Gmod-ajax] jbrowse_help

[anubhav r. <anu...@gm...>]

I have loaded Rice gff3 file but in GUI no genes or transcripts or any
information is shown.why?
I want genes in my gff3 file to be shown in GUI. kindly help.
screenshot is Attached.

Re: [Gmod-ajax] JBrowse 2 features

[Vaneet L. <van...@uc...>]

Hey Coling

Thanks for the useful info and your prompt reply.  I will certainly try out JBrowse 2 soon to take advantage of all of its new features.

It’s great to know that grouped track autoscaling is still in future plans.  I guess I was subscribed to the original issue, just couldn’t remember where  it was so thanks.  I subscribed to this new issue as well.  I always appreciate your help with JBrowse troubleshooting.

Vaneet

Vaneet Lotay
Xenbase Bioinformatician
716 ICT Building – University of Calgary
2500 University Drive NW
Calgary, AB T2N 1N4
CANADA

From: Colin <col...@gm...>
Sent: Wednesday, March 17, 2021 6:12 PM
To: Vaneet Lotay <van...@uc...>
Cc: gmod-ajax <gmo...@li...>
Subject: Re: [Gmod-ajax] JBrowse 2 features

[△EXTERNAL]

Hi Vaneet,
JBrowse 2 is definitely where most of our effort is now,

JBrowse 1 will probably continue on in maintenance mode with not a lot of new development. We did just release a new 1.16.11 for JBrowse 1 for example, but most of our work is on JBrowse 2

We currently have a developer working on the gene name/ID search for JBrowse 2, so that should be incorporated soon.

Also, having multibigwig style feature in JBrowse 2, or grouped track autoscaling, would also be great. We don't have this yet but these needs are very common

I created this issue to track grouped track autoscaling, you can subscribe to the issue if you have a github account

https://github.com/GMOD/jbrowse-components/issues/1809


-Colin

On Wed, Mar 17, 2021 at 7:10 PM Vaneet Lotay <van...@uc...<mailto:van...@uc...>> wrote:
Hello,

I am interested in trying out JBrowse 2 but I was just wondering is version 2 something that will eventually replace JBrowse 1 meaning that it could become the only supported version of JBrowse?  Or is it more looked at as an alternative browser for displaying more visualization types and a different variety of features than version 1?

I noticed that the ability to search for a particular gene name or ID is not included in JBrowse 2 yet.  Is this a priority going forward to include it in JBrowse 2 or is it just something that will remain in JBrowse 1?

One feature that I’ve always wished for is the ability to dynamically scale a group tracks together with same maximum score on the y-axis.  Perhaps scaling tracks in the same subcategory together with the same maximum would be one avenue that would work well for most.  I’ve seen different issue threads related to this on the Github JBrowse repository, so I wasn’t sure if this still a feature that’s being worked on for JBrowse 1 or perhaps JBrowse 2?  I know that the multibigwig plugin does accomplish this if configured as that type of track and I’ve been grateful to use it for different subsets of our tracks at Xenbase but I was just wondering if there are any alternatives being worked on while keeping the tracks separated as well.

Thanks,

Vaneet
Vaneet Lotay
Xenbase Bioinformatician
716 ICT Building – University of Calgary
2500 University Drive NW
Calgary, AB T2N 1N4
CANADA

_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] JBrowse 2 features

[Colin <col...@gm...>]

Hi Vaneet,
JBrowse 2 is definitely where most of our effort is now,

JBrowse 1 will probably continue on in maintenance mode with not a lot of
new development. We did just release a new 1.16.11 for JBrowse 1 for
example, but most of our work is on JBrowse 2

We currently have a developer working on the gene name/ID search for
JBrowse 2, so that should be incorporated soon.

Also, having multibigwig style feature in JBrowse 2, or grouped track
autoscaling, would also be great. We don't have this yet but these needs
are very common

I created this issue to track grouped track autoscaling, you can subscribe
to the issue if you have a github account

https://github.com/GMOD/jbrowse-components/issues/1809


-Colin

On Wed, Mar 17, 2021 at 7:10 PM Vaneet Lotay <van...@uc...>
wrote:

> Hello,
>
>
>
> I am interested in trying out JBrowse 2 but I was just wondering is
> version 2 something that will eventually replace JBrowse 1 meaning that it
> could become the only supported version of JBrowse?  Or is it more looked
> at as an alternative browser for displaying more visualization types and a
> different variety of features than version 1?
>
>
>
> I noticed that the ability to search for a particular gene name or ID is
> not included in JBrowse 2 yet.  Is this a priority going forward to include
> it in JBrowse 2 or is it just something that will remain in JBrowse 1?
>
>
>
> One feature that I’ve always wished for is the ability to dynamically
> scale a group tracks together with same maximum score on the y-axis.
> Perhaps scaling tracks in the same subcategory together with the same
> maximum would be one avenue that would work well for most.  I’ve seen
> different issue threads related to this on the Github JBrowse repository,
> so I wasn’t sure if this still a feature that’s being worked on for JBrowse
> 1 or perhaps JBrowse 2?  I know that the multibigwig plugin does accomplish
> this if configured as that type of track and I’ve been grateful to use it
> for different subsets of our tracks at Xenbase but I was just wondering if
> there are any alternatives being worked on while keeping the tracks
> separated as well.
>
>
>
> Thanks,
>
>
>
> Vaneet
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *716 ICT Building – University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary, AB T2N 1N4*
>
> *CANADA*
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse 2 features

[Vaneet L. <van...@uc...>]

Hello,

I am interested in trying out JBrowse 2 but I was just wondering is version 2 something that will eventually replace JBrowse 1 meaning that it could become the only supported version of JBrowse?  Or is it more looked at as an alternative browser for displaying more visualization types and a different variety of features than version 1?

I noticed that the ability to search for a particular gene name or ID is not included in JBrowse 2 yet.  Is this a priority going forward to include it in JBrowse 2 or is it just something that will remain in JBrowse 1?

One feature that I've always wished for is the ability to dynamically scale a group tracks together with same maximum score on the y-axis.  Perhaps scaling tracks in the same subcategory together with the same maximum would be one avenue that would work well for most.  I've seen different issue threads related to this on the Github JBrowse repository, so I wasn't sure if this still a feature that's being worked on for JBrowse 1 or perhaps JBrowse 2?  I know that the multibigwig plugin does accomplish this if configured as that type of track and I've been grateful to use it for different subsets of our tracks at Xenbase but I was just wondering if there are any alternatives being worked on while keeping the tracks separated as well.

Thanks,

Vaneet
Vaneet Lotay
Xenbase Bioinformatician
716 ICT Building - University of Calgary
2500 University Drive NW
Calgary, AB T2N 1N4
CANADA

Re: [Gmod-ajax] Unable to add track in gff3

[Robert B. <rb...@gm...>]

Might it be useful for us to have a `jbrowse list-assemblies` or similar
command for this situation?

On Tue, Mar 16, 2021 at 2:32 AM anubhav roy <anu...@gm...> wrote:

> Thanks, I'll check it out.
>
> On Tue, Mar 16, 2021 at 1:54 AM Colin <col...@gm...> wrote:
>
>> Hi there!
>>
>> Glad to hear interest in jbrowse 2
>>
>> Our basic tutorial assumes that you only have one assembly in your
>> config, and in that case it automatically infers which assembly you are
>> loading your track for
>>
>> If you have multiple in your config, then you will need to specify which
>> assembly you are loading for
>>
>> If you look in the config.json then it will be the "name" field for the
>> assembly of interest, which you can add to your command so it might be like
>>
>> So if you had ran
>>
>> jbrowse add-assembly yourfile.fasta --name rice --load copy
>>
>> Then you can then run
>>
>> jbrowse add-track yourfile.sorted.gff.gz --load copy --assemblyNames rice
>>
>>
>>
>> -Colin
>>
>> On Mon, Mar 15, 2021 at 11:54 AM anubhav roy <anu...@gm...>
>> wrote:
>>
>>> hello sir/mam,
>>> i am trying to add gff3 annotation track into jbrowse by following code
>>> given in tutorial-
>>> "jbrowse add-track yourfile.sorted.gff.gz --load copy" but this code
>>> executes following error
>>> T*oo many assemblies, cannot default to one. Please specify the
>>> assembly with the --assemblyNames flag*
>>> kindly help to get it done.
>>> _______________________________________________
>>> 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
>

Re: [Gmod-ajax] Unable to add track in gff3

[anubhav r. <anu...@gm...>]

Thanks, I'll check it out.

On Tue, Mar 16, 2021 at 1:54 AM Colin <col...@gm...> wrote:

> Hi there!
>
> Glad to hear interest in jbrowse 2
>
> Our basic tutorial assumes that you only have one assembly in your config,
> and in that case it automatically infers which assembly you are loading
> your track for
>
> If you have multiple in your config, then you will need to specify which
> assembly you are loading for
>
> If you look in the config.json then it will be the "name" field for the
> assembly of interest, which you can add to your command so it might be like
>
> So if you had ran
>
> jbrowse add-assembly yourfile.fasta --name rice --load copy
>
> Then you can then run
>
> jbrowse add-track yourfile.sorted.gff.gz --load copy --assemblyNames rice
>
>
>
> -Colin
>
> On Mon, Mar 15, 2021 at 11:54 AM anubhav roy <anu...@gm...>
> wrote:
>
>> hello sir/mam,
>> i am trying to add gff3 annotation track into jbrowse by following code
>> given in tutorial-
>> "jbrowse add-track yourfile.sorted.gff.gz --load copy" but this code
>> executes following error
>> T*oo many assemblies, cannot default to one. Please specify the assembly
>> with the --assemblyNames flag*
>> kindly help to get it done.
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] Unable to add track in gff3

[Colin <col...@gm...>]

Hi there!

