gmod-ajax — JBrowse list

Re: [Gmod-ajax] ColorBySize settings

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

Also note: I described changing a config parameter. If you are not an admin
of the jbrowse instance you might have to ask your admin to do this

-Colin

On Tue, Aug 11, 2020 at 11:40 AM Colin <col...@gm...> wrote:

> Hi Caterina,
>
> Glad to hear about interest in paired end read viewing, it is not a
> feature that we've received a lot of feedback about since it was launched.
> There are not a lot of manual tuning parameters currently, but I try will
> describe the algorithm it uses.
>
> - First, if there are too few features, e.g. less than 100
> (config.insertStatsCacheMin) then it exits because the statistics might not
> be good
>
> - Next, it calculates mean and variance of insert size for all reads in
> view except for read pairs that have insert size below a configurable
> minimum (config.insertStatsMinSize) and maximum (config.insertStatsMaxSize)
>
> - Then it colors things if they are below or above mean+/-3*sd
>
> The default minimum is 100 (config.insertStatsMinSize), the maximum is
> 50,000 (config.insertStatsMaxSize)
>
> If you think maybe reads with long insert size (e.g. in the range
> 450-50,000) are affecting the calculation, you could try changing
> "insertStatsMaxSize": 500 so this way it will actually only take into
> account reads below insert size 500 for the stats calculation, and then it
> will more clearly show anything above this range
>
>
> Let me know if that helps
>
> -Colin
>
> On Tue, Aug 11, 2020 at 9:56 AM Caterina Marconi <
> cat...@ho...> wrote:
>
>> Hello,
>> I have two question regarding the ColorBySize option.
>> What is the correct way to use the "re-estimate insert size stats"
>> function?
>> Is it possible to set a fix thresholds for insert size for the
>> ColorBySize option?
>> I have some troubles in visualizing abnormal read-pairs. The avg insert
>> size is around 450bp, but only reads with insert size higher than 1000 are
>> highlighted. Moreover, if I switch from paired to unpaired view and then
>> again to pair view, I lost the highlighting.
>>
>> Thanks for your help.
>> Caterina
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] ColorBySize settings

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

Hi Caterina,

Glad to hear about interest in paired end read viewing, it is not a feature
that we've received a lot of feedback about since it was launched. There
are not a lot of manual tuning parameters currently, but I try will
describe the algorithm it uses.

- First, if there are too few features, e.g. less than 100
(config.insertStatsCacheMin) then it exits because the statistics might not
be good

- Next, it calculates mean and variance of insert size for all reads in
view except for read pairs that have insert size below a configurable
minimum (config.insertStatsMinSize) and maximum (config.insertStatsMaxSize)

- Then it colors things if they are below or above mean+/-3*sd

The default minimum is 100 (config.insertStatsMinSize), the maximum is
50,000 (config.insertStatsMaxSize)

If you think maybe reads with long insert size (e.g. in the range
450-50,000) are affecting the calculation, you could try changing
"insertStatsMaxSize": 500 so this way it will actually only take into
account reads below insert size 500 for the stats calculation, and then it
will more clearly show anything above this range


Let me know if that helps

-Colin

On Tue, Aug 11, 2020 at 9:56 AM Caterina Marconi <cat...@ho...>
wrote:

> Hello,
> I have two question regarding the ColorBySize option.
> What is the correct way to use the "re-estimate insert size stats"
> function?
> Is it possible to set a fix thresholds for insert size for the
> ColorBySize option?
> I have some troubles in visualizing abnormal read-pairs. The avg insert
> size is around 450bp, but only reads with insert size higher than 1000 are
> highlighted. Moreover, if I switch from paired to unpaired view and then
> again to pair view, I lost the highlighting.
>
> Thanks for your help.
> Caterina
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] ColorBySize settings

[Caterina M. <cat...@ho...>]

Hello,
I have two question regarding the ColorBySize option.
What is the correct way to use the "re-estimate insert size stats" function?
Is it possible to set a fix thresholds for insert size for the ColorBySize option?
I have some troubles in visualizing abnormal read-pairs. The avg insert size is around 450bp, but only reads with insert size higher than 1000 are highlighted. Moreover, if I switch from paired to unpaired view and then again to pair view, I lost the highlighting.

Thanks for your help.
Caterina

Re: [Gmod-ajax] Combining BigWig Tracks

[ARORA, S. <sz...@ps...>]

Great, thanks for taking care of that so quickly!
________________________________
From: Colin <col...@gm...>
Sent: Friday, August 7, 2020 3:23 PM
To: ARORA, SONNY <sz...@ps...>
Cc: gmo...@li... <gmo...@li...>
Subject: Re: [Gmod-ajax] Combining BigWig Tracks

Good catch

The fix is similar to the above answer, but needed fixing in our core codebase

https://github.com/GMOD/jbrowse/pull/1536<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse%2Fpull%2F1536&data=02%7C01%7Csza149%40psu.edu%7C9a381f6d188a4ab31ec408d83b0774dc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637324250497994478&sdata=txhdawuYNFp2NGX6s%2Fk9ajO6Yvzc2tstEUr76XImpUk%3D&reserved=0>

This is an example of where we have had combination tracks for a long time but we never got this bug noticed, I think they are also very cool but indeed not often used.

If you are interested you can check out this branch and create a custom build

git clone https://github.com/gmod/jbrowse<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fgmod%2Fjbrowse&data=02%7C01%7Csza149%40psu.edu%7C9a381f6d188a4ab31ec408d83b0774dc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637324250498004479&sdata=UvL7lbsGFocN63YO4bpJtjl1XjrWr3W8MeekOikvIgI%3D&reserved=0>
cd jbrowse
git checkout fix_local_combination
./setup.sh

Should be able to get merged and released sometime soon though

-Colin

On Fri, Aug 7, 2020 at 2:07 PM ARORA, SONNY <sz...@ps...<mailto:sz...@ps...>> wrote:
Thanks! That worked great when adding tracks with the API.

Any idea what was going wrong when I was adding bigwigs through the navbar and trying to use a combination track? Sometimes users would like to add local tracks to JBrowse and I was hoping to allow them to do that through the navbar with the ability to use them in a combination track.

> Note that we don't use combination tracks often so there are probably some weird corners there, but I am curious how your experience goes

That's a shame that they are not used so often. A big reason my lab is interested in JBrowse is because we were looking for a well supported web-based browser with the combination track feature. Often members of our lab want to visually combine replicates for experiments and it's a bit of a pain to create a merged big wig for those cases. Are you aware of any areas where I might run into issues with combination tracks? Thanks again for all your help so far!
________________________________
From: Colin <col...@gm...<mailto:col...@gm...>>
Sent: Wednesday, August 5, 2020 8:28 PM
To: ARORA, SONNY <sz...@ps...<mailto:sz...@ps...>>
Cc: gmo...@li...<mailto:gmo...@li...> <gmo...@li...<mailto:gmo...@li...>>
Subject: Re: [Gmod-ajax] Combining BigWig Tracks

I think this is sort of related to your last question (xref https://sourceforge.net/p/gmod/mailman/message/37078566/<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fp%2Fgmod%2Fmailman%2Fmessage%2F37078566%2F&data=02%7C01%7Csza149%40psu.edu%7C9a381f6d188a4ab31ec408d83b0774dc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637324250498004479&sdata=ljVFg6%2BAP70c%2Fw07VeWg6OwJW97M6zptgyoQRU5U4CY%3D&reserved=0>)

I took a little shortcut and made an abbreviated config in that thread, but if you add the storeClass to the track config, then the Combination track recognizes it properly and should allow it


var storeName = JBrowse.addStoreConfig(null, {
  browser: JBrowse,
  type: "JBrowse/Store/SeqFeature/BigWig",
  baseUrl: ".",
  urlTemplate: "sample_data/raw/volvox/volvox_microarray.bw<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fvolvox_microarray.bw%2F&data=02%7C01%7Csza149%40psu.edu%7C9a381f6d188a4ab31ec408d83b0774dc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637324250498014469&sdata=2bEgTZsjtuf%2BO4%2BZSHNQI1PVW0xp4ZNp0DzV%2FlgMSIk%3D&reserved=0>",
});
JBrowse.publish("/jbrowse/v1/v/tracks/replace", [
  { label: "My Track2", store: storeName, storeClass: "JBrowse/Store/SeqFeature/BigWig" },
]);

Note that we don't use combination tracks often so there are probably some weird corners there, but I am curious how your experience goes

-Colin

On Wed, Aug 5, 2020 at 5:42 PM ARORA, SONNY <sz...@ps...<mailto:sz...@ps...>> wrote:
Hi,

I'm looking to add two bigwigs together in JBrowse. I'm working on Chrome Version 84.0.4147.89 (Official Build) (64-bit).

