gmod-ajax — JBrowse list

Re: [Gmod-ajax] [apollo] Errors when running ucsc-to-json.pl script

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

In general ucsc-to-json doesn't have the capability to load all types of
tracks from the UCSC database


For the phyloP i'd use a bigwig file
http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phyloP100way/

For the mrna track that gives a PSL error, I am not sure which track this
refers to as no track is named mrna in the UCSC database there (e.g. no
mrna.sql or mrna.txt.gz)
If needed though, probably would need to convert the PSL to some gff type
thing or bigBed, similar to the other thread. bigPsl is an option, it is
just a particular type of bigBed, and then load as bigBed (won't display
all the alignments in the PSL but might help enough)


-Colin

On Tue, Nov 17, 2020 at 5:55 AM smm <sm...@eb...> wrote:

> Hello,
>
> Thanks. I have increased ulimit as suggested. I will let you know if it
> worked. In the meantime, running these commands raise an error-
>
> ~/web-apollo-test-server/Apollo-2.6.1/bin/ucsc-to-json.pl --in source_loc
> --track mrna --out dest_loc
>
> Cannot convert mrna track; this script is not capable of handling psl
> tracks.
>  at
> /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm
> line 7.
>     Bio::JBrowse::ConfigurationManager::__ANON__("Cannot convert mrna
> track; this script is not capable of hand"...) called at
> /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/bin/
> ucsc-to-json.pl line 202
>
> ~/web-apollo-test-server/Apollo-2.6.1/bin/ucsc-to-json.pl --in source_loc
> --track phyloP100way --out dest_loc
>
> Cannot convert phyloP100way track; this script is not capable of handling
> wig tracks.
>  at
> /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm
> line 7.
>     Bio::JBrowse::ConfigurationManager::__ANON__("Cannot convert
> phyloP100way track; this script is not capable"...) called at
> /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/bin/
> ucsc-to-json.pl line 202
>
> I have downloaded the .sql and .txt files from here-
> http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/. Please let me
> know if I should set some flag or if there is some other way to load UCSC
> MySQL database.
>
> Regards,
> Shamika
>
> On 16/11/2020 16:35, Nathan Dunn wrote:
>
> If you type in the
>
> ulimit -n
>
> command what do you see?
>
> My guess is that this needs to be upped.  Ulimit -n 10000 e.g.,
>
>
> http://gmod.827538.n3.nabble.com/Gmod-ajax-restrict-zoom-level-tp4042205p4043034.html
>
>
>
> Nathan
>
>
> On Nov 16, 2020, at 7:47 AM, Shamika Mohanan <sm...@eb...> wrote:
>
> Hello,
>
> When trying to load data from
> http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/
> using Apollo-2.6.1/bin/ucsc-to-json.pl script, I get errors like
>
> Cannot convert gwipsvizRiboseq track; this script is not capable of
> handling bigWig tracks.
> (or)
> Cannot convert phyloP100way track; this script is not capable of handling
> wig tracks.
> (or)
> Cannot convert mrna track; this script is not capable of handling psl
> tracks.
> (or)
> couldn't open /tmp/0FT2Jm8Ge5.sort: Too many open files
>  at /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/bin/
> ucsc-to-json.pl line 286.
>  at
> /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm
> line 7.
> Bio::JBrowse::ConfigurationManager::__ANON__("couldn't open
> /tmp/0FT2Jm8Ge5.sort: Too many open files\x{a} at /"...) called at
> /usr/share/perl/5.22/Carp.pm line 166
> Carp::croak("couldn't open /tmp/0FT2Jm8Ge5.sort: Too many open
> files\x{a}") called at
> /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/jbrowse/bin/../src/perl5/Bio/JBrowse/ExternalSorter.pm
> line 98
> Bio::JBrowse::ExternalSorter::finish(Bio::JBrowse::ExternalSorter=HASH(0x2e4efe0))
> called at
> /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/bin/
> ucsc-to-json.pl line 286
>
> The final error was seen when loading a large file. Is there a way to get
> past these errors?
>
> Regards,
> Shamika
>
>
>
> --
> To unsubscribe from this group and stop receiving emails from it, send an
> email to apo...@lb....
>

Re: [Gmod-ajax] [apollo] Issues with data visualisation on Apollo

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

Hi there,

This is an interesting thread, basically it appears you want to make some
hg38 type instance for JBrowse data. It might be nice if this was just
already available so that it didn't require a lot of legwork but certainly
happy to help here (we do have one here but I think it could be better
organized http://hg38.jbrowse.org/)

Here is a short summary of some options based on the files you listed

>Capture_seq gencode_pasa_Captureseq_2.pasa_assemblies.gtf
/nfs/production/panda/ensembl/havana/warehouse_th_group/jmg/long_read_pipeline/Capture_seq_2/gencode_pasa_Captureseq_2.pasa_assemblies.gtf.gz
GTF

Convert the gtf to gff, and load with flatfile-to-json (or use gff3tabix,
but I'd suggest flatfile-to-json probably)