Glad to hear interest in jbrowse 2

Our basic tutorial assumes that you only have one assembly in your config,
and in that case it automatically infers which assembly you are loading
your track for

If you have multiple in your config, then you will need to specify which
assembly you are loading for

If you look in the config.json then it will be the "name" field for the
assembly of interest, which you can add to your command so it might be like

So if you had ran

jbrowse add-assembly yourfile.fasta --name rice --load copy

Then you can then run

jbrowse add-track yourfile.sorted.gff.gz --load copy --assemblyNames rice



-Colin

On Mon, Mar 15, 2021 at 11:54 AM anubhav roy <anu...@gm...>
wrote:

> hello sir/mam,
> i am trying to add gff3 annotation track into jbrowse by following code
> given in tutorial-
> "jbrowse add-track yourfile.sorted.gff.gz --load copy" but this code
> executes following error
> T*oo many assemblies, cannot default to one. Please specify the assembly
> with the --assemblyNames flag*
> kindly help to get it done.
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Unable to add track in gff3

[anubhav r. <anu...@gm...>]

hello sir/mam,
i am trying to add gff3 annotation track into jbrowse by following code
given in tutorial-
"jbrowse add-track yourfile.sorted.gff.gz --load copy" but this code
executes following error
T*oo many assemblies, cannot default to one. Please specify the assembly
with the --assemblyNames flag*
kindly help to get it done.

Re: [Gmod-ajax] [apollo] Blast server

[Nathan D. <nat...@lb...>]

Oh, even easier in just using the `Save sequence` drop down.  Not sure why I forgot that. 



Nathan


> On Mar 11, 2021, at 4:25 PM, Nathan Dunn <nat...@lb...> wrote:
> 
> 
> For the reference sequence track at the top you choose:
> 
> <PastedGraphic-1.tiff>
> 
> And then the highlighted region:
> 
> <PastedGraphic-2.tiff>
> 
> 
> With respect to JB-connect, I don’t think we’d tried that experiment, but I don’t know of any reason it wouldn’t work, though it may require a bit of configuration.  
> 
> Nathan
> 
> 
> 
>> On Mar 11, 2021, at 4:01 PM, Michał T. Lorenc <m.t...@gm... <mailto:m.t...@gm...>> wrote:
>> 
>> Hi Nathan,
>> Thank you for the list. It appears that NAL-i5k uses under the hood https://github.com/NAL-i5K/django-blast <https://github.com/NAL-i5K/django-blast> . By any chance, do you know how to allow the user to click on the blast result, and apollo will open and highlight the BLAST hit region?
>> 
>> I am also interested in Eric's https://github.com/GMOD/jblast-jbconnect-hook <https://github.com/GMOD/jblast-jbconnect-hook> . Is the installation documentation (https://jblast.readthedocs.io/en/latest/#install <https://jblast.readthedocs.io/en/latest/#install>) compatible with Apollo?
>> 
>> Thank you in advance,
>> 
>> Michal
>> 
>> On Fri, Dec 11, 2020 at 10:12 AM Nathan Dunn <nat...@lb... <mailto:nat...@lb...>> wrote:
>> 
>> 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. 
>> 
>> <PastedGraphic-3.tiff>
>> 
>> 
>> 
>> 2 - The i5k workspace is here: https://github.com/NAL-i5K <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... <mailto: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
>> 
>> 
>> -- 
>> To unsubscribe from this group and stop receiving emails from it, send an email to apo...@lb... <mailto:apo...@lb...>.
> 
> 
> -- 
> To unsubscribe from this group and stop receiving emails from it, send an email to apo...@lb... <mailto:apo...@lb...>.

[Gmod-ajax] JBrowse 1.16.11 maintanence release

[Colin <col...@gm...>]

Hi all,

This is a small maintenance release that fixes an issue that was seen with
very long CRAM reads and an issue that was seen with some users installing
with setup.sh producing an error. Thanks to everyone for their bug reports
and requests and for being patient with jbrowse 1 releases as we speed
ahead with jbrowse 2!



   - JBrowse-1.16.11.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.11-release/JBrowse-1.16.11.zip>
-
   minified release
   - JBrowse-1.16.11-dev.zip
   <https://github.com/GMOD/jbrowse/archive/1.16.11-release.zip> - use this
   if you modify jbrowse source code or use plugins
   - JBrowse-1.16.11-desktop-win32-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.11-release/JBrowse-1.16.11-desktop-win32-x64.zip>
   - JBrowse-1.16.11-desktop-linux-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.11-release/JBrowse-1.16.11-desktop-linux-x64.zip>
   - JBrowse-1.16.11-desktop-darwin-x64.zip
   <https://github.com/GMOD/jbrowse/releases/download/1.16.11-release/JBrowse-1.16.11-desktop-darwin-x64.zip>

<https://jbrowse.org/blog/#minor-improvements>Minor improvements

   -

   Add optional track label field for RegexSequenceSearch (issue #1553
   <https://github.com/gmod/jbrowse/issues/1553>, @cmdcolin
   <https://github.com/cmdcolin>, @Rhinogradentia
   <https://github.com/Rhinogradentia>)
   -

   Bump @gmod <https://github.com/gmod>/tabix for textdecoder speedup for
   very large tabix files (@arpanda <https://github.com/arpanda>, @cmdcolin
   <https://github.com/cmdcolin>, issue #1569
   <https://github.com/gmod/jbrowse/pull/1569>)
   -

   Increase GFF3Tabix chunkSizeLimit to avoid it being hit on relatively
   small files

<https://jbrowse.org/blog/#bug-fixes>Bug fixes

   -

   Bump @gmod <https://github.com/gmod>/cram for fix for ultra long reads (
   https://github.com/GMOD/cram-js/pull/84)
   -

   Fix issue that some users were seeing with "Commit hash required" when
   running setup.sh. Thanks to @GFJHogue <https://github.com/GFJHogue> and
   @hans-vg <https://github.com/hans-vg> for reporting (issue #1555
   <https://github.com/gmod/jbrowse/issues/1555>)
   -

   Bump @gmod <https://github.com/gmod>/bam which fixes some unsigned BAM
   tags being reported with a negative number
   -

   Bump @gmod <https://github.com/gmod>/bam and @gmod
   <https://github.com/gmod>/tabix for and some fixes with reg2bins and
   chunk merging for large chromosomes e.g. wheat. Thanks to @jrobinso
   <https://github.com/jrobinso> for reporting (
   https://github.com/GMOD/tabix-js/issues/118)


Thanks
-Colin

Re: [Gmod-ajax] [apollo] Blast server

[Nathan D. <nat...@lb...>]

For the reference sequence track at the top you choose:



And then the highlighted region:




With respect to JB-connect, I don’t think we’d tried that experiment, but I don’t know of any reason it wouldn’t work, though it may require a bit of configuration.  

Nathan



> On Mar 11, 2021, at 4:01 PM, Michał T. Lorenc <m.t...@gm...> wrote:
> 
> Hi Nathan,
> Thank you for the list. It appears that NAL-i5k uses under the hood https://github.com/NAL-i5K/django-blast <https://github.com/NAL-i5K/django-blast> . By any chance, do you know how to allow the user to click on the blast result, and apollo will open and highlight the BLAST hit region?
> 
> I am also interested in Eric's https://github.com/GMOD/jblast-jbconnect-hook <https://github.com/GMOD/jblast-jbconnect-hook> . Is the installation documentation (https://jblast.readthedocs.io/en/latest/#install <https://jblast.readthedocs.io/en/latest/#install>) compatible with Apollo?
> 
> Thank you in advance,
> 
> Michal
> 
> On Fri, Dec 11, 2020 at 10:12 AM Nathan Dunn <nat...@lb... <mailto:nat...@lb...>> wrote:
> 
> 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. 
> 
> <PastedGraphic-3.tiff>
> 
> 
> 
> 2 - The i5k workspace is here: https://github.com/NAL-i5K <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... <mailto: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
> 
> 
> -- 
> To unsubscribe from this group and stop receiving emails from it, send an email to apo...@lb... <mailto:apo...@lb...>.

Re: [Gmod-ajax] [apollo] Blast server

[Michał T. L. <m.t...@gm...>]

Hi Nathan,
Thank you for the list. It appears that NAL-i5k uses under the hood
https://github.com/NAL-i5K/django-blast . By any chance, do you know how to
allow the user to click on the blast result, and apollo will open and
highlight the BLAST hit region?

I am also interested in Eric's https://github.com/GMOD/jblast-jbconnect-hook .
Is the installation documentation (
https://jblast.readthedocs.io/en/latest/#install) compatible with Apollo?

Thank you in advance,

Michal

On Fri, Dec 11, 2020 at 10:12 AM Nathan Dunn <nat...@lb...> wrote:

>
> 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://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 ) .
>
> 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 ?  (For JBrowse)
> maintained by Eric Yao.
>
> 4 - I believe the galaxy.eu server has one:
> https://annotation.usegalaxy.eu/
>
> 5 - 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/) 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
>
>
>

Re: [Gmod-ajax] Problems installing jbrowse1

[Hans Vasquez-G. <hav...@uc...>]

Hi Colin,

I just tried installing from the latest dev branch. Everything went
smoothly this time. Thank you!