Going to the address:

http://jbrowse.org/code/JBrowse-1.16.9/?data=sample_data%2Fjson%2Fvolvox&loc=ctgA%3A19987..24704&tracks=DNA%2Cvolvox_microarray_bw_density%2Cvolvox_sine_density&highlight=<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fjbrowse.org%2Fcode%2FJBrowse-1.16.9%2F%3Fdata%3Dsample_data%252Fjson%252Fvolvox%26loc%3DctgA%253A19987..24704%26tracks%3DDNA%252Cvolvox_microarray_bw_density%252Cvolvox_sine_density%26highlight%3D&data=02%7C01%7Csza149%40psu.edu%7C9a381f6d188a4ab31ec408d83b0774dc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637324250498014469&sdata=kTmKJnyt28wmhydGOTJNBBp6V5P4QmFnn1zyj%2Ftlmyo%3D&reserved=0>

I add a genome by clicking Genome -> Open Sequence File -> Local Files -> Select Files. I then select my mm10.fa and mm10.fa.fai files and click open.

I then load two bigwigs: Track -> Open track file or URL -> Local Files -> Select Files. The bigwigs appear to display fine.

I create a combination track: Track -> Add combination track.

When I try to drag over one of the bigwigs to the combination track I get a red stop sign and am not able to add the bigwig to the track. I've attached a screenshot. Let me know what I'm doing wrong, thanks!

Best,

Sonny


_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=02%7C01%7Csza149%40psu.edu%7C9a381f6d188a4ab31ec408d83b0774dc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637324250498024469&sdata=2EvBOmwf3dtBcGPrZAOVbiOOh%2Ft%2BuWT3kOxLnkPLcMc%3D&reserved=0>

Re: [Gmod-ajax] Combining BigWig Tracks

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

Good catch

The fix is similar to the above answer, but needed fixing in our core
codebase

https://github.com/GMOD/jbrowse/pull/1536

This is an example of where we have had combination tracks for a long time
but we never got this bug noticed, I think they are also very cool but
indeed not often used.

If you are interested you can check out this branch and create a custom
build

git clone https://github.com/gmod/jbrowse
cd jbrowse
git checkout fix_local_combination
./setup.sh

Should be able to get merged and released sometime soon though

-Colin

On Fri, Aug 7, 2020 at 2:07 PM ARORA, SONNY <sz...@ps...> wrote:

> Thanks! That worked great when adding tracks with the API.
>
> Any idea what was going wrong when I was adding bigwigs through the navbar
> and trying to use a combination track? Sometimes users would like to add
> local tracks to JBrowse and I was hoping to allow them to do that through
> the navbar with the ability to use them in a combination track.
>
> > Note that we don't use combination tracks often so there are probably
> some weird corners there, but I am curious how your experience goes
>
> That's a shame that they are not used so often. A big reason my lab is
> interested in JBrowse is because we were looking for a well supported
> web-based browser with the combination track feature. Often members of our
> lab want to visually combine replicates for experiments and it's a bit of a
> pain to create a merged big wig for those cases. Are you aware of any areas
> where I might run into issues with combination tracks? Thanks again for all
> your help so far!
> ------------------------------
> *From:* Colin <col...@gm...>
> *Sent:* Wednesday, August 5, 2020 8:28 PM
> *To:* ARORA, SONNY <sz...@ps...>
> *Cc:* gmo...@li... <gmo...@li...>
> *Subject:* Re: [Gmod-ajax] Combining BigWig Tracks
>
> I think this is sort of related to your last question (xref
> https://sourceforge.net/p/gmod/mailman/message/37078566/
> <https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fp%2Fgmod%2Fmailman%2Fmessage%2F37078566%2F&data=02%7C01%7Csza149%40psu.edu%7Ce01d5630504d430a136208d8399fb416%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637322705374494356&sdata=SfwFQ0uT5uEfnRHKxZUCy20YzRIS4K%2BsIprPJaM1jLg%3D&reserved=0>
> )
>
> I took a little shortcut and made an abbreviated config in that thread,
> but if you add the storeClass to the track config, then the Combination
> track recognizes it properly and should allow it
>
>
> var storeName = JBrowse.addStoreConfig(null, {
>   browser: JBrowse,
>   type: "JBrowse/Store/SeqFeature/BigWig",
>   baseUrl: ".",
>   urlTemplate: "sample_data/raw/volvox/volvox_microarray.bw
> <https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fvolvox_microarray.bw%2F&data=02%7C01%7Csza149%40psu.edu%7Ce01d5630504d430a136208d8399fb416%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637322705374504350&sdata=c7ZlfwvpGLRSurpON%2FbexVulpsAugoC2QUG7cOv%2BCqk%3D&reserved=0>
> ",
> });
> JBrowse.publish("/jbrowse/v1/v/tracks/replace", [
>   { label: "My Track2", store: storeName, storeClass:
> "JBrowse/Store/SeqFeature/BigWig" },
> ]);
>
> Note that we don't use combination tracks often so there are probably some
> weird corners there, but I am curious how your experience goes
>
> -Colin
>
> On Wed, Aug 5, 2020 at 5:42 PM ARORA, SONNY <sz...@ps...> wrote:
>
> Hi,
>
> I'm looking to add two bigwigs together in JBrowse. I'm working on Chrome Version
> 84.0.4147.89 (Official Build) (64-bit).
>
> Going to the address:
>
>
> http://jbrowse.org/code/JBrowse-1.16.9/?data=sample_data%2Fjson%2Fvolvox&loc=ctgA%3A19987..24704&tracks=DNA%2Cvolvox_microarray_bw_density%2Cvolvox_sine_density&highlight=
> <https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fjbrowse.org%2Fcode%2FJBrowse-1.16.9%2F%3Fdata%3Dsample_data%252Fjson%252Fvolvox%26loc%3DctgA%253A19987..24704%26tracks%3DDNA%252Cvolvox_microarray_bw_density%252Cvolvox_sine_density%26highlight%3D&data=02%7C01%7Csza149%40psu.edu%7Ce01d5630504d430a136208d8399fb416%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637322705374504350&sdata=gNua150N%2BaRtEDXCOhCEIz9%2BLIvC1g6XpPWUhKMxjQk%3D&reserved=0>
>
> I add a genome by clicking Genome -> Open Sequence File -> Local Files ->
> Select Files. I then select my mm10.fa and mm10.fa.fai files and click
> open.
>
> I then load two bigwigs: Track -> Open track file or URL -> Local Files ->
> Select Files. The bigwigs appear to display fine.
>
> I create a combination track: Track -> Add combination track.
>
> When I try to drag over one of the bigwigs to the combination track I get
> a red stop sign and am not able to add the bigwig to the track. I've
> attached a screenshot. Let me know what I'm doing wrong, thanks!
>
> Best,
>
> Sonny
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> <https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=02%7C01%7Csza149%40psu.edu%7Ce01d5630504d430a136208d8399fb416%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637322705374514341&sdata=7WCbqkp9kdndC0rIhY%2FS8Hg4rg7Zo0a6EGLkaFylkJg%3D&reserved=0>
>
>

Re: [Gmod-ajax] Combining BigWig Tracks

[ARORA, S. <sz...@ps...>]

Thanks! That worked great when adding tracks with the API.

Any idea what was going wrong when I was adding bigwigs through the navbar and trying to use a combination track? Sometimes users would like to add local tracks to JBrowse and I was hoping to allow them to do that through the navbar with the ability to use them in a combination track.