Best,
-Hans

On Thu, Mar 11, 2021 at 1:38 PM Colin <col...@gm...> wrote:

> I just pushed a fix to the "dev" branch of jbrowse with a possible fix for
> the "Commit hash required" message I saw in your log file
>
>
> If you are able to test it out, and see if you can run setup.sh on the dev
> branch, let me know
>
> Try
>
>
> git clone https://github.com/GMOD/jbrowse
> cd jbrowse
> git checkout dev
> ./setup.sh
>
> We could then make a quick new release with that if it works
>
>
> -Colin
>
> On Thu, Mar 11, 2021 at 12:30 PM Hans Vasquez-Gross <
> hav...@uc...> wrote:
>
>> Hi Robert,
>>
>> No I haven't. In my previous lab, I had extended viroblast PHP code to
>> keep track of source BLAST databases and pull up the specific genome
>> reference in JBrowse using URL encoded tracks. However, this was all very
>> specific to that lab.
>>
>> In the new lab I joined, I was going to use SequenceServer to connect the
>> BLAST service to different JBrowse genome projects. Right now, It doesn't
>> sound like there is an easy way to integrate SequenceServer with JB2. Thank
>> you for your suggestion though.
>>
>> Colin: thank you for the issue report. I'll try the workaround.
>>
>> Best,
>> -Hans
>>
>> On Thu, Mar 11, 2021 at 11:05 AM Robert Buels <rb...@gm...> wrote:
>>
>>> Regarding url encoded tracks, the currently best “jbrowse 2 way” of
>>> creating tracks and injecting them into the browser is to directly embed a
>>> jb2 embedded linear genome view in your application that you can fully
>>> control. Have you considered going in that direction?
>>>
>>>
>>> On Wed, Mar 10, 2021 at 6:22 PM Colin <col...@gm...> wrote:
>>>
>>>> Interesting... I think this error was also noted here
>>>> https://github.com/GMOD/jbrowse/issues/1555
>>>>
>>>>
>>>> Probably we should remove our dependency in jbrowse 1 from installing a
>>>> package directly from GitHub to properly fix, I think it is the jszlib
>>>> dependency that we use
>>>>
>>>>
>>>> -Colin
>>>>
>>>> On Wed, Mar 10, 2021, 6:39 PM Hans Vasquez-Gross via Gmod-ajax <
>>>> gmo...@li...> wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> I recently installed jbrowse2 on a new system, but some of the
>>>>> functionality that was in jbrowse1 is missing in jbrowse2 (URL encoded
>>>>> tracks). Today, I tried installing jbrowse1, but am running into some
>>>>> nodejs issues.
>>>>>
>>>>> When I try loading up the page, I can see my main.bundle.js is missing
>>>>> (404 error) which I think is related to the nodejs problems.
>>>>>
>>>>> Please see setup log below.
>>>>>
>>>>> Any advice would be greatly appreciated.
>>>>>
>>>>> Thank you,
>>>>> -Hans
>>>>>
>>>>>
>>>>> > bash setup.sh
>>>>> Gathering system information ...done.
>>>>> NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been
>>>>> removed from setup. Their functionality has been superseded by
>>>>> add-bam-track.pl and add-bw-track.pl. If you require the old
>>>>> versions, please use JBrowse 1.12.3 or earlier.
>>>>> Installing node.js dependencies and building with webpack ... failed.
>>>>> See setup.log file for error messages.
>>>>> setup cannot continue, aborting.
>>>>>
>>>>> Gathering system information ...
>>>>> ============== System information ====
>>>>> + lsb_release -a
>>>>> No LSB modules are available.
>>>>> Distributor ID: Ubuntu
>>>>> Description:    Ubuntu 20.04.1 LTS
>>>>> Release:        20.04
>>>>> Codename:       focal
>>>>> + uname -a
>>>>> Linux borlaug 5.8.0-36-generic #40~20.04.1-Ubuntu SMP Wed Jan 6
>>>>> 10:15:55 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
>>>>> + sw_vers
>>>>> setup.sh: line 89: sw_vers: command not found
>>>>> + grep MemTotal /proc/meminfo
>>>>> MemTotal:       65733500 kB
>>>>> + echo
>>>>>
>>>>> + echo
>>>>>
>>>>>
>>>>> done.
>>>>>
>>>>>
>>>>> NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been
>>>>> removed from setup. Their functionality has been superseded by
>>>>> add-bam-track.pl and add-bw-track.pl. If you require the old
>>>>> versions, please use JBrowse 1.12.3 or earlier.
>>>>>
>>>>>
>>>>> Installing node.js dependencies and building with webpack ...
>>>>> Node v15.11.0 installed at /usr/bin/node with npm 7.6.0
>>>>> npm WARN deprecated ini@1.3.5: Please update to ini >=1.3.6 to avoid
>>>>> a prototype pollution issue
>>>>> npm WARN deprecated urix@0.1.0: Please see
>>>>> https://github.com/lydell/urix#deprecated
>>>>> npm WARN deprecated sprintf@0.1.5: The sprintf package is deprecated
>>>>> in favor of sprintf-js.
>>>>> npm WARN deprecated har-validator@5.1.3: this library is no longer
>>>>> supported
>>>>> npm WARN deprecated mkdirp@0.5.3: Legacy versions of mkdirp are no
>>>>> longer supported. Please update to mkdirp 1.x. (Note that the API surface
>>>>> has changed to use Promises in 1.x.)
>>>>> npm WARN deprecated resolve-url@0.2.1:
>>>>> https://github.com/lydell/resolve-url#deprecated
>>>>> npm WARN deprecated chokidar@1.7.0: Chokidar 2 will break on node
>>>>> v14+. Upgrade to chokidar 3 with 15x less dependencies.
>>>>> npm WARN deprecated circular-json@0.3.3: CircularJSON is in
>>>>> maintenance only, flatted is its successor.
>>>>> npm WARN deprecated xmldom@0.1.31: Deprecated due to CVE-2021-21366
>>>>> resolved in 0.5.0
>>>>> npm WARN deprecated filesaver.js@0.2.0: Unmaintained namespace.
>>>>> Please use the file-saver package:
>>>>> https://www.npmjs.com/package/file-saver
>>>>> npm WARN deprecated debug@3.2.6: Debug versions >=3.2.0 <3.2.7 || >=4
>>>>> <4.3.1 have a low-severity ReDos regression when used in a Node.js
>>>>> environment. It is recommended you upgrade to 3.2.7 or 4.3.1. (
>>>>> https://github.com/visionmedia/debug/issues/797)
>>>>> npm WARN deprecated chokidar@2.1.8: Chokidar 2 will break on node
>>>>> v14+. Upgrade to chokidar 3 with 15x less dependencies.
>>>>>  WARN deprecated debug@4.1.1: Debug versions >=3.2.0 <3.2.7 || >=4
>>>>> <4.3.1 have a low-severity ReDos regression when used in a Node.js
>>>>> environment. It is recommended you upgrade to 3.2.7 or 4.3.1. (
>>>>> https://github.com/visionmedia/debug/issues/797)
>>>>> npm WARN deprecated mkdirp@0.3.5: Legacy versions of mkdirp are no
>>>>> longer supported. Please update to mkdirp 1.x. (Note that the API surface
>>>>> has changed to use Promises in 1.x.)
>>>>> npm WARN deprecated mkdirp@0.3.5: Legacy versions of mkdirp are no
>>>>> longer supported. Please update to mkdirp 1.x. (Note that the API surface
>>>>> has changed to use Promises in 1.x.)
>>>>> npm WARN deprecated babel-eslint@8.2.6: babel-eslint is now
>>>>> @babel/eslint-parser. This package will no longer receive updates.
>>>>> npm WARN deprecated mkdirp@0.5.1: Legacy versions of mkdirp are no
>>>>> longer supported. Please update to mkdirp 1.x. (Note that the API surface
>>>>> has changed to use Promises in 1.x.)
>>>>> npm WARN deprecated request@2.88.2: request has been deprecated, see
>>>>> https://github.com/request/request/issues/3142
>>>>> npm WARN deprecated uglify-es@3.3.9: support for ECMAScript is
>>>>> superseded by `uglify-js` as of v3.13.0
>>>>> npm WARN deprecated webdriverio@4.14.4: outdated version, please use
>>>>> @next
>>>>> npm WARN deprecated core-js@2.6.11: core-js@<3 is no longer
>>>>> maintained and not recommended for usage due to the number of issues.
>>>>> Please, upgrade your dependencies to the actual version of core-js@3.
>>>>>
>>>>> added 1500 packages, and audited 1501 packages in 3m
>>>>>
>>>>> 24 packages are looking for funding
>>>>>   run `npm fund` for details
>>>>>
>>>>> 35 vulnerabilities (21 low, 3 moderate, 11 high)
>>>>>
>>>>> To address issues that do not require attention, run:
>>>>>   npm audit fix
>>>>>
>>>>> To address all issues possible (including breaking changes), run:
>>>>>   npm audit fix --force
>>>>>
>>>>> Some issues need review, and may require choosing
>>>>> a different dependency.
>>>>>
>>>>> Run `npm audit` for details.
>>>>> 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 inconsistencies caused by
>>>>> unsynchronized lock files. To clear this warning, remove package-lock.json.
>>>>> [1/4] Resolving packages...
>>>>> warning ava > chokidar > fsevents@1.2.13: fsevents 1 will break on
>>>>> node v14+ and could be using insecure binaries. Upgrade to fsevents 2.
>>>>> warning webpack > watchpack > chokidar > fsevents@1.2.13: fsevents 1
>>>>> will break on node v14+ and could be using insecure binaries. Upgrade to
>>>>> fsevents 2.
>>>>> [2/4] Fetching packages...
>>>>> error An unexpected error occurred: "Commit hash required".
>>>>> info If you think this is a bug, please open a bug report with the
>>>>> information provided in
>>>>> "/var/www/html/jbrowse-1.16.10-release/yarn-error.log".
>>>>> info Visit https://yarnpkg.com/en/docs/cli/install for documentation
>>>>> about this command.
>>>>>
>>>>>
>>>>> Formatting Volvox example data ...done.
>>>>> To see the volvox example data, browse to
>>>>> http://your.jbrowse.root/index.html?data=sample_data/json/volvox.
>>>>>
>>>>> Formatting Yeast example data ...done.
>>>>> To see the yeast example data, browse to
>>>>> http://your.jbrowse.root/index.html?data=sample_data/json/yeast.
>>>>> _______________________________________________
>>>>> 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