> Note that we don't use combination tracks often so there are probably some weird corners there, but I am curious how your experience goes

That's a shame that they are not used so often. A big reason my lab is interested in JBrowse is because we were looking for a well supported web-based browser with the combination track feature. Often members of our lab want to visually combine replicates for experiments and it's a bit of a pain to create a merged big wig for those cases. Are you aware of any areas where I might run into issues with combination tracks? Thanks again for all your help so far!
________________________________
From: Colin <col...@gm...>
Sent: Wednesday, August 5, 2020 8:28 PM
To: ARORA, SONNY <sz...@ps...>
Cc: gmo...@li... <gmo...@li...>
Subject: Re: [Gmod-ajax] Combining BigWig Tracks

I think this is sort of related to your last question (xref https://sourceforge.net/p/gmod/mailman/message/37078566/<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsourceforge.net%2Fp%2Fgmod%2Fmailman%2Fmessage%2F37078566%2F&data=02%7C01%7Csza149%40psu.edu%7Ce01d5630504d430a136208d8399fb416%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637322705374494356&sdata=SfwFQ0uT5uEfnRHKxZUCy20YzRIS4K%2BsIprPJaM1jLg%3D&reserved=0>)

I took a little shortcut and made an abbreviated config in that thread, but if you add the storeClass to the track config, then the Combination track recognizes it properly and should allow it


var storeName = JBrowse.addStoreConfig(null, {
  browser: JBrowse,
  type: "JBrowse/Store/SeqFeature/BigWig",
  baseUrl: ".",
  urlTemplate: "sample_data/raw/volvox/volvox_microarray.bw<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fvolvox_microarray.bw%2F&data=02%7C01%7Csza149%40psu.edu%7Ce01d5630504d430a136208d8399fb416%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637322705374504350&sdata=c7ZlfwvpGLRSurpON%2FbexVulpsAugoC2QUG7cOv%2BCqk%3D&reserved=0>",
});
JBrowse.publish("/jbrowse/v1/v/tracks/replace", [
  { label: "My Track2", store: storeName, storeClass: "JBrowse/Store/SeqFeature/BigWig" },
]);

Note that we don't use combination tracks often so there are probably some weird corners there, but I am curious how your experience goes

-Colin

On Wed, Aug 5, 2020 at 5:42 PM ARORA, SONNY <sz...@ps...<mailto:sz...@ps...>> wrote:
Hi,

I'm looking to add two bigwigs together in JBrowse. I'm working on Chrome Version 84.0.4147.89 (Official Build) (64-bit).

Going to the address:

http://jbrowse.org/code/JBrowse-1.16.9/?data=sample_data%2Fjson%2Fvolvox&loc=ctgA%3A19987..24704&tracks=DNA%2Cvolvox_microarray_bw_density%2Cvolvox_sine_density&highlight=<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fjbrowse.org%2Fcode%2FJBrowse-1.16.9%2F%3Fdata%3Dsample_data%252Fjson%252Fvolvox%26loc%3DctgA%253A19987..24704%26tracks%3DDNA%252Cvolvox_microarray_bw_density%252Cvolvox_sine_density%26highlight%3D&data=02%7C01%7Csza149%40psu.edu%7Ce01d5630504d430a136208d8399fb416%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637322705374504350&sdata=gNua150N%2BaRtEDXCOhCEIz9%2BLIvC1g6XpPWUhKMxjQk%3D&reserved=0>

I add a genome by clicking Genome -> Open Sequence File -> Local Files -> Select Files. I then select my mm10.fa and mm10.fa.fai files and click open.

I then load two bigwigs: Track -> Open track file or URL -> Local Files -> Select Files. The bigwigs appear to display fine.

I create a combination track: Track -> Add combination track.

When I try to drag over one of the bigwigs to the combination track I get a red stop sign and am not able to add the bigwig to the track. I've attached a screenshot. Let me know what I'm doing wrong, thanks!

Best,

Sonny


_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=02%7C01%7Csza149%40psu.edu%7Ce01d5630504d430a136208d8399fb416%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637322705374514341&sdata=7WCbqkp9kdndC0rIhY%2FS8Hg4rg7Zo0a6EGLkaFylkJg%3D&reserved=0>

Re: [Gmod-ajax] Combining BigWig Tracks

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

I think this is sort of related to your last question (xref
https://sourceforge.net/p/gmod/mailman/message/37078566/)

I took a little shortcut and made an abbreviated config in that thread, but
if you add the storeClass to the track config, then the Combination track
recognizes it properly and should allow it


var storeName = JBrowse.addStoreConfig(null, {
  browser: JBrowse,
  type: "JBrowse/Store/SeqFeature/BigWig",
  baseUrl: ".",
  urlTemplate: "sample_data/raw/volvox/volvox_microarray.bw",
});
JBrowse.publish("/jbrowse/v1/v/tracks/replace", [
  { label: "My Track2", store: storeName, storeClass:
"JBrowse/Store/SeqFeature/BigWig" },
]);

Note that we don't use combination tracks often so there are probably some
weird corners there, but I am curious how your experience goes

-Colin

On Wed, Aug 5, 2020 at 5:42 PM ARORA, SONNY <sz...@ps...> wrote:

> Hi,
>
> I'm looking to add two bigwigs together in JBrowse. I'm working on Chrome Version
> 84.0.4147.89 (Official Build) (64-bit).
>
> Going to the address:
>
>
> http://jbrowse.org/code/JBrowse-1.16.9/?data=sample_data%2Fjson%2Fvolvox&loc=ctgA%3A19987..24704&tracks=DNA%2Cvolvox_microarray_bw_density%2Cvolvox_sine_density&highlight=
>
> I add a genome by clicking Genome -> Open Sequence File -> Local Files ->
> Select Files. I then select my mm10.fa and mm10.fa.fai files and click
> open.
>
> I then load two bigwigs: Track -> Open track file or URL -> Local Files ->
> Select Files. The bigwigs appear to display fine.
>
> I create a combination track: Track -> Add combination track.
>
> When I try to drag over one of the bigwigs to the combination track I get
> a red stop sign and am not able to add the bigwig to the track. I've
> attached a screenshot. Let me know what I'm doing wrong, thanks!
>
> Best,
>
> Sonny
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Combining BigWig Tracks

[ARORA, S. <sz...@ps...>]

Hi,

I'm looking to add two bigwigs together in JBrowse. I'm working on Chrome Version 84.0.4147.89 (Official Build) (64-bit).

Going to the address:

http://jbrowse.org/code/JBrowse-1.16.9/?data=sample_data%2Fjson%2Fvolvox&loc=ctgA%3A19987..24704&tracks=DNA%2Cvolvox_microarray_bw_density%2Cvolvox_sine_density&highlight=

I add a genome by clicking Genome -> Open Sequence File -> Local Files -> Select Files. I then select my mm10.fa and mm10.fa.fai files and click open.

I then load two bigwigs: Track -> Open track file or URL -> Local Files -> Select Files. The bigwigs appear to display fine.

I create a combination track: Track -> Add combination track.

When I try to drag over one of the bigwigs to the combination track I get a red stop sign and am not able to add the bigwig to the track. I've attached a screenshot. Let me know what I'm doing wrong, thanks!

Best,

Sonny

Re: [Gmod-ajax] Loading a Track to JBrowse using the API

[ARORA, S. <sz...@ps...>]

That example was exactly what I was looking for, thanks!
________________________________
From: Colin <col...@gm...>
Sent: Wednesday, August 5, 2020 9:01 AM
To: ARORA, SONNY <sz...@ps...>
Cc: gmo...@li... <gmo...@li...>
Subject: Re: [Gmod-ajax] Loading a Track to JBrowse using the API

If I understand correctly, you might use the addTracks URL parameter can be used to add custom tracks via the URL

http://jbrowse.org/docs/url_strings.html<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fjbrowse.org%2Fdocs%2Furl_strings.html&data=02%7C01%7Csza149%40psu.edu%7Ca33564f490eb4935f11708d8393fb98e%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637322293140549760&sdata=gPH4NyOaE77YYS6Expg%2B6X3IQWA7t1%2B20nePKX4Brfo%3D&reserved=0>


If you are talking about dynamically adding tracks at runtime, that would probably use the events API, not the URL. That events documentation page has always been kind of difficult to interpret, it needs examples...here is one example of adding a track at runtime

var storeName = JBrowse.addStoreConfig(null, {
  browser: JBrowse,
  type: "JBrowse/Store/SeqFeature/BAM",
  baseUrl: ".",
  urlTemplate: "sample_data/raw/volvox/volvox-sorted.bam",
});
JBrowse.publish("/jbrowse/v1/v/tracks/replace", [
  { label: "My track", store: storeName },
]);

If you run this from inside of the javascript console on http://jbrowse.org/code/JBrowse-1.16.9/?data=sample_data/json/volvox<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fjbrowse.org%2Fcode%2FJBrowse-1.16.9%2F%3Fdata%3Dsample_data%2Fjson%2Fvolvox&data=02%7C01%7Csza149%40psu.edu%7Ca33564f490eb4935f11708d8393fb98e%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637322293140549760&sdata=wSPifRLx7hGJbXoZyWVojhgFOfhRsyf0w1cWFtSkF8w%3D&reserved=0> then you'll see the track get added


-Colin

On Wed, Aug 5, 2020 at 3:30 AM ARORA, SONNY <sz...@ps...<mailto:sz...@ps...>> wrote:
Hi,

I'm interested in embedding JBrowse in my website. I saw the documentation for loading a config at start up here:

https://jbrowse.org/docs/embedding.html<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fjbrowse.org%2Fdocs%2Fembedding.html&data=02%7C01%7Csza149%40psu.edu%7Ca33564f490eb4935f11708d8393fb98e%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637322293140559754&sdata=7x13hiL1mf7AJWFuK8Wp9Ir5JnUGZlVB1L9EP%2FTgi6o%3D&reserved=0>

On my website users can select tracks and I would like to add these tracks to JBrowse by URL after JBrowse is loaded. I was wondering if JBrowse provides an API to load tracks? The link here mentions being able to publish events to JBrowse:

https://jbrowse.org/docs/events.html<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fjbrowse.org%2Fdocs%2Fevents.html&data=02%7C01%7Csza149%40psu.edu%7Ca33564f490eb4935f11708d8393fb98e%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637322293140559754&sdata=Y%2Bs0cwS1hmKOqfgW9jB9yaIi5D0l5pRG0E3Frvc%2FRbg%3D&reserved=0>

To me the link above seemed to suggest that it's possible to load a track using an API, but correct me if I'm wrong (I'm not familiar with dojo). If it is possible to load a track from a url using the API, how would I go about doing that? Thanks in advance for your help!

Best,

Sonny
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...<mailto:Gmo...@li...>
https://lists.sourceforge.net/lists/listinfo/gmod-ajax<https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fgmod-ajax&data=02%7C01%7Csza149%40psu.edu%7Ca33564f490eb4935f11708d8393fb98e%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637322293140569753&sdata=O3qqkQgy6iMRk%2BiR1zgdL0ZDkyNvKhpTTyXOoHQfcn4%3D&reserved=0>

Re: [Gmod-ajax] Loading a Track to JBrowse using the API

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

If I understand correctly, you might use the addTracks URL parameter can be
used to add custom tracks via the URL

http://jbrowse.org/docs/url_strings.html


If you are talking about dynamically adding tracks at runtime, that would
probably use the events API, not the URL. That events documentation page
has always been kind of difficult to interpret, it needs examples...here is
one example of adding a track at runtime

var storeName = JBrowse.addStoreConfig(null, {
  browser: JBrowse,
  type: "JBrowse/Store/SeqFeature/BAM",
  baseUrl: ".",
  urlTemplate: "sample_data/raw/volvox/volvox-sorted.bam",
});
JBrowse.publish("/jbrowse/v1/v/tracks/replace", [
  { label: "My track", store: storeName },
]);

If you run this from inside of the javascript console on
http://jbrowse.org/code/JBrowse-1.16.9/?data=sample_data/json/volvox then
you'll see the track get added


-Colin

On Wed, Aug 5, 2020 at 3:30 AM ARORA, SONNY <sz...@ps...> wrote:

> Hi,
>
> I'm interested in embedding JBrowse in my website. I saw the documentation
> for loading a config at start up here:
>
> https://jbrowse.org/docs/embedding.html
>
> On my website users can select tracks and I would like to add these tracks
> to JBrowse by URL after JBrowse is loaded. I was wondering if JBrowse
> provides an API to load tracks? The link here mentions being able to
> publish events to JBrowse:
>
> https://jbrowse.org/docs/events.html
>
> To me the link above seemed to suggest that it's possible to load a track
> using an API, but correct me if I'm wrong (I'm not familiar with dojo). If
> it is possible to load a track from a url using the API, how would I go
> about doing that? Thanks in advance for your help!
>
> Best,
>
> Sonny
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Loading a Track to JBrowse using the API

[ARORA, S. <sz...@ps...>]

Hi,

I'm interested in embedding JBrowse in my website. I saw the documentation for loading a config at start up here:

https://jbrowse.org/docs/embedding.html

On my website users can select tracks and I would like to add these tracks to JBrowse by URL after JBrowse is loaded. I was wondering if JBrowse provides an API to load tracks? The link here mentions being able to publish events to JBrowse:

https://jbrowse.org/docs/events.html

To me the link above seemed to suggest that it's possible to load a track using an API, but correct me if I'm wrong (I'm not familiar with dojo). If it is possible to load a track from a url using the API, how would I go about doing that? Thanks in advance for your help!

Best,

Sonny

Re: [Gmod-ajax] Perl lib version question

[Zhiliang Hu <hu...@an...>]

On Tue, 14 Jul 2020, Zhiliang Hu wrote:

> Date: Tue, 14 Jul 2020 15:10:27 -0500 (CDT)
> From: Zhiliang Hu <hu...@an...>
> To: Colin <col...@gm...>
> Cc: gmod-ajax <gmo...@li...>
> Subject: Re: [Gmod-ajax] Perl lib version question
> 
> Thank you Colin!  This was an eye openning for me to cpanm... My ran of 
> "cpanm Bio::Perl@1.7.2" seemed an success.
>
> I was able to get rid of multiple "Segmentation fault (core dumped)" by 
> changing the line in 'setup.sh' where perl was called with a full path: 
> "have_db=`/usr/local/bin/perl -MConfig=myconfig -e".  The setup was a 
> success!
>
> Now I am getting "Segmentation fault (core dumped)" running 
> "flatfile-to-json.pl", even after I changed its "#!/usr/bin/env perl" line
> to "#!/usr/local/bin/perl".

Just a follow up - "flatfile-to-json.pl" ran without errors when I 
changed its first line to "#!/usr/bin/env /usr/bin/perl". I guess there 
was a confusion with regard to multiple install locations by each of the 
'cpan', 'cpanm', and other installers, over the time.

Zhiliang

Re: [Gmod-ajax] Perl lib version question

[Zhiliang Hu <hu...@an...>]

On Tue, 14 Jul 2020, Zhiliang Hu wrote:

> Date: Tue, 14 Jul 2020 16:12:36 -0500 (CDT)
> From: Zhiliang Hu <hu...@an...>
> To: Colin <col...@gm...>
> Cc: gmod-ajax <gmo...@li...>
> Subject: Re: [Gmod-ajax] Perl lib version question
> 
> Hi Colin,
>
> Yes, upon my first run of 'setup.sh' of the new download, it complained about 
> "... perl v5.12 ...not compatible with perl v5.30" or something like that. My 
> ssh window does not scroll back that far.  I thought I read something similar 
> on jbrowse web site but can't locate it this moment.

Or it detected I have multiple versions of perl installed on the system.

Re: [Gmod-ajax] Perl lib version question

[Zhiliang Hu <hu...@an...>]

Hi Colin,

Yes, upon my first run of 'setup.sh' of the new download, it complained 
about "... perl v5.12 ...not compatible with perl v5.30" or something like 
that. My ssh window does not scroll back that far.  I thought I read 
something similar on jbrowse web site but can't locate it this moment.

Zhiliang


On Tue, 14 Jul 2020, Colin wrote:

> Date: Tue, 14 Jul 2020 16:39:57 -0400
> From: Colin <col...@gm...>
> To: Zhiliang Hu <hu...@an...>
> Cc: gmod-ajax <gmo...@li...>
> Subject: Re: [Gmod-ajax] Perl lib version question
> 
> I am not really sure but I wanted to revisit your other email
>
>> As needed by new JBrowse, I installed perl 5.30 into the
> /usr/local/bin/ location (my /usr/bin/ location has perl 5.16)
>
> There is no requirement to use a new version of perl with newer versions of
> JBrowse as far as I know, we should be backwards compatible with pretty old
> versions of perl
>
> Did you see something that seemed to need an upgraded perl?
>
>
> -Colin
>
> On Tue, Jul 14, 2020 at 4:10 PM Zhiliang Hu <hu...@an...> wrote:
>
>> Thank you Colin!  This was an eye openning for me to cpanm... My ran of
>> "cpanm Bio::Perl@1.7.2" seemed an success.
>>
>> I was able to get rid of multiple "Segmentation fault (core dumped)"
>> by changing the line in 'setup.sh' where perl was called with a full path:
>> "have_db=`/usr/local/bin/perl -MConfig=myconfig -e".  The setup was a
>> success!
>>
>> Now I am getting "Segmentation fault (core dumped)" running
>> "flatfile-to-json.pl", even after I changed its "#!/usr/bin/env perl" line
>> to "#!/usr/local/bin/perl".
>>
>> Any suggestion please?
>>
>> Zhiliang
>>
>>
>> On Tue, 14 Jul 2020, Colin wrote:
>>
>>> Date: Tue, 14 Jul 2020 13:03:54 -0400
>>> From: Colin <col...@gm...>
>>> To: Zhiliang Hu <hu...@an...>
>>> Cc: gmod-ajax <gmo...@li...>
>>> Subject: Re: [Gmod-ajax] Perl lib version question
>>>
>>> If you have cpanm installed globally on your system you can try to
>> manually
>>> run this command
>>>
>>> cpanm Bio::Perl@1.7.2
>>>
>>> A similar thing can likely be done with the plain cpan executable also,
>>> possibly this
>>>
>>> cpan CJFIELDS/BioPerl-1.007002.tar.gz
>>>
>>>
>>> We require 1.7.2 because later versions really significantly modified the
>>> BioPerl ecosystem (see changelog here
>>> https://github.com/bioperl/bioperl-live/blob/master/Changes)
>>>
>>>
>>> -Colin
>>>
>>>
>>> On Tue, Jul 14, 2020 at 11:59 AM Zhiliang Hu <hu...@an...>
>> wrote:
>>>
>>>>
>>>> Thanks Colin for addressing the issue.  I took the path to reinstall the
>>>> JBrowse.  As needed by new JBrowse, I installed perl 5.30 into the
>>>> /usr/local/bin/ location (my /usr/bin/ location has perl 5.16)
>>>>
>>>> My newly downloaded JBrowse setup.sh (at a location different from
>>>> previous installations; on a RedHat CentOS 7 system) got complains like:
>>>>
>>>> Installing Perl prerequisites ...
>>>> + bin/cpanm -v --notest -l extlib/ Bio::Perl@1.7.2
>>>> ./setup.sh: line 142: 10708 Segmentation fault      (core dumped)
>>>>
>>>> I understand it might be caused by multiple perl versions on my system
>> but
>>>> by cleaning my shell environment PERLLIB/ PERL5LIB didn't help. I wonder
>>>> is there alternative ways to install "Bio::Perl@1.7.2" (actually which
>>>> modules?).
>>>>
>>>> I searched for old JBrowse troubleshooting and did:
>>>>> sudo yum groupinstall "Development Tools"
>>>>> sudo yum install libpng-devel gd-devel zlib-devel
>> perl-ExtUtils-MakeMaker
>>>> and it didn't help.
>>>>
>>>> Any further suggestion please? (I know on this RH Centos7 system there
>> are
>>>> perl GD, Zlib, and libpng installed but how to make the JBrowse setup
>> know
>>>> where they are?)
>>>>
>>>> Zhiliang
>>>>
>>>> On Wed, 3 Jun 2020, Colin wrote:
>>>>
>>>>> Date: Wed, 3 Jun 2020 20:34:24 -0400
>>>>> From: Colin <col...@gm...>
>>>>> To: Zhiliang Hu <hu...@an...>
>>>>> Cc: gmod-ajax <gmo...@li...>
>>>>> Subject: Re: [Gmod-ajax] Perl lib version question
>>>>>
>>>>> There have been a couple people experiencing this lately. I am not
>>>> exactly
>>>>> sure why, maybe it is related people who have older versions of jbrowse
>>>>> upgrading to perl 5.30+.
>>>>>
>>>>> JBrowse generally installs all it's perl dependencies to a folder
>> inside
>>>>> JBROWSE_ROOT/extlib
>>>>>
>>>>> I would try rm -rf extlib, maybe also ~/.cpanm and ~/.cpan, then re-run
>>>>> setup.sh
>>>>>
>>>>> Here is a chat log of a user on our chat that also did these steps but
>> it
>>>>> was  on macOS
>>>>>
>>>>>> * nuke all traces of perl in /User (brew, .cpan, .cpanm etc.)
>>>>>> * `sudo installer -pkg
>>>>>
>>>>
>> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>>>>> -target` - allows  Extern_H compile problem to  pass
>>>>>> * use `cpan` to `install JSON::XS` (for some reason the dependency
>> won't
>>>>> install during setup.sh)
>>>>>> * run `setup.sh`
>>>>>
>>>>>
>>>>>
>>>>> -Colin
>>>>>
>>>>> On Wed, Jun 3, 2020 at 7:37 PM Zhiliang Hu <hu...@an...>
>> wrote:
>>>>>
>>>>>> When I tried to load data to JBrowse, I got the following complain:
>>>>>>
>>>>>> Perl lib version (5.16.3) doesn't match executable
>>>>>> '/home/apache/doc/jbrowse/bin/flatfile-to-json.pl' version (v5.30.0)
>> at
>>>>>> /usr/lib64/perl5/Config.pm line 60.
>>>>>> Compilation failed in require at /usr/lib64/perl5/lib.pm line 6.
>>>>>>
>>>>>> In cpan I did "reload cpan" and "install lib" and it says:
>>>>>>
>>>>>>    lib is up to date (0.63)
>>>>>>
>>>>>> I am at a lost as how to update my "perl lib". Any advice please?
>>>>>>
>>>>>> Zhiliang
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Gmod-ajax mailing list
>>>>>> Gmo...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>>>
>>>>>
>>>>
>>>
>>
>

Re: [Gmod-ajax] Perl lib version question

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

I am not really sure but I wanted to revisit your other email

>As needed by new JBrowse, I installed perl 5.30 into the
/usr/local/bin/ location (my /usr/bin/ location has perl 5.16)

There is no requirement to use a new version of perl with newer versions of
JBrowse as far as I know, we should be backwards compatible with pretty old
versions of perl

Did you see something that seemed to need an upgraded perl?


-Colin

On Tue, Jul 14, 2020 at 4:10 PM Zhiliang Hu <hu...@an...> wrote:

> Thank you Colin!  This was an eye openning for me to cpanm... My ran of
> "cpanm Bio::Perl@1.7.2" seemed an success.
>
> I was able to get rid of multiple "Segmentation fault (core dumped)"
> by changing the line in 'setup.sh' where perl was called with a full path:
> "have_db=`/usr/local/bin/perl -MConfig=myconfig -e".  The setup was a
> success!
>
> Now I am getting "Segmentation fault (core dumped)" running
> "flatfile-to-json.pl", even after I changed its "#!/usr/bin/env perl" line
> to "#!/usr/local/bin/perl".
>
> Any suggestion please?
>
> Zhiliang
>
>
> On Tue, 14 Jul 2020, Colin wrote:
>
> > Date: Tue, 14 Jul 2020 13:03:54 -0400
> > From: Colin <col...@gm...>
> > To: Zhiliang Hu <hu...@an...>
> > Cc: gmod-ajax <gmo...@li...>
> > Subject: Re: [Gmod-ajax] Perl lib version question
> >
> > If you have cpanm installed globally on your system you can try to
> manually
> > run this command
> >
> > cpanm Bio::Perl@1.7.2
> >
> > A similar thing can likely be done with the plain cpan executable also,
> > possibly this
> >
> > cpan CJFIELDS/BioPerl-1.007002.tar.gz
> >
> >
> > We require 1.7.2 because later versions really significantly modified the
> > BioPerl ecosystem (see changelog here
> > https://github.com/bioperl/bioperl-live/blob/master/Changes)
> >
> >
> > -Colin
> >
> >
> > On Tue, Jul 14, 2020 at 11:59 AM Zhiliang Hu <hu...@an...>
> wrote:
> >
> >>
> >> Thanks Colin for addressing the issue.  I took the path to reinstall the
> >> JBrowse.  As needed by new JBrowse, I installed perl 5.30 into the
> >> /usr/local/bin/ location (my /usr/bin/ location has perl 5.16)
> >>
> >> My newly downloaded JBrowse setup.sh (at a location different from
> >> previous installations; on a RedHat CentOS 7 system) got complains like:
> >>
> >> Installing Perl prerequisites ...
> >> + bin/cpanm -v --notest -l extlib/ Bio::Perl@1.7.2
> >> ./setup.sh: line 142: 10708 Segmentation fault      (core dumped)
> >>
> >> I understand it might be caused by multiple perl versions on my system
> but
> >> by cleaning my shell environment PERLLIB/ PERL5LIB didn't help. I wonder
> >> is there alternative ways to install "Bio::Perl@1.7.2" (actually which
> >> modules?).
> >>
> >> I searched for old JBrowse troubleshooting and did:
> >>> sudo yum groupinstall "Development Tools"
> >>> sudo yum install libpng-devel gd-devel zlib-devel
> perl-ExtUtils-MakeMaker
> >> and it didn't help.
> >>
> >> Any further suggestion please? (I know on this RH Centos7 system there
> are
> >> perl GD, Zlib, and libpng installed but how to make the JBrowse setup
> know
> >> where they are?)
> >>
> >> Zhiliang
> >>
> >> On Wed, 3 Jun 2020, Colin wrote:
> >>
> >>> Date: Wed, 3 Jun 2020 20:34:24 -0400
> >>> From: Colin <col...@gm...>
> >>> To: Zhiliang Hu <hu...@an...>
> >>> Cc: gmod-ajax <gmo...@li...>
> >>> Subject: Re: [Gmod-ajax] Perl lib version question
> >>>
> >>> There have been a couple people experiencing this lately. I am not
> >> exactly
> >>> sure why, maybe it is related people who have older versions of jbrowse
> >>> upgrading to perl 5.30+.
> >>>
> >>> JBrowse generally installs all it's perl dependencies to a folder
> inside
> >>> JBROWSE_ROOT/extlib
> >>>
> >>> I would try rm -rf extlib, maybe also ~/.cpanm and ~/.cpan, then re-run
> >>> setup.sh
> >>>
> >>> Here is a chat log of a user on our chat that also did these steps but
> it
> >>> was  on macOS
> >>>
> >>>> * nuke all traces of perl in /User (brew, .cpan, .cpanm etc.)
> >>>> * `sudo installer -pkg
> >>>
> >>
> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
> >>> -target` - allows  Extern_H compile problem to  pass
> >>>> * use `cpan` to `install JSON::XS` (for some reason the dependency
> won't
> >>> install during setup.sh)
> >>>> * run `setup.sh`
> >>>
> >>>
> >>>
> >>> -Colin
> >>>
> >>> On Wed, Jun 3, 2020 at 7:37 PM Zhiliang Hu <hu...@an...>
> wrote:
> >>>
> >>>> When I tried to load data to JBrowse, I got the following complain:
> >>>>
> >>>> Perl lib version (5.16.3) doesn't match executable
> >>>> '/home/apache/doc/jbrowse/bin/flatfile-to-json.pl' version (v5.30.0)
> at
> >>>> /usr/lib64/perl5/Config.pm line 60.
> >>>> Compilation failed in require at /usr/lib64/perl5/lib.pm line 6.
> >>>>
> >>>> In cpan I did "reload cpan" and "install lib" and it says:
> >>>>
> >>>>    lib is up to date (0.63)
> >>>>
> >>>> I am at a lost as how to update my "perl lib". Any advice please?
> >>>>
> >>>> Zhiliang
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> Gmod-ajax mailing list
> >>>> Gmo...@li...
> >>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> >>>>
> >>>
> >>
> >
>