Re: [Gmod-ajax] Problems installing jbrowse1

[Colin <col...@gm...>]

I just pushed a fix to the "dev" branch of jbrowse with a possible fix for
the "Commit hash required" message I saw in your log file


If you are able to test it out, and see if you can run setup.sh on the dev
branch, let me know

Try


git clone https://github.com/GMOD/jbrowse
cd jbrowse
git checkout dev
./setup.sh

We could then make a quick new release with that if it works


-Colin

On Thu, Mar 11, 2021 at 12:30 PM Hans Vasquez-Gross <
hav...@uc...> wrote:

> Hi Robert,
>
> No I haven't. In my previous lab, I had extended viroblast PHP code to
> keep track of source BLAST databases and pull up the specific genome
> reference in JBrowse using URL encoded tracks. However, this was all very
> specific to that lab.
>
> In the new lab I joined, I was going to use SequenceServer to connect the
> BLAST service to different JBrowse genome projects. Right now, It doesn't
> sound like there is an easy way to integrate SequenceServer with JB2. Thank
> you for your suggestion though.
>
> Colin: thank you for the issue report. I'll try the workaround.
>
> Best,
> -Hans
>
> On Thu, Mar 11, 2021 at 11:05 AM Robert Buels <rb...@gm...> wrote:
>
>> Regarding url encoded tracks, the currently best “jbrowse 2 way” of
>> creating tracks and injecting them into the browser is to directly embed a
>> jb2 embedded linear genome view in your application that you can fully
>> control. Have you considered going in that direction?
>>
>>
>> On Wed, Mar 10, 2021 at 6:22 PM Colin <col...@gm...> wrote:
>>
>>> Interesting... I think this error was also noted here
>>> https://github.com/GMOD/jbrowse/issues/1555
>>>
>>>
>>> Probably we should remove our dependency in jbrowse 1 from installing a
>>> package directly from GitHub to properly fix, I think it is the jszlib
>>> dependency that we use
>>>
>>>
>>> -Colin
>>>
>>> On Wed, Mar 10, 2021, 6:39 PM Hans Vasquez-Gross via Gmod-ajax <
>>> gmo...@li...> wrote:
>>>
>>>> Hello,
>>>>
>>>> I recently installed jbrowse2 on a new system, but some of the
>>>> functionality that was in jbrowse1 is missing in jbrowse2 (URL encoded
>>>> tracks). Today, I tried installing jbrowse1, but am running into some
>>>> nodejs issues.
>>>>
>>>> When I try loading up the page, I can see my main.bundle.js is missing
>>>> (404 error) which I think is related to the nodejs problems.
>>>>
>>>> Please see setup log below.
>>>>
>>>> Any advice would be greatly appreciated.
>>>>
>>>> Thank you,
>>>> -Hans
>>>>
>>>>
>>>> > bash setup.sh
>>>> Gathering system information ...done.
>>>> NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been
>>>> removed from setup. Their functionality has been superseded by
>>>> add-bam-track.pl and add-bw-track.pl. If you require the old versions,
>>>> please use JBrowse 1.12.3 or earlier.
>>>> Installing node.js dependencies and building with webpack ... failed.
>>>> See setup.log file for error messages.
>>>> setup cannot continue, aborting.
>>>>
>>>> Gathering system information ...
>>>> ============== System information ====
>>>> + lsb_release -a
>>>> No LSB modules are available.
>>>> Distributor ID: Ubuntu
>>>> Description:    Ubuntu 20.04.1 LTS
>>>> Release:        20.04
>>>> Codename:       focal
>>>> + uname -a
>>>> Linux borlaug 5.8.0-36-generic #40~20.04.1-Ubuntu SMP Wed Jan 6
>>>> 10:15:55 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
>>>> + sw_vers
>>>> setup.sh: line 89: sw_vers: command not found
>>>> + grep MemTotal /proc/meminfo
>>>> MemTotal:       65733500 kB
>>>> + echo
>>>>
>>>> + echo
>>>>
>>>>
>>>> done.
>>>>
>>>>
>>>> NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been
>>>> removed from setup. Their functionality has been superseded by
>>>> add-bam-track.pl and add-bw-track.pl. If you require the old versions,
>>>> please use JBrowse 1.12.3 or earlier.
>>>>
>>>>
>>>> Installing node.js dependencies and building with webpack ...
>>>> Node v15.11.0 installed at /usr/bin/node with npm 7.6.0
>>>> npm WARN deprecated ini@1.3.5: Please update to ini >=1.3.6 to avoid a
>>>> prototype pollution issue
>>>> npm WARN deprecated urix@0.1.0: Please see
>>>> https://github.com/lydell/urix#deprecated
>>>> npm WARN deprecated sprintf@0.1.5: The sprintf package is deprecated
>>>> in favor of sprintf-js.
>>>> npm WARN deprecated har-validator@5.1.3: this library is no longer
>>>> supported
>>>> npm WARN deprecated mkdirp@0.5.3: Legacy versions of mkdirp are no
>>>> longer supported. Please update to mkdirp 1.x. (Note that the API surface
>>>> has changed to use Promises in 1.x.)
>>>> npm WARN deprecated resolve-url@0.2.1:
>>>> https://github.com/lydell/resolve-url#deprecated
>>>> npm WARN deprecated chokidar@1.7.0: Chokidar 2 will break on node
>>>> v14+. Upgrade to chokidar 3 with 15x less dependencies.
>>>> npm WARN deprecated circular-json@0.3.3: CircularJSON is in
>>>> maintenance only, flatted is its successor.
>>>> npm WARN deprecated xmldom@0.1.31: Deprecated due to CVE-2021-21366
>>>> resolved in 0.5.0
>>>> npm WARN deprecated filesaver.js@0.2.0: Unmaintained namespace. Please
>>>> use the file-saver package: https://www.npmjs.com/package/file-saver
>>>> npm WARN deprecated debug@3.2.6: Debug versions >=3.2.0 <3.2.7 || >=4
>>>> <4.3.1 have a low-severity ReDos regression when used in a Node.js
>>>> environment. It is recommended you upgrade to 3.2.7 or 4.3.1. (
>>>> https://github.com/visionmedia/debug/issues/797)
>>>> npm WARN deprecated chokidar@2.1.8: Chokidar 2 will break on node
>>>> v14+. Upgrade to chokidar 3 with 15x less dependencies.
>>>>  WARN deprecated debug@4.1.1: Debug versions >=3.2.0 <3.2.7 || >=4
>>>> <4.3.1 have a low-severity ReDos regression when used in a Node.js
>>>> environment. It is recommended you upgrade to 3.2.7 or 4.3.1. (
>>>> https://github.com/visionmedia/debug/issues/797)
>>>> npm WARN deprecated mkdirp@0.3.5: Legacy versions of mkdirp are no
>>>> longer supported. Please update to mkdirp 1.x. (Note that the API surface
>>>> has changed to use Promises in 1.x.)
>>>> npm WARN deprecated mkdirp@0.3.5: Legacy versions of mkdirp are no
>>>> longer supported. Please update to mkdirp 1.x. (Note that the API surface
>>>> has changed to use Promises in 1.x.)
>>>> npm WARN deprecated babel-eslint@8.2.6: babel-eslint is now
>>>> @babel/eslint-parser. This package will no longer receive updates.
>>>> npm WARN deprecated mkdirp@0.5.1: Legacy versions of mkdirp are no
>>>> longer supported. Please update to mkdirp 1.x. (Note that the API surface
>>>> has changed to use Promises in 1.x.)
>>>> npm WARN deprecated request@2.88.2: request has been deprecated, see
>>>> https://github.com/request/request/issues/3142
>>>> npm WARN deprecated uglify-es@3.3.9: support for ECMAScript is
>>>> superseded by `uglify-js` as of v3.13.0
>>>> npm WARN deprecated webdriverio@4.14.4: outdated version, please use
>>>> @next
>>>> npm WARN deprecated core-js@2.6.11: core-js@<3 is no longer maintained
>>>> and not recommended for usage due to the number of issues. Please, upgrade
>>>> your dependencies to the actual version of core-js@3.
>>>>
>>>> added 1500 packages, and audited 1501 packages in 3m
>>>>
>>>> 24 packages are looking for funding
>>>>   run `npm fund` for details
>>>>
>>>> 35 vulnerabilities (21 low, 3 moderate, 11 high)
>>>>
>>>> To address issues that do not require attention, run:
>>>>   npm audit fix
>>>>
>>>> To address all issues possible (including breaking changes), run:
>>>>   npm audit fix --force
>>>>
>>>> Some issues need review, and may require choosing
>>>> a different dependency.
>>>>
>>>> Run `npm audit` for details.
>>>> 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 inconsistencies caused by
>>>> unsynchronized lock files. To clear this warning, remove package-lock.json.
>>>> [1/4] Resolving packages...
>>>> warning ava > chokidar > fsevents@1.2.13: fsevents 1 will break on
>>>> node v14+ and could be using insecure binaries. Upgrade to fsevents 2.
>>>> warning webpack > watchpack > chokidar > fsevents@1.2.13: fsevents 1
>>>> will break on node v14+ and could be using insecure binaries. Upgrade to
>>>> fsevents 2.
>>>> [2/4] Fetching packages...
>>>> error An unexpected error occurred: "Commit hash required".
>>>> info If you think this is a bug, please open a bug report with the
>>>> information provided in
>>>> "/var/www/html/jbrowse-1.16.10-release/yarn-error.log".
>>>> info Visit https://yarnpkg.com/en/docs/cli/install for documentation
>>>> about this command.
>>>>
>>>>
>>>> Formatting Volvox example data ...done.
>>>> To see the volvox example data, browse to
>>>> http://your.jbrowse.root/index.html?data=sample_data/json/volvox.
>>>>
>>>> Formatting Yeast example data ...done.
>>>> To see the yeast example data, browse to
>>>> http://your.jbrowse.root/index.html?data=sample_data/json/yeast.
>>>> _______________________________________________
>>>> 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
>

Re: [Gmod-ajax] Problems installing jbrowse1

[Hans Vasquez-G. <hav...@uc...>]

Hi Robert,

No I haven't. In my previous lab, I had extended viroblast PHP code to keep
track of source BLAST databases and pull up the specific genome reference
in JBrowse using URL encoded tracks. However, this was all very specific to
that lab.

In the new lab I joined, I was going to use SequenceServer to connect the
BLAST service to different JBrowse genome projects. Right now, It doesn't
sound like there is an easy way to integrate SequenceServer with JB2. Thank
you for your suggestion though.

Colin: thank you for the issue report. I'll try the workaround.

Best,
-Hans

On Thu, Mar 11, 2021 at 11:05 AM Robert Buels <rb...@gm...> wrote:

> Regarding url encoded tracks, the currently best “jbrowse 2 way” of
> creating tracks and injecting them into the browser is to directly embed a
> jb2 embedded linear genome view in your application that you can fully
> control. Have you considered going in that direction?
>
>
> On Wed, Mar 10, 2021 at 6:22 PM Colin <col...@gm...> wrote:
>
>> Interesting... I think this error was also noted here
>> https://github.com/GMOD/jbrowse/issues/1555
>>
>>
>> Probably we should remove our dependency in jbrowse 1 from installing a
>> package directly from GitHub to properly fix, I think it is the jszlib
>> dependency that we use
>>
>>
>> -Colin
>>
>> On Wed, Mar 10, 2021, 6:39 PM Hans Vasquez-Gross via Gmod-ajax <
>> gmo...@li...> wrote:
>>
>>> Hello,
>>>
>>> I recently installed jbrowse2 on a new system, but some of the
>>> functionality that was in jbrowse1 is missing in jbrowse2 (URL encoded
>>> tracks). Today, I tried installing jbrowse1, but am running into some
>>> nodejs issues.
>>>
>>> When I try loading up the page, I can see my main.bundle.js is missing
>>> (404 error) which I think is related to the nodejs problems.
>>>
>>> Please see setup log below.
>>>
>>> Any advice would be greatly appreciated.
>>>
>>> Thank you,
>>> -Hans
>>>
>>>
>>> > bash setup.sh
>>> Gathering system information ...done.
>>> NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been
>>> removed from setup. Their functionality has been superseded by
>>> add-bam-track.pl and add-bw-track.pl. If you require the old versions,
>>> please use JBrowse 1.12.3 or earlier.
>>> Installing node.js dependencies and building with webpack ... failed.
>>> See setup.log file for error messages.
>>> setup cannot continue, aborting.
>>>
>>> Gathering system information ...
>>> ============== System information ====
>>> + lsb_release -a
>>> No LSB modules are available.
>>> Distributor ID: Ubuntu
>>> Description:    Ubuntu 20.04.1 LTS
>>> Release:        20.04
>>> Codename:       focal
>>> + uname -a
>>> Linux borlaug 5.8.0-36-generic #40~20.04.1-Ubuntu SMP Wed Jan 6 10:15:55
>>> UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
>>> + sw_vers
>>> setup.sh: line 89: sw_vers: command not found
>>> + grep MemTotal /proc/meminfo
>>> MemTotal:       65733500 kB
>>> + echo
>>>
>>> + echo
>>>
>>>
>>> done.
>>>
>>>
>>> NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been
>>> removed from setup. Their functionality has been superseded by
>>> add-bam-track.pl and add-bw-track.pl. If you require the old versions,
>>> please use JBrowse 1.12.3 or earlier.
>>>
>>>
>>> Installing node.js dependencies and building with webpack ...
>>> Node v15.11.0 installed at /usr/bin/node with npm 7.6.0
>>> npm WARN deprecated ini@1.3.5: Please update to ini >=1.3.6 to avoid a
>>> prototype pollution issue
>>> npm WARN deprecated urix@0.1.0: Please see
>>> https://github.com/lydell/urix#deprecated
>>> npm WARN deprecated sprintf@0.1.5: The sprintf package is deprecated in
>>> favor of sprintf-js.
>>> npm WARN deprecated har-validator@5.1.3: this library is no longer
>>> supported
>>> npm WARN deprecated mkdirp@0.5.3: Legacy versions of mkdirp are no
>>> longer supported. Please update to mkdirp 1.x. (Note that the API surface
>>> has changed to use Promises in 1.x.)
>>> npm WARN deprecated resolve-url@0.2.1:
>>> https://github.com/lydell/resolve-url#deprecated
>>> npm WARN deprecated chokidar@1.7.0: Chokidar 2 will break on node v14+.
>>> Upgrade to chokidar 3 with 15x less dependencies.
>>> npm WARN deprecated circular-json@0.3.3: CircularJSON is in maintenance
>>> only, flatted is its successor.
>>> npm WARN deprecated xmldom@0.1.31: Deprecated due to CVE-2021-21366
>>> resolved in 0.5.0
>>> npm WARN deprecated filesaver.js@0.2.0: Unmaintained namespace. Please
>>> use the file-saver package: https://www.npmjs.com/package/file-saver
>>> npm WARN deprecated debug@3.2.6: Debug versions >=3.2.0 <3.2.7 || >=4
>>> <4.3.1 have a low-severity ReDos regression when used in a Node.js
>>> environment. It is recommended you upgrade to 3.2.7 or 4.3.1. (
>>> https://github.com/visionmedia/debug/issues/797)
>>> npm WARN deprecated chokidar@2.1.8: Chokidar 2 will break on node v14+.
>>> Upgrade to chokidar 3 with 15x less dependencies.
>>>  WARN deprecated debug@4.1.1: Debug versions >=3.2.0 <3.2.7 || >=4
>>> <4.3.1 have a low-severity ReDos regression when used in a Node.js
>>> environment. It is recommended you upgrade to 3.2.7 or 4.3.1. (
>>> https://github.com/visionmedia/debug/issues/797)
>>> npm WARN deprecated mkdirp@0.3.5: Legacy versions of mkdirp are no
>>> longer supported. Please update to mkdirp 1.x. (Note that the API surface
>>> has changed to use Promises in 1.x.)
>>> npm WARN deprecated mkdirp@0.3.5: Legacy versions of mkdirp are no
>>> longer supported. Please update to mkdirp 1.x. (Note that the API surface
>>> has changed to use Promises in 1.x.)
>>> npm WARN deprecated babel-eslint@8.2.6: babel-eslint is now
>>> @babel/eslint-parser. This package will no longer receive updates.
>>> npm WARN deprecated mkdirp@0.5.1: Legacy versions of mkdirp are no
>>> longer supported. Please update to mkdirp 1.x. (Note that the API surface
>>> has changed to use Promises in 1.x.)
>>> npm WARN deprecated request@2.88.2: request has been deprecated, see
>>> https://github.com/request/request/issues/3142
>>> npm WARN deprecated uglify-es@3.3.9: support for ECMAScript is
>>> superseded by `uglify-js` as of v3.13.0
>>> npm WARN deprecated webdriverio@4.14.4: outdated version, please use
>>> @next
>>> npm WARN deprecated core-js@2.6.11: core-js@<3 is no longer maintained
>>> and not recommended for usage due to the number of issues. Please, upgrade
>>> your dependencies to the actual version of core-js@3.
>>>
>>> added 1500 packages, and audited 1501 packages in 3m
>>>
>>> 24 packages are looking for funding
>>>   run `npm fund` for details
>>>
>>> 35 vulnerabilities (21 low, 3 moderate, 11 high)
>>>
>>> To address issues that do not require attention, run:
>>>   npm audit fix
>>>
>>> To address all issues possible (including breaking changes), run:
>>>   npm audit fix --force
>>>
>>> Some issues need review, and may require choosing
>>> a different dependency.
>>>
>>> Run `npm audit` for details.
>>> 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 inconsistencies caused by
>>> unsynchronized lock files. To clear this warning, remove package-lock.json.
>>> [1/4] Resolving packages...
>>> warning ava > chokidar > fsevents@1.2.13: fsevents 1 will break on node
>>> v14+ and could be using insecure binaries. Upgrade to fsevents 2.
>>> warning webpack > watchpack > chokidar > fsevents@1.2.13: fsevents 1
>>> will break on node v14+ and could be using insecure binaries. Upgrade to
>>> fsevents 2.
>>> [2/4] Fetching packages...
>>> error An unexpected error occurred: "Commit hash required".
>>> info If you think this is a bug, please open a bug report with the
>>> information provided in
>>> "/var/www/html/jbrowse-1.16.10-release/yarn-error.log".
>>> info Visit https://yarnpkg.com/en/docs/cli/install for documentation
>>> about this command.
>>>
>>>
>>> Formatting Volvox example data ...done.
>>> To see the volvox example data, browse to
>>> http://your.jbrowse.root/index.html?data=sample_data/json/volvox.
>>>
>>> Formatting Yeast example data ...done.
>>> To see the yeast example data, browse to
>>> http://your.jbrowse.root/index.html?data=sample_data/json/yeast.
>>> _______________________________________________
>>> 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

Re: [Gmod-ajax] Problems installing jbrowse1

[Robert B. <rb...@gm...>]

Regarding url encoded tracks, the currently best “jbrowse 2 way” of
creating tracks and injecting them into the browser is to directly embed a
jb2 embedded linear genome view in your application that you can fully
control. Have you considered going in that direction?