Re: [Gmod-ajax] Perl lib version question

[Zhiliang Hu <hu...@an...>]

Thank you Colin!  This was an eye openning for me to cpanm... My ran of 
"cpanm Bio::Perl@1.7.2" seemed an success.

I was able to get rid of multiple "Segmentation fault (core dumped)" 
by changing the line in 'setup.sh' where perl was called with a full path: 
"have_db=`/usr/local/bin/perl -MConfig=myconfig -e".  The setup was a 
success!

Now I am getting "Segmentation fault (core dumped)" running 
"flatfile-to-json.pl", even after I changed its "#!/usr/bin/env perl" line
to "#!/usr/local/bin/perl".

Any suggestion please?

Zhiliang


On Tue, 14 Jul 2020, Colin wrote:

> Date: Tue, 14 Jul 2020 13:03:54 -0400
> From: Colin <col...@gm...>
> To: Zhiliang Hu <hu...@an...>
> Cc: gmod-ajax <gmo...@li...>
> Subject: Re: [Gmod-ajax] Perl lib version question
> 
> If you have cpanm installed globally on your system you can try to manually
> run this command
>
> cpanm Bio::Perl@1.7.2
>
> A similar thing can likely be done with the plain cpan executable also,
> possibly this
>
> cpan CJFIELDS/BioPerl-1.007002.tar.gz
>
>
> We require 1.7.2 because later versions really significantly modified the
> BioPerl ecosystem (see changelog here
> https://github.com/bioperl/bioperl-live/blob/master/Changes)
>
>
> -Colin
>
>
> On Tue, Jul 14, 2020 at 11:59 AM Zhiliang Hu <hu...@an...> wrote:
>
>>
>> Thanks Colin for addressing the issue.  I took the path to reinstall the
>> JBrowse.  As needed by new JBrowse, I installed perl 5.30 into the
>> /usr/local/bin/ location (my /usr/bin/ location has perl 5.16)
>>
>> My newly downloaded JBrowse setup.sh (at a location different from
>> previous installations; on a RedHat CentOS 7 system) got complains like:
>>
>> Installing Perl prerequisites ...
>> + bin/cpanm -v --notest -l extlib/ Bio::Perl@1.7.2
>> ./setup.sh: line 142: 10708 Segmentation fault      (core dumped)
>>
>> I understand it might be caused by multiple perl versions on my system but
>> by cleaning my shell environment PERLLIB/ PERL5LIB didn't help. I wonder
>> is there alternative ways to install "Bio::Perl@1.7.2" (actually which
>> modules?).
>>
>> I searched for old JBrowse troubleshooting and did:
>>> sudo yum groupinstall "Development Tools"
>>> sudo yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker
>> and it didn't help.
>>
>> Any further suggestion please? (I know on this RH Centos7 system there are
>> perl GD, Zlib, and libpng installed but how to make the JBrowse setup know
>> where they are?)
>>
>> Zhiliang
>>
>> On Wed, 3 Jun 2020, Colin wrote:
>>
>>> Date: Wed, 3 Jun 2020 20:34:24 -0400
>>> From: Colin <col...@gm...>
>>> To: Zhiliang Hu <hu...@an...>
>>> Cc: gmod-ajax <gmo...@li...>
>>> Subject: Re: [Gmod-ajax] Perl lib version question
>>>
>>> There have been a couple people experiencing this lately. I am not
>> exactly
>>> sure why, maybe it is related people who have older versions of jbrowse
>>> upgrading to perl 5.30+.
>>>
>>> JBrowse generally installs all it's perl dependencies to a folder inside
>>> JBROWSE_ROOT/extlib
>>>
>>> I would try rm -rf extlib, maybe also ~/.cpanm and ~/.cpan, then re-run
>>> setup.sh
>>>
>>> Here is a chat log of a user on our chat that also did these steps but it
>>> was  on macOS
>>>
>>>> * nuke all traces of perl in /User (brew, .cpan, .cpanm etc.)
>>>> * `sudo installer -pkg
>>>
>> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
>>> -target` - allows  Extern_H compile problem to  pass
>>>> * use `cpan` to `install JSON::XS` (for some reason the dependency won't
>>> install during setup.sh)
>>>> * run `setup.sh`
>>>
>>>
>>>
>>> -Colin
>>>
>>> On Wed, Jun 3, 2020 at 7:37 PM Zhiliang Hu <hu...@an...> wrote:
>>>
>>>> When I tried to load data to JBrowse, I got the following complain:
>>>>
>>>> Perl lib version (5.16.3) doesn't match executable
>>>> '/home/apache/doc/jbrowse/bin/flatfile-to-json.pl' version (v5.30.0) at
>>>> /usr/lib64/perl5/Config.pm line 60.
>>>> Compilation failed in require at /usr/lib64/perl5/lib.pm line 6.
>>>>
>>>> In cpan I did "reload cpan" and "install lib" and it says:
>>>>
>>>>    lib is up to date (0.63)
>>>>
>>>> I am at a lost as how to update my "perl lib". Any advice please?
>>>>
>>>> Zhiliang
>>>>
>>>>
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>
>>
>

Re: [Gmod-ajax] Perl lib version question

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

The "extlib" folder is inside of the jbrowse folder


-Colin

On Tue, Jul 14, 2020 at 1:04 PM Zhiliang Hu <hu...@an...> wrote:

> On Tue, 14 Jul 2020, Zhiliang Hu wrote:
>
> > Date: Tue, 14 Jul 2020 10:59:21 -0500 (CDT)
> > From: Zhiliang Hu <hu...@an...>
> > To: Colin <col...@gm...>
> > Cc: gmod-ajax <gmo...@li...>
> > Subject: Re: [Gmod-ajax] Perl lib version question
> >
> >
> > Thanks Colin for addressing the issue.  I took the path to reinstall the
> > JBrowse.  As needed by new JBrowse, I installed perl 5.30 into the
> > /usr/local/bin/ location (my /usr/bin/ location has perl 5.16)
> >
> > My newly downloaded JBrowse setup.sh (at a location different from
> previous
> > installations; on a RedHat CentOS 7 system) got complains like:
> >
> > Installing Perl prerequisites ...
> > + bin/cpanm -v --notest -l extlib/ Bio::Perl@1.7.2
> > ./setup.sh: line 142: 10708 Segmentation fault      (core dumped)
> >
> > I understand it might be caused by multiple perl versions on my system
> but by
> > cleaning my shell environment PERLLIB/ PERL5LIB didn't help. I wonder is
> > there alternative ways to install "Bio::Perl@1.7.2" (actually which
> > modules?).
> >
> > I searched for old JBrowse troubleshooting and did:
> >> sudo yum groupinstall "Development Tools"
> >> sudo yum install libpng-devel gd-devel zlib-devel
> perl-ExtUtils-MakeMaker
> > and it didn't help.
> >
> > Any further suggestion please? (I know on this RH Centos7 system there
> are
> > perl GD, Zlib, and libpng installed but how to make the JBrowse setup
> know
> > where they are?)
>
> By the way I did rm -rf ~/.cpanm and ~/.cpan, but don't know how to remove
> "extlib".  I also did 'install JSON::XS' with cpan.
>
> Zhiliang
>