On Wed, Mar 10, 2021 at 6:22 PM Colin <col...@gm...> wrote:

> Interesting... I think this error was also noted here
> https://github.com/GMOD/jbrowse/issues/1555
>
>
> Probably we should remove our dependency in jbrowse 1 from installing a
> package directly from GitHub to properly fix, I think it is the jszlib
> dependency that we use
>
>
> -Colin
>
> On Wed, Mar 10, 2021, 6:39 PM Hans Vasquez-Gross via Gmod-ajax <
> gmo...@li...> wrote:
>
>> Hello,
>>
>> I recently installed jbrowse2 on a new system, but some of the
>> functionality that was in jbrowse1 is missing in jbrowse2 (URL encoded
>> tracks). Today, I tried installing jbrowse1, but am running into some
>> nodejs issues.
>>
>> When I try loading up the page, I can see my main.bundle.js is missing
>> (404 error) which I think is related to the nodejs problems.
>>
>> Please see setup log below.
>>
>> Any advice would be greatly appreciated.
>>
>> Thank you,
>> -Hans
>>
>>
>> > bash setup.sh
>> Gathering system information ...done.
>> NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been removed
>> from setup. Their functionality has been superseded by add-bam-track.pl
>> and add-bw-track.pl. If you require the old versions, please use JBrowse
>> 1.12.3 or earlier.
>> Installing node.js dependencies and building with webpack ... failed.
>> See setup.log file for error messages.
>> setup cannot continue, aborting.
>>
>> Gathering system information ...
>> ============== System information ====
>> + lsb_release -a
>> No LSB modules are available.
>> Distributor ID: Ubuntu
>> Description:    Ubuntu 20.04.1 LTS
>> Release:        20.04
>> Codename:       focal
>> + uname -a
>> Linux borlaug 5.8.0-36-generic #40~20.04.1-Ubuntu SMP Wed Jan 6 10:15:55
>> UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
>> + sw_vers
>> setup.sh: line 89: sw_vers: command not found
>> + grep MemTotal /proc/meminfo
>> MemTotal:       65733500 kB
>> + echo
>>
>> + echo
>>
>>
>> done.
>>
>>
>> NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been removed
>> from setup. Their functionality has been superseded by add-bam-track.pl
>> and add-bw-track.pl. If you require the old versions, please use JBrowse
>> 1.12.3 or earlier.
>>
>>
>> Installing node.js dependencies and building with webpack ...
>> Node v15.11.0 installed at /usr/bin/node with npm 7.6.0
>> npm WARN deprecated ini@1.3.5: Please update to ini >=1.3.6 to avoid a
>> prototype pollution issue
>> npm WARN deprecated urix@0.1.0: Please see
>> https://github.com/lydell/urix#deprecated
>> npm WARN deprecated sprintf@0.1.5: The sprintf package is deprecated in
>> favor of sprintf-js.
>> npm WARN deprecated har-validator@5.1.3: this library is no longer
>> supported
>> npm WARN deprecated mkdirp@0.5.3: Legacy versions of mkdirp are no
>> longer supported. Please update to mkdirp 1.x. (Note that the API surface
>> has changed to use Promises in 1.x.)
>> npm WARN deprecated resolve-url@0.2.1:
>> https://github.com/lydell/resolve-url#deprecated
>> npm WARN deprecated chokidar@1.7.0: Chokidar 2 will break on node v14+.
>> Upgrade to chokidar 3 with 15x less dependencies.
>> npm WARN deprecated circular-json@0.3.3: CircularJSON is in maintenance
>> only, flatted is its successor.
>> npm WARN deprecated xmldom@0.1.31: Deprecated due to CVE-2021-21366
>> resolved in 0.5.0
>> npm WARN deprecated filesaver.js@0.2.0: Unmaintained namespace. Please
>> use the file-saver package: https://www.npmjs.com/package/file-saver
>> npm WARN deprecated debug@3.2.6: Debug versions >=3.2.0 <3.2.7 || >=4
>> <4.3.1 have a low-severity ReDos regression when used in a Node.js
>> environment. It is recommended you upgrade to 3.2.7 or 4.3.1. (
>> https://github.com/visionmedia/debug/issues/797)
>> npm WARN deprecated chokidar@2.1.8: Chokidar 2 will break on node v14+.
>> Upgrade to chokidar 3 with 15x less dependencies.
>>  WARN deprecated debug@4.1.1: Debug versions >=3.2.0 <3.2.7 || >=4
>> <4.3.1 have a low-severity ReDos regression when used in a Node.js
>> environment. It is recommended you upgrade to 3.2.7 or 4.3.1. (
>> https://github.com/visionmedia/debug/issues/797)
>> npm WARN deprecated mkdirp@0.3.5: Legacy versions of mkdirp are no
>> longer supported. Please update to mkdirp 1.x. (Note that the API surface
>> has changed to use Promises in 1.x.)
>> npm WARN deprecated mkdirp@0.3.5: Legacy versions of mkdirp are no
>> longer supported. Please update to mkdirp 1.x. (Note that the API surface
>> has changed to use Promises in 1.x.)
>> npm WARN deprecated babel-eslint@8.2.6: babel-eslint is now
>> @babel/eslint-parser. This package will no longer receive updates.
>> npm WARN deprecated mkdirp@0.5.1: Legacy versions of mkdirp are no
>> longer supported. Please update to mkdirp 1.x. (Note that the API surface
>> has changed to use Promises in 1.x.)
>> npm WARN deprecated request@2.88.2: request has been deprecated, see
>> https://github.com/request/request/issues/3142
>> npm WARN deprecated uglify-es@3.3.9: support for ECMAScript is
>> superseded by `uglify-js` as of v3.13.0
>> npm WARN deprecated webdriverio@4.14.4: outdated version, please use
>> @next
>> npm WARN deprecated core-js@2.6.11: core-js@<3 is no longer maintained
>> and not recommended for usage due to the number of issues. Please, upgrade
>> your dependencies to the actual version of core-js@3.
>>
>> added 1500 packages, and audited 1501 packages in 3m
>>
>> 24 packages are looking for funding
>>   run `npm fund` for details
>>
>> 35 vulnerabilities (21 low, 3 moderate, 11 high)
>>
>> To address issues that do not require attention, run:
>>   npm audit fix
>>
>> To address all issues possible (including breaking changes), run:
>>   npm audit fix --force
>>
>> Some issues need review, and may require choosing
>> a different dependency.
>>
>> Run `npm audit` for details.
>> 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 inconsistencies caused by
>> unsynchronized lock files. To clear this warning, remove package-lock.json.
>> [1/4] Resolving packages...
>> warning ava > chokidar > fsevents@1.2.13: fsevents 1 will break on node
>> v14+ and could be using insecure binaries. Upgrade to fsevents 2.
>> warning webpack > watchpack > chokidar > fsevents@1.2.13: fsevents 1
>> will break on node v14+ and could be using insecure binaries. Upgrade to
>> fsevents 2.
>> [2/4] Fetching packages...
>> error An unexpected error occurred: "Commit hash required".
>> info If you think this is a bug, please open a bug report with the
>> information provided in
>> "/var/www/html/jbrowse-1.16.10-release/yarn-error.log".
>> info Visit https://yarnpkg.com/en/docs/cli/install for documentation
>> about this command.
>>
>>
>> Formatting Volvox example data ...done.
>> To see the volvox example data, browse to
>> http://your.jbrowse.root/index.html?data=sample_data/json/volvox.
>>
>> Formatting Yeast example data ...done.
>> To see the yeast example data, browse to
>> http://your.jbrowse.root/index.html?data=sample_data/json/yeast.
>> _______________________________________________
>> 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
>

Re: [Gmod-ajax] Problems installing jbrowse1

[Colin <col...@gm...>]

Interesting... I think this error was also noted here
https://github.com/GMOD/jbrowse/issues/1555


Probably we should remove our dependency in jbrowse 1 from installing a
package directly from GitHub to properly fix, I think it is the jszlib
dependency that we use


-Colin

On Wed, Mar 10, 2021, 6:39 PM Hans Vasquez-Gross via Gmod-ajax <
gmo...@li...> wrote:

> Hello,
>
> I recently installed jbrowse2 on a new system, but some of the
> functionality that was in jbrowse1 is missing in jbrowse2 (URL encoded
> tracks). Today, I tried installing jbrowse1, but am running into some
> nodejs issues.
>
> When I try loading up the page, I can see my main.bundle.js is missing
> (404 error) which I think is related to the nodejs problems.
>
> Please see setup log below.
>
> Any advice would be greatly appreciated.
>
> Thank you,
> -Hans
>
>
> > bash setup.sh
> Gathering system information ...done.
> NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been removed
> from setup. Their functionality has been superseded by add-bam-track.pl
> and add-bw-track.pl. If you require the old versions, please use JBrowse
> 1.12.3 or earlier.
> Installing node.js dependencies and building with webpack ... failed.  See
> setup.log file for error messages.
> setup cannot continue, aborting.
>
> Gathering system information ...
> ============== System information ====
> + lsb_release -a
> No LSB modules are available.
> Distributor ID: Ubuntu
> Description:    Ubuntu 20.04.1 LTS
> Release:        20.04
> Codename:       focal
> + uname -a
> Linux borlaug 5.8.0-36-generic #40~20.04.1-Ubuntu SMP Wed Jan 6 10:15:55
> UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
> + sw_vers
> setup.sh: line 89: sw_vers: command not found
> + grep MemTotal /proc/meminfo
> MemTotal:       65733500 kB
> + echo
>
> + echo
>
>
> done.
>
>
> NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been removed
> from setup. Their functionality has been superseded by add-bam-track.pl
> and add-bw-track.pl. If you require the old versions, please use JBrowse
> 1.12.3 or earlier.
>
>
> Installing node.js dependencies and building with webpack ...
> Node v15.11.0 installed at /usr/bin/node with npm 7.6.0
> npm WARN deprecated ini@1.3.5: Please update to ini >=1.3.6 to avoid a
> prototype pollution issue
> npm WARN deprecated urix@0.1.0: Please see
> https://github.com/lydell/urix#deprecated
> npm WARN deprecated sprintf@0.1.5: The sprintf package is deprecated in
> favor of sprintf-js.
> npm WARN deprecated har-validator@5.1.3: this library is no longer
> supported
> npm WARN deprecated mkdirp@0.5.3: Legacy versions of mkdirp are no longer
> supported. Please update to mkdirp 1.x. (Note that the API surface has
> changed to use Promises in 1.x.)
> npm WARN deprecated resolve-url@0.2.1:
> https://github.com/lydell/resolve-url#deprecated
> npm WARN deprecated chokidar@1.7.0: Chokidar 2 will break on node v14+.
> Upgrade to chokidar 3 with 15x less dependencies.
> npm WARN deprecated circular-json@0.3.3: CircularJSON is in maintenance
> only, flatted is its successor.
> npm WARN deprecated xmldom@0.1.31: Deprecated due to CVE-2021-21366
> resolved in 0.5.0
> npm WARN deprecated filesaver.js@0.2.0: Unmaintained namespace. Please
> use the file-saver package: https://www.npmjs.com/package/file-saver
> npm WARN deprecated debug@3.2.6: Debug versions >=3.2.0 <3.2.7 || >=4
> <4.3.1 have a low-severity ReDos regression when used in a Node.js
> environment. It is recommended you upgrade to 3.2.7 or 4.3.1. (
> https://github.com/visionmedia/debug/issues/797)
> npm WARN deprecated chokidar@2.1.8: Chokidar 2 will break on node v14+.
> Upgrade to chokidar 3 with 15x less dependencies.
>  WARN deprecated debug@4.1.1: Debug versions >=3.2.0 <3.2.7 || >=4 <4.3.1
> have a low-severity ReDos regression when used in a Node.js environment. It
> is recommended you upgrade to 3.2.7 or 4.3.1. (
> https://github.com/visionmedia/debug/issues/797)
> npm WARN deprecated mkdirp@0.3.5: Legacy versions of mkdirp are no longer
> supported. Please update to mkdirp 1.x. (Note that the API surface has
> changed to use Promises in 1.x.)
> npm WARN deprecated mkdirp@0.3.5: Legacy versions of mkdirp are no longer
> supported. Please update to mkdirp 1.x. (Note that the API surface has
> changed to use Promises in 1.x.)
> npm WARN deprecated babel-eslint@8.2.6: babel-eslint is now
> @babel/eslint-parser. This package will no longer receive updates.
> npm WARN deprecated mkdirp@0.5.1: Legacy versions of mkdirp are no longer
> supported. Please update to mkdirp 1.x. (Note that the API surface has
> changed to use Promises in 1.x.)
> npm WARN deprecated request@2.88.2: request has been deprecated, see
> https://github.com/request/request/issues/3142
> npm WARN deprecated uglify-es@3.3.9: support for ECMAScript is superseded
> by `uglify-js` as of v3.13.0
> npm WARN deprecated webdriverio@4.14.4: outdated version, please use @next
> npm WARN deprecated core-js@2.6.11: core-js@<3 is no longer maintained
> and not recommended for usage due to the number of issues. Please, upgrade
> your dependencies to the actual version of core-js@3.
>
> added 1500 packages, and audited 1501 packages in 3m
>
> 24 packages are looking for funding
>   run `npm fund` for details
>
> 35 vulnerabilities (21 low, 3 moderate, 11 high)
>
> To address issues that do not require attention, run:
>   npm audit fix
>
> To address all issues possible (including breaking changes), run:
>   npm audit fix --force
>
> Some issues need review, and may require choosing
> a different dependency.
>
> Run `npm audit` for details.
> 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 inconsistencies caused by
> unsynchronized lock files. To clear this warning, remove package-lock.json.
> [1/4] Resolving packages...
> warning ava > chokidar > fsevents@1.2.13: fsevents 1 will break on node
> v14+ and could be using insecure binaries. Upgrade to fsevents 2.
> warning webpack > watchpack > chokidar > fsevents@1.2.13: fsevents 1 will
> break on node v14+ and could be using insecure binaries. Upgrade to
> fsevents 2.
> [2/4] Fetching packages...
> error An unexpected error occurred: "Commit hash required".
> info If you think this is a bug, please open a bug report with the
> information provided in
> "/var/www/html/jbrowse-1.16.10-release/yarn-error.log".
> info Visit https://yarnpkg.com/en/docs/cli/install for documentation
> about this command.
>
>
> Formatting Volvox example data ...done.
> To see the volvox example data, browse to
> http://your.jbrowse.root/index.html?data=sample_data/json/volvox.
>
> Formatting Yeast example data ...done.
> To see the yeast example data, browse to
> http://your.jbrowse.root/index.html?data=sample_data/json/yeast.
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Problems installing jbrowse1

[Hans Vasquez-G. <hav...@uc...>]

Hello,

I recently installed jbrowse2 on a new system, but some of the
functionality that was in jbrowse1 is missing in jbrowse2 (URL encoded
tracks). Today, I tried installing jbrowse1, but am running into some
nodejs issues.

When I try loading up the page, I can see my main.bundle.js is missing (404
error) which I think is related to the nodejs problems.

Please see setup log below.

Any advice would be greatly appreciated.

Thank you,
-Hans


> bash setup.sh
Gathering system information ...done.
NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been removed
from setup. Their functionality has been superseded by add-bam-track.pl and
add-bw-track.pl. If you require the old versions, please use JBrowse 1.12.3
or earlier.
Installing node.js dependencies and building with webpack ... failed.  See
setup.log file for error messages.
setup cannot continue, aborting.

Gathering system information ...
============== System information ====
+ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 20.04.1 LTS
Release:        20.04
Codename:       focal
+ uname -a
Linux borlaug 5.8.0-36-generic #40~20.04.1-Ubuntu SMP Wed Jan 6 10:15:55
UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
+ sw_vers
setup.sh: line 89: sw_vers: command not found
+ grep MemTotal /proc/meminfo
MemTotal:       65733500 kB
+ echo

+ echo


done.


NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been removed
from setup. Their functionality has been superseded by add-bam-track.pl and
add-bw-track.pl. If you require the old versions, please use JBrowse 1.12.3
or earlier.


Installing node.js dependencies and building with webpack ...
Node v15.11.0 installed at /usr/bin/node with npm 7.6.0
npm WARN deprecated ini@1.3.5: Please update to ini >=1.3.6 to avoid a
prototype pollution issue
npm WARN deprecated urix@0.1.0: Please see
https://github.com/lydell/urix#deprecated
npm WARN deprecated sprintf@0.1.5: The sprintf package is deprecated in
favor of sprintf-js.
npm WARN deprecated har-validator@5.1.3: this library is no longer supported
npm WARN deprecated mkdirp@0.5.3: Legacy versions of mkdirp are no longer
supported. Please update to mkdirp 1.x. (Note that the API surface has
changed to use Promises in 1.x.)
npm WARN deprecated resolve-url@0.2.1:
https://github.com/lydell/resolve-url#deprecated
npm WARN deprecated chokidar@1.7.0: Chokidar 2 will break on node v14+.
Upgrade to chokidar 3 with 15x less dependencies.
npm WARN deprecated circular-json@0.3.3: CircularJSON is in maintenance
only, flatted is its successor.
npm WARN deprecated xmldom@0.1.31: Deprecated due to CVE-2021-21366
resolved in 0.5.0
npm WARN deprecated filesaver.js@0.2.0: Unmaintained namespace. Please use
the file-saver package: https://www.npmjs.com/package/file-saver
npm WARN deprecated debug@3.2.6: Debug versions >=3.2.0 <3.2.7 || >=4
<4.3.1 have a low-severity ReDos regression when used in a Node.js
environment. It is recommended you upgrade to 3.2.7 or 4.3.1. (
https://github.com/visionmedia/debug/issues/797)
npm WARN deprecated chokidar@2.1.8: Chokidar 2 will break on node v14+.
Upgrade to chokidar 3 with 15x less dependencies.
 WARN deprecated debug@4.1.1: Debug versions >=3.2.0 <3.2.7 || >=4 <4.3.1
have a low-severity ReDos regression when used in a Node.js environment. It
is recommended you upgrade to 3.2.7 or 4.3.1. (
https://github.com/visionmedia/debug/issues/797)
npm WARN deprecated mkdirp@0.3.5: Legacy versions of mkdirp are no longer
supported. Please update to mkdirp 1.x. (Note that the API surface has
changed to use Promises in 1.x.)
npm WARN deprecated mkdirp@0.3.5: Legacy versions of mkdirp are no longer
supported. Please update to mkdirp 1.x. (Note that the API surface has
changed to use Promises in 1.x.)
npm WARN deprecated babel-eslint@8.2.6: babel-eslint is now
@babel/eslint-parser. This package will no longer receive updates.
npm WARN deprecated mkdirp@0.5.1: Legacy versions of mkdirp are no longer
supported. Please update to mkdirp 1.x. (Note that the API surface has
changed to use Promises in 1.x.)
npm WARN deprecated request@2.88.2: request has been deprecated, see
https://github.com/request/request/issues/3142
npm WARN deprecated uglify-es@3.3.9: support for ECMAScript is superseded
by `uglify-js` as of v3.13.0
npm WARN deprecated webdriverio@4.14.4: outdated version, please use @next
npm WARN deprecated core-js@2.6.11: core-js@<3 is no longer maintained and
not recommended for usage due to the number of issues. Please, upgrade your
dependencies to the actual version of core-js@3.

added 1500 packages, and audited 1501 packages in 3m

24 packages are looking for funding
  run `npm fund` for details

35 vulnerabilities (21 low, 3 moderate, 11 high)

To address issues that do not require attention, run:
  npm audit fix

To address all issues possible (including breaking changes), run:
  npm audit fix --force

Some issues need review, and may require choosing
a different dependency.

Run `npm audit` for details.
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 inconsistencies caused by unsynchronized lock
files. To clear this warning, remove package-lock.json.
[1/4] Resolving packages...
warning ava > chokidar > fsevents@1.2.13: fsevents 1 will break on node
v14+ and could be using insecure binaries. Upgrade to fsevents 2.
warning webpack > watchpack > chokidar > fsevents@1.2.13: fsevents 1 will
break on node v14+ and could be using insecure binaries. Upgrade to
fsevents 2.
[2/4] Fetching packages...
error An unexpected error occurred: "Commit hash required".
info If you think this is a bug, please open a bug report with the
information provided in
"/var/www/html/jbrowse-1.16.10-release/yarn-error.log".
info Visit https://yarnpkg.com/en/docs/cli/install for documentation about
this command.


Formatting Volvox example data ...done.
To see the volvox example data, browse to
http://your.jbrowse.root/index.html?data=sample_data/json/volvox.

Formatting Yeast example data ...done.
To see the yeast example data, browse to
http://your.jbrowse.root/index.html?data=sample_data/json/yeast.

Re: [Gmod-ajax] multibigwig for JBrowse2

[Colin <col...@gm...>]

Hi Ke,
It is so great to hear that jb2 is working well for you :)

I agree that multibigwig is an important feature. I can't say anything
about timeline for it but it would really be great

Fun factoid: we initially started by trying to make our base wiggle track
"multi bigwig capable" from the start but that got tabled so just one
bigwig per track for the time being.

Do check out some of our new features in our new jbrowse 2 release,
screenshot of some new track menu items

[image:
localhost_3000__config=test_data%2Fconfig_demo.json&session=local-rLeCB65dK.png]

-Colin

On Mon, Mar 8, 2021 at 8:27 AM Ke Jiang <bio...@gm...> wrote:

> Hi,
>
> I've been playing with JBrowse2 for a while, and it works really great so
> far! Thanks to the developers for the refreshing new tool!
>
> Currently, the one feature I missed the most from JBrowse1 was the
> multibigwig plugin, which makes it really easy to get a high-level view of
> a series of BigWig tracks. Is there any plan to bring it to JBrowse2?
>
> Thanks!
>
> Ke
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] multibigwig for JBrowse2

[Ke J. <bio...@gm...>]

Hi,

I've been playing with JBrowse2 for a while, and it works really great so
far! Thanks to the developers for the refreshing new tool!

Currently, the one feature I missed the most from JBrowse1 was the
multibigwig plugin, which makes it really easy to get a high-level view of
a series of BigWig tracks. Is there any plan to bring it to JBrowse2?

Thanks!

Ke

[Gmod-ajax] Apollo 2.6.3 released

[Nathan D. <nat...@lb...>]

Apollo 2.6.3 has been released:  https://github.com/GMOD/Apollo/releases/tag/2.6.3 <https://github.com/GMOD/Apollo/releases/tag/2.6.3>



Features

Fix empty attribute list in annotation panel 2552 <https://github.com/GMOD/Apollo/issues/2552>.
Added ability to use posts to sequence methods 2555 <https://github.com/GMOD/Apollo/pull/2558>.
Added system info web service 2557 <https://github.com/GMOD/Apollo/pull/2557>.
Add "merged from" comment to merged in transcript and gene 2567 <https://github.com/GMOD/Apollo/issues/2567>.
Added support for "obsolete", and partials in the interface for GFF3s 2573 <https://github.com/GMOD/Apollo/pull/2573>.
Allow overlap filter to be configurable 2582 <https://github.com/GMOD/Apollo/issues/2582>.
Bug Fixes:

Bad coordinate value in genomic element details screen in annotator panel 2559 <https://github.com/GMOD/Apollo/issues/2559>.
Web services indicated user had no organism permissions when checking the login 2554 <https://github.com/GMOD/Apollo/issues/2554>.
Vcf reads as ISO-8859-1 instead of UTF-8 from reader mangling some symbols. 2498 <https://github.com/GMOD/Apollo/issues/2498>.
Added security fixes for web services. 2564 <https://github.com/GMOD/Apollo/pull/2564>, 2587 <https://github.com/GMOD/Apollo/pull/2587>.
In some cases web services tries to create a preference which results in incorrect results 2580 <https://github.com/GMOD/Apollo/issues/2580>.
For the track service, the overlap filter is too restrictive when converting NCList to JSON 2586 <https://github.com/GMOD/Apollo/issues/2586>.
Infrastructure Changes

Removed travis in favor of GitHub Actions 2546 <https://github.com/GMOD/Apollo/issues/2546>.
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>.

Re: [Gmod-ajax] JBrowse2 with JBrowse1

[Colin <col...@gm...>]

Ya for BLAST -> JBrowse I'd probably use jbrowse 1 right now e.g.
https://jbrowse.org/docs/faq.html#how-can-i-link-blast-results-to-jbrowse


I'd stay tuned for doing sequenceserver/jbrowse 2 integration. There is not
a URL params API for jbrowse 2 but it should be coming soon.


-Colin

On Tue, Feb 2, 2021 at 10:51 AM Hans Vasquez-Gross <
hav...@uc...> wrote:

> Hi Colin,
>
> So if I need to get BLAST -> JBrowse working, my only option right now is
> JBrowse1? I used to use a heavily modified viroblast php installation to
> generate the links to JBrowse. However, in my new lab, I have setup
> sequenceServer and have started configuring that for BLAST.
>
> There is some documentation on the FAQ (https://jbrowse.org/docs/faq.html)
> mentioning sequenceserver configuration, but I believe this is only for
> JBrowse1. Do you know of any talks about getting sequenceserver working
> with JBrowse2?
>
> Thank you,
> -Hans
>
> On Mon, Feb 1, 2021 at 4:21 PM Colin <col...@gm...> wrote:
>
>> > 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.
>>
>> Currently there is not yet a feature for this but we plan on making it.
>> It would actually be possible with the session url but it'd be a bit
>> tedious. If possible I'd recommend keeping track of this issue for updates
>> https://github.com/GMOD/jbrowse-components/issues/1464
>>
>> > 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.
>>
>> Using the "share" button at the top of the screen is the best way to
>> share links with your colleagues.
>>
>> The share link that this generates is uses a URL shortener that we made
>> (no data on users is collected when using this, and the system can be
>> considered "end to end encrypted"), but you can also get an expanded link
>> from the gear icon in the share dialog that skips the URL shortener
>>
>> Screenshot:
>>
>> [image:
>> localhost_3000__config=test_data%2Fconfig_demo.json&session=local-hHHLBr_Jn
>> (1).png]
>>
>>
>> -Colin
>>
>> On Mon, Feb 1, 2021 at 4:00 PM Hans Vasquez-Gross <
>> hav...@uc...> wrote:
>>
>>> 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
>>>
>>
>
> --
> 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
>

Re: [Gmod-ajax] JBrowse2 with JBrowse1

[Hans Vasquez-G. <hav...@uc...>]

Hi Colin,

So if I need to get BLAST -> JBrowse working, my only option right now is
JBrowse1? I used to use a heavily modified viroblast php installation to
generate the links to JBrowse. However, in my new lab, I have setup
sequenceServer and have started configuring that for BLAST.

There is some documentation on the FAQ (https://jbrowse.org/docs/faq.html)
mentioning sequenceserver configuration, but I believe this is only for
JBrowse1. Do you know of any talks about getting sequenceserver working
with JBrowse2?

Thank you,
-Hans

On Mon, Feb 1, 2021 at 4:21 PM Colin <col...@gm...> wrote:

> > 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.
>
> Currently there is not yet a feature for this but we plan on making it. It
> would actually be possible with the session url but it'd be a bit tedious.
> If possible I'd recommend keeping track of this issue for updates
> https://github.com/GMOD/jbrowse-components/issues/1464
>
> > 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.
>
> Using the "share" button at the top of the screen is the best way to share
> links with your colleagues.
>
> The share link that this generates is uses a URL shortener that we made
> (no data on users is collected when using this, and the system can be
> considered "end to end encrypted"), but you can also get an expanded link
> from the gear icon in the share dialog that skips the URL shortener
>
> Screenshot:
>
> [image:
> localhost_3000__config=test_data%2Fconfig_demo.json&session=local-hHHLBr_Jn
> (1).png]
>
>
> -Colin
>
> On Mon, Feb 1, 2021 at 4:00 PM Hans Vasquez-Gross <
> hav...@uc...> wrote:
>
>> 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
>>
>

-- 
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

Re: [Gmod-ajax] JBrowse2 with JBrowse1

[Colin <col...@gm...>]

> 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.

Currently there is not yet a feature for this but we plan on making it. It
would actually be possible with the session url but it'd be a bit tedious.
If possible I'd recommend keeping track of this issue for updates
https://github.com/GMOD/jbrowse-components/issues/1464

> 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.

Using the "share" button at the top of the screen is the best way to share
links with your colleagues.

The share link that this generates is uses a URL shortener that we made (no
data on users is collected when using this, and the system can be
considered "end to end encrypted"), but you can also get an expanded link
from the gear icon in the share dialog that skips the URL shortener

Screenshot:

[image:
localhost_3000__config=test_data%2Fconfig_demo.json&session=local-hHHLBr_Jn
(1).png]


-Colin

On Mon, Feb 1, 2021 at 4:00 PM Hans Vasquez-Gross <
hav...@uc...> wrote:

> 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
>