Re: [Gmod-ajax] Perl lib version question

[Zhiliang Hu <hu...@an...>]

On Tue, 14 Jul 2020, Zhiliang Hu wrote:

> Date: Tue, 14 Jul 2020 10:59:21 -0500 (CDT)
> From: Zhiliang Hu <hu...@an...>
> To: Colin <col...@gm...>
> Cc: gmod-ajax <gmo...@li...>
> Subject: Re: [Gmod-ajax] Perl lib version question
> 
>
> Thanks Colin for addressing the issue.  I took the path to reinstall the 
> JBrowse.  As needed by new JBrowse, I installed perl 5.30 into the 
> /usr/local/bin/ location (my /usr/bin/ location has perl 5.16)
>
> My newly downloaded JBrowse setup.sh (at a location different from previous 
> installations; on a RedHat CentOS 7 system) got complains like:
>
> Installing Perl prerequisites ...
> + bin/cpanm -v --notest -l extlib/ Bio::Perl@1.7.2
> ./setup.sh: line 142: 10708 Segmentation fault      (core dumped)
>
> I understand it might be caused by multiple perl versions on my system but by 
> cleaning my shell environment PERLLIB/ PERL5LIB didn't help. I wonder is 
> there alternative ways to install "Bio::Perl@1.7.2" (actually which 
> modules?).
>
> I searched for old JBrowse troubleshooting and did:
>> sudo yum groupinstall "Development Tools"
>> sudo yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker
> and it didn't help.
>
> Any further suggestion please? (I know on this RH Centos7 system there are 
> perl GD, Zlib, and libpng installed but how to make the JBrowse setup know 
> where they are?)

By the way I did rm -rf ~/.cpanm and ~/.cpan, but don't know how to remove 
"extlib".  I also did 'install JSON::XS' with cpan.

Zhiliang

Re: [Gmod-ajax] Perl lib version question

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

If you have cpanm installed globally on your system you can try to manually
run this command

cpanm Bio::Perl@1.7.2

A similar thing can likely be done with the plain cpan executable also,
possibly this

cpan CJFIELDS/BioPerl-1.007002.tar.gz


We require 1.7.2 because later versions really significantly modified the
BioPerl ecosystem (see changelog here
https://github.com/bioperl/bioperl-live/blob/master/Changes)


-Colin


On Tue, Jul 14, 2020 at 11:59 AM Zhiliang Hu <hu...@an...> wrote:

>
> Thanks Colin for addressing the issue.  I took the path to reinstall the
> JBrowse.  As needed by new JBrowse, I installed perl 5.30 into the
> /usr/local/bin/ location (my /usr/bin/ location has perl 5.16)
>
> My newly downloaded JBrowse setup.sh (at a location different from
> previous installations; on a RedHat CentOS 7 system) got complains like:
>
> Installing Perl prerequisites ...
> + bin/cpanm -v --notest -l extlib/ Bio::Perl@1.7.2
> ./setup.sh: line 142: 10708 Segmentation fault      (core dumped)
>
> I understand it might be caused by multiple perl versions on my system but
> by cleaning my shell environment PERLLIB/ PERL5LIB didn't help. I wonder
> is there alternative ways to install "Bio::Perl@1.7.2" (actually which
> modules?).
>
> I searched for old JBrowse troubleshooting and did:
> > sudo yum groupinstall "Development Tools"
> > sudo yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker
> and it didn't help.
>
> Any further suggestion please? (I know on this RH Centos7 system there are
> perl GD, Zlib, and libpng installed but how to make the JBrowse setup know
> where they are?)
>
> Zhiliang
>
> On Wed, 3 Jun 2020, Colin wrote:
>
> > Date: Wed, 3 Jun 2020 20:34:24 -0400
> > From: Colin <col...@gm...>
> > To: Zhiliang Hu <hu...@an...>
> > Cc: gmod-ajax <gmo...@li...>
> > Subject: Re: [Gmod-ajax] Perl lib version question
> >
> > There have been a couple people experiencing this lately. I am not
> exactly
> > sure why, maybe it is related people who have older versions of jbrowse
> > upgrading to perl 5.30+.
> >
> > JBrowse generally installs all it's perl dependencies to a folder inside
> > JBROWSE_ROOT/extlib
> >
> > I would try rm -rf extlib, maybe also ~/.cpanm and ~/.cpan, then re-run
> > setup.sh
> >
> > Here is a chat log of a user on our chat that also did these steps but it
> > was  on macOS
> >
> >> * nuke all traces of perl in /User (brew, .cpan, .cpanm etc.)
> >> * `sudo installer -pkg
> >
> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
> > -target` - allows  Extern_H compile problem to  pass
> >> * use `cpan` to `install JSON::XS` (for some reason the dependency won't
> > install during setup.sh)
> >> * run `setup.sh`
> >
> >
> >
> > -Colin
> >
> > On Wed, Jun 3, 2020 at 7:37 PM Zhiliang Hu <hu...@an...> wrote:
> >
> >> When I tried to load data to JBrowse, I got the following complain:
> >>
> >> Perl lib version (5.16.3) doesn't match executable
> >> '/home/apache/doc/jbrowse/bin/flatfile-to-json.pl' version (v5.30.0) at
> >> /usr/lib64/perl5/Config.pm line 60.
> >> Compilation failed in require at /usr/lib64/perl5/lib.pm line 6.
> >>
> >> In cpan I did "reload cpan" and "install lib" and it says:
> >>
> >>    lib is up to date (0.63)
> >>
> >> I am at a lost as how to update my "perl lib". Any advice please?
> >>
> >> Zhiliang
> >>
> >>
> >> _______________________________________________
> >> Gmod-ajax mailing list
> >> Gmo...@li...
> >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> >>
> >
>

Re: [Gmod-ajax] Perl lib version question

[Zhiliang Hu <hu...@an...>]

Thanks Colin for addressing the issue.  I took the path to reinstall the 
JBrowse.  As needed by new JBrowse, I installed perl 5.30 into the 
/usr/local/bin/ location (my /usr/bin/ location has perl 5.16)

My newly downloaded JBrowse setup.sh (at a location different from 
previous installations; on a RedHat CentOS 7 system) got complains like:

Installing Perl prerequisites ...
+ bin/cpanm -v --notest -l extlib/ Bio::Perl@1.7.2
./setup.sh: line 142: 10708 Segmentation fault      (core dumped)

I understand it might be caused by multiple perl versions on my system but 
by cleaning my shell environment PERLLIB/ PERL5LIB didn't help. I wonder 
is there alternative ways to install "Bio::Perl@1.7.2" (actually which 
modules?).

I searched for old JBrowse troubleshooting and did:
> sudo yum groupinstall "Development Tools"
> sudo yum install libpng-devel gd-devel zlib-devel perl-ExtUtils-MakeMaker
and it didn't help.

Any further suggestion please? (I know on this RH Centos7 system there are 
perl GD, Zlib, and libpng installed but how to make the JBrowse setup know 
where they are?)

Zhiliang

On Wed, 3 Jun 2020, Colin wrote:

> Date: Wed, 3 Jun 2020 20:34:24 -0400
> From: Colin <col...@gm...>
> To: Zhiliang Hu <hu...@an...>
> Cc: gmod-ajax <gmo...@li...>
> Subject: Re: [Gmod-ajax] Perl lib version question
> 
> There have been a couple people experiencing this lately. I am not exactly
> sure why, maybe it is related people who have older versions of jbrowse
> upgrading to perl 5.30+.
>
> JBrowse generally installs all it's perl dependencies to a folder inside
> JBROWSE_ROOT/extlib
>
> I would try rm -rf extlib, maybe also ~/.cpanm and ~/.cpan, then re-run
> setup.sh
>
> Here is a chat log of a user on our chat that also did these steps but it
> was  on macOS
>
>> * nuke all traces of perl in /User (brew, .cpan, .cpanm etc.)
>> * `sudo installer -pkg
> /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
> -target` - allows  Extern_H compile problem to  pass
>> * use `cpan` to `install JSON::XS` (for some reason the dependency won't
> install during setup.sh)
>> * run `setup.sh`
>
>
>
> -Colin
>
> On Wed, Jun 3, 2020 at 7:37 PM Zhiliang Hu <hu...@an...> wrote:
>
>> When I tried to load data to JBrowse, I got the following complain:
>>
>> Perl lib version (5.16.3) doesn't match executable
>> '/home/apache/doc/jbrowse/bin/flatfile-to-json.pl' version (v5.30.0) at
>> /usr/lib64/perl5/Config.pm line 60.
>> Compilation failed in require at /usr/lib64/perl5/lib.pm line 6.
>>
>> In cpan I did "reload cpan" and "install lib" and it says:
>>
>>    lib is up to date (0.63)
>>
>> I am at a lost as how to update my "perl lib". Any advice please?
>>
>> Zhiliang
>>
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

[Gmod-ajax] Apollo 2.6.1 released

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

Apollo 2.6.1 has been released. 

Mostly a few infrastructure changes and minor bug fixes. 

https://github.com/GMOD/Apollo/releases/tag/2.6.1 <https://github.com/GMOD/Apollo/releases/tag/2.6.1>

Let us know if you have any issues here or via a GitHub issue https://github.com/GMOD/Apollo/issues <https://github.com/GMOD/Apollo/issues>

Cheers,

Apollo team

Re: [Gmod-ajax] Perl lib version question

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

There have been a couple people experiencing this lately. I am not exactly
sure why, maybe it is related people who have older versions of jbrowse
upgrading to perl 5.30+.

JBrowse generally installs all it's perl dependencies to a folder inside
JBROWSE_ROOT/extlib

I would try rm -rf extlib, maybe also ~/.cpanm and ~/.cpan, then re-run
setup.sh

Here is a chat log of a user on our chat that also did these steps but it
was  on macOS

> * nuke all traces of perl in /User (brew, .cpan, .cpanm etc.)
> * `sudo installer -pkg
/Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
-target` - allows  Extern_H compile problem to  pass
> * use `cpan` to `install JSON::XS` (for some reason the dependency won't
install during setup.sh)
> * run `setup.sh`



-Colin

On Wed, Jun 3, 2020 at 7:37 PM Zhiliang Hu <hu...@an...> wrote:

> When I tried to load data to JBrowse, I got the following complain:
>
> Perl lib version (5.16.3) doesn't match executable
> '/home/apache/doc/jbrowse/bin/flatfile-to-json.pl' version (v5.30.0) at
> /usr/lib64/perl5/Config.pm line 60.
> Compilation failed in require at /usr/lib64/perl5/lib.pm line 6.
>
> In cpan I did "reload cpan" and "install lib" and it says:
>
>    lib is up to date (0.63)
>
> I am at a lost as how to update my "perl lib". Any advice please?
>
> Zhiliang
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Perl lib version question

[Zhiliang Hu <hu...@an...>]

When I tried to load data to JBrowse, I got the following complain:

Perl lib version (5.16.3) doesn't match executable 
'/home/apache/doc/jbrowse/bin/flatfile-to-json.pl' version (v5.30.0) at 
/usr/lib64/perl5/Config.pm line 60.
Compilation failed in require at /usr/lib64/perl5/lib.pm line 6.

In cpan I did "reload cpan" and "install lib" and it says:

   lib is up to date (0.63)

I am at a lost as how to update my "perl lib". Any advice please?

Zhiliang

Re: [Gmod-ajax] [apollo] Command to display marker track in Apollo

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

Meant to link to this documentation page not localhost
https://jbrowse.org/docs/html_features.html  :)

-Colin

On Wed, Jun 3, 2020 at 1:02 PM Colin <col...@gm...> wrote:

> Here is a command I used to load triangle shaped markers with HTMLFeatures
> on JBrowse
>
>
> bin/flatfile-to-json.pl --bed here.bed --bed here.bed --out
> sample_data/json/volvox --trackLabel MyTrack --className "triangle hgred"
> --clientConfig '{"arrowheadClass":null}'
>
> http://localhost:3000/docs/html_features.html
>
> I had to manually pass clientConfig for arrowheadClass instead of
> --arrowheadClass because of setting null properly on it to disable the
> strand arrows
>
> Screenshot here
>
> [image: Screenshot from 2020-06-03 13-02-35.png]
>
>
> -Colin
>
>
> On Tue, Jun 2, 2020 at 10:36 AM Nathan Dunn <nat...@lb...> wrote:
>
>>
>> Abhjit,
>>
>> I am going to expand this to the JBrowse general mailing list as this is
>> more of a JBrowse question.
>>
>> I’ve never actually tried to do this specifically.
>>
>> If for some reason you get this to work in JBrowse, but not Apollo,
>> please let me know.
>>
>> Nathan
>>
>>
>>
>> On Jun 2, 2020, at 6:59 AM, Abhijit Sanyal <abh...@gm...>
>> wrote:
>>
>> Hello All,
>>
>> I would like to display markers on Apollo as tracks. I am still a novice
>> in using Apollo, so still learning the basics. I have the following command
>> for displaying gene tracks
>>
>> /app/Apollo/bin/flatfile-to-json.pl --gff /Apollo-TEMP/displayname.gff3
>> --arrowheadClass trellis-arrowhead --subfeatureClasses
>> '{"CDS":"pink-90pct", "five_prime_UTR":"purple-60pct",
>> "three_prime_UTR":"purple-60pct", "exon":"container-100pct"}' --className
>> container-16px --type mRNA --trackLabel Gene-Models --out
>> /apollo-annotation/genome/maize/Annot1/data/
>>
>> I would like to modify that to display SNP markers as arrowheads or
>> little triangles, and other genetic markers as rectangles, both magenta in
>> colour. I have gotten as far as below. Need a little help modifying the
>> rest of the code.
>>
>> /app/Apollo/bin/flatfile-to-json.pl --gff
>> /Apollo-TEMP/gsap645_markers.gff3 --arrowheadClass trellis-arrowhead
>> --className ?? --type genetic_marker --key blast --subfeatureClasses
>> '{"??"}' --trackLabel GENETIC-MARKER --out
>> /apollo-annotation/genome/maize/Annot1/data/
>>
>> The "??" are the places where I do not know what value to put, in order
>> to get the desired effect of triangle or a rectangle. Also I do not know
>> where to specify the color. Thank you for your help
>>
>> -Abhijit
>>
>>
>> --
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to apo...@lb....
>>
>

Re: [Gmod-ajax] [apollo] Command to display marker track in Apollo

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

Here is a command I used to load triangle shaped markers with HTMLFeatures
on JBrowse


bin/flatfile-to-json.pl --bed here.bed --bed here.bed --out
sample_data/json/volvox --trackLabel MyTrack --className "triangle hgred"
--clientConfig '{"arrowheadClass":null}'

http://localhost:3000/docs/html_features.html

I had to manually pass clientConfig for arrowheadClass instead of
--arrowheadClass because of setting null properly on it to disable the
strand arrows

Screenshot here

[image: Screenshot from 2020-06-03 13-02-35.png]


-Colin


On Tue, Jun 2, 2020 at 10:36 AM Nathan Dunn <nat...@lb...> wrote:

>
> Abhjit,
>
> I am going to expand this to the JBrowse general mailing list as this is
> more of a JBrowse question.
>
> I’ve never actually tried to do this specifically.
>
> If for some reason you get this to work in JBrowse, but not Apollo, please
> let me know.
>
> Nathan
>
>
>
> On Jun 2, 2020, at 6:59 AM, Abhijit Sanyal <abh...@gm...> wrote:
>
> Hello All,
>
> I would like to display markers on Apollo as tracks. I am still a novice
> in using Apollo, so still learning the basics. I have the following command
> for displaying gene tracks
>
> /app/Apollo/bin/flatfile-to-json.pl --gff /Apollo-TEMP/displayname.gff3
> --arrowheadClass trellis-arrowhead --subfeatureClasses
> '{"CDS":"pink-90pct", "five_prime_UTR":"purple-60pct",
> "three_prime_UTR":"purple-60pct", "exon":"container-100pct"}' --className
> container-16px --type mRNA --trackLabel Gene-Models --out
> /apollo-annotation/genome/maize/Annot1/data/
>
> I would like to modify that to display SNP markers as arrowheads or little
> triangles, and other genetic markers as rectangles, both magenta in colour.
> I have gotten as far as below. Need a little help modifying the rest of the
> code.
>
> /app/Apollo/bin/flatfile-to-json.pl --gff
> /Apollo-TEMP/gsap645_markers.gff3 --arrowheadClass trellis-arrowhead
> --className ?? --type genetic_marker --key blast --subfeatureClasses
> '{"??"}' --trackLabel GENETIC-MARKER --out
> /apollo-annotation/genome/maize/Annot1/data/
>
> The "??" are the places where I do not know what value to put, in order to
> get the desired effect of triangle or a rectangle. Also I do not know where
> to specify the color. Thank you for your help
>
> -Abhijit
>
>
> --
> To unsubscribe from this group and stop receiving emails from it, send an
> email to apo...@lb....
>