Here is one option for how to convert gtf to gff
https://jbrowse.org/docs/faq.html#how-do-i-convert-gtf-to-gff

>GENCODE gencode.v35.annotation.gff3
ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_35/gencode.v35.annotation.gtf.gz
GFF3

Load with flatfile-to-json --gff

>GENCODE_Ensembl Homo_sapiens.GRCh38.101.gff3
ftp://ftp.ensembl.org/pub/release-101/gff3/homo_sapiens/Homo_sapiens.GRCh38.101.gff3.gz
GFF3

Load with flatfile-to-json --gff

>RefSeq hg38.ncbiRefSeq.gtf
http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/hg38.ncbiRefSeq.gtf.gz
GTF

Probably convert gtf to gff, and then load with flatfile-to-json

Note that another option is to convert to bigBed. First gtfToGenePred and
then https://gist.github.com/gireeshkbogu/f478ad8495dca56545746cd391615b93

If you want a searchable gene names though, suggest using flatfile-to-json

>RefSeq_GRCh38 GRCh38_latest_genomic.gff
ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.gff.gz
GFF

This one is tricky because it uses NCBI refnames so you'll have to convert
them to chr1, chr2, etc. from NC_000001.11 etc.

>SLRseq_2 SLRseq.GRCh38.gtf
/nfs/production/panda/ensembl/havana/warehouse_th_group/jmg/long_read_pipeline/SLRseq_2/SLRseq.GRCh38.gtf.gz
GTF

Probably convert to gff3, load with flatfile-to-json

>SLRseq_merged SLRseq_merged.bam
ftp://ftp.ebi.ac.uk/pub/databases/havana/ngs_havana/havana/SLRseq/human/SLRseq_merged.bam
//
ftp://ftp.ebi.ac.uk/pub/databases/havana/ngs_havana/havana/SLRseq/human/SLRseq_merged.bam.bai
BAM

Manually download the BAM and BAI into your data folder, and edit it into
tracks.conf with a text editor, don't have a great add track workflow for
BAM files

[tracks.SLRseq_merged_bam]
urlTemplate=SLRseq_merged.bam

That is all that is needed for your config

>UCSC_MANE mane.0.9.bed
https://hgdownload.soe.ucsc.edu/gbdb/hg38/mane/mane.0.9.ix //
https://hgdownload.soe.ucsc.edu/gbdb/hg38/mane/mane.0.9.ixx //
https://hgdownload.soe.ucsc.edu/gbdb/hg38/mane/mane.0.9.bb BigBed -> BED

You can do two things

1) load this as is in bigBed format. Manually edit this into your
tracks.conf file with a text editor, the bigBed is natively supported

[tracks.MANE]
key=MANE 0.9 BigBed
urlTemplate=mane.0.9.bb

2) convert to gff, load with flatfile-to-json

Note that the trix index (ix and ixx) are not able to be used by jbrowse
currently (that would allow searching for genes in the bigBed files) so if
you want searchable gene names, convert to gff, use flatfile-to-json

>UCSC_ncbiRefSeqOther ncbiRefSeqOther.bed
https://hgdownload.soe.ucsc.edu/gbdb/hg38/ncbiRefSeq/ncbiRefSeqOther.bb
BigBed -> BED

Manually download this into your tracks.conf file with a text editor, the
bigBed is natively supported

[tracks.ncbiRefSeqOther]
key=NCBI RefSeq (other) BigBed
urlTemplate=ncbiRefSeqOther.bb


>UNIPROT UP000005640_9606_proteome.bed
ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/knowledgebase/genome_annotation_tracks/UP000005640_9606_beds/UP000005640_9606_proteome.bed
BED

Convert to bigBed or GFF. The extra columns are not loaded if using
flatfile-to-json.pl --bed

>gtexGene --
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/gtexGene.sql //
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/gtexGene.txt.gz SQL

Use ucsc-to-json.pl with these "database" files

>unipAliSwissprot unipAliSwissprot.bed

Convert to bigBed or GFF, extra columns will not be loaded



-Colin



On Tue, Nov 17, 2020 at 1:35 PM Nathan Dunn <nat...@lb...> wrote:

>
> Shamika,
>
> I don’t know the exact answer to your question, but usually you have to
> supply a —type argument to process the top-level information you want to
> display, so you could potentially put in multiple tracks.
>
> e.g., for just coding genes:
>
> ~/web-apollo-test-server/Apollo-2.6.1/bin/flatfile-to-json.pl --gff
> GRCh38_latest_genomic.gff —type mRNA --trackLabel RefSeq_GRCh38_mRNA --out
> dest_loc
>
>
> For multiple types, from the script itself you get:
>
> =item --type <feature types to process>
>
> Only process features of the given type.  Can take either single type
> names, e.g. "mRNA", or type names qualified by "source" name, for
> whatever definition of "source" your data file might have.  For
> example, "mRNA:exonerate" will filter for only mRNA features that have
> a source of "exonerate".
>
> Multiple type names can be specified by separating the type names with
> commas, e.g. C<--type mRNA:exonerate,ncRNA>.
>
> Might be easier to play with a small scaffold at first until you get what
> you want.
>
> Someone on the gmod-ajax panel will likely know more than me about the
> UCSC piece.
>
> Nathan
>
>
> On Nov 17, 2020, at 2:33 AM, smm <sm...@eb...> wrote:
>
> Hello,
>
> These are three example commands that I have run. None of them show any
> error. But the visualization is not ideal on Apollo.
>
> 1. GFF
> ~/web-apollo-test-server/Apollo-2.6.1/bin/flatfile-to-json.pl --gff
> GRCh38_latest_genomic.gff --trackLabel RefSeq_GRCh38 --out dest_loc
>
> 2. BigBED to BED
> ./bigBedToBed mane.0.9.bb mane.0.9.bed
> ~/web-apollo-test-server/Apollo-2.6.1/bin/flatfile-to-json.pl --bed
> mane.0.9.bed --trackLabel UCSC_MANE --out dest_loc
>
> 3. SQL
> ~/web-apollo-test-server/Apollo-2.6.1/bin/ucsc-to-json.pl --in source_loc
> --track gtexGene --out dest_loc
>
> Please let me know if you require any other information. The source for
> each file is available here-
> https://docs.google.com/spreadsheets/d/1l_O-GYGqyU6Sk9hBSWFwp-ehjr0RAQndpylnYOrzmzA/edit?usp=sharing
>
> Regards,
> Shamika
>
> On 16/11/2020 16:41, Nathan Dunn wrote:
>
>
> I’d have to see the individual data and commands you were using for each.
>
> More info can be found here https://jbrowse.org/docs/html_features.html and
> here https://jbrowse.org/docs/flatfile-to-json.pl.html
>
> That being said, it LOOKS like the filter you are running is for genes,
> where typically the top-level should be mRNA (for your working attachment),
> but that is just a guess.
>
> If you provide a snippet, command, and output I can provide some more
> direct feedback.
>
> Nathan
>
>
>
> On Nov 16, 2020, at 7:26 AM, Shamika Mohanan <sm...@eb...> wrote:
>
> Hello,
>
> I am trying to load GFF/GTF/BED/BigBED/BAM/UCSC SQL files using the
> command line scripts available in Apollo-2.6.1/bin.
>
> Most files load properly and are available on Apollo as seen in
> attachment_1. There are few files that do load but do not display the data
> properly as seen in attachment_2.
>
> I have listed the files that show this problem here-
> https://docs.google.com/spreadsheets/d/1l_O-GYGqyU6Sk9hBSWFwp-ehjr0RAQndpylnYOrzmzA/edit?usp=sharing
>
> Should I set some option when running the scripts?
>
> Regards,
> Shamika
> <attachment_2.png><attachment_1.png>
>
>
> --
> To unsubscribe from this group and stop receiving emails from it, send an
> email to apo...@lb....
>

Re: [Gmod-ajax] [apollo] Issues with data visualisation on Apollo

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

Shamika,

I don’t know the exact answer to your question, but usually you have to supply a —type argument to process the top-level information you want to display, so you could potentially put in multiple tracks. 

e.g., for just coding genes:

> ~/web-apollo-test-server/Apollo-2.6.1/bin/flatfile-to-json.pl --gff GRCh38_latest_genomic.gff —type mRNA --trackLabel RefSeq_GRCh38_mRNA --out dest_loc


For multiple types, from the script itself you get:

=item --type <feature types to process>

Only process features of the given type.  Can take either single type
names, e.g. "mRNA", or type names qualified by "source" name, for
whatever definition of "source" your data file might have.  For
example, "mRNA:exonerate" will filter for only mRNA features that have
a source of "exonerate".

Multiple type names can be specified by separating the type names with
commas, e.g. C<--type mRNA:exonerate,ncRNA>.

Might be easier to play with a small scaffold at first until you get what you want. 

Someone on the gmod-ajax panel will likely know more than me about the UCSC piece. 

Nathan


> On Nov 17, 2020, at 2:33 AM, smm <sm...@eb...> wrote:
> 
> Hello,
> 
> These are three example commands that I have run. None of them show any error. But the visualization is not ideal on Apollo.
> 
> 1. GFF
> ~/web-apollo-test-server/Apollo-2.6.1/bin/flatfile-to-json.pl --gff GRCh38_latest_genomic.gff --trackLabel RefSeq_GRCh38 --out dest_loc
> 
> 2. BigBED to BED
> ./bigBedToBed mane.0.9.bb mane.0.9.bed
> ~/web-apollo-test-server/Apollo-2.6.1/bin/flatfile-to-json.pl --bed mane.0.9.bed --trackLabel UCSC_MANE --out dest_loc
> 
> 3. SQL
> ~/web-apollo-test-server/Apollo-2.6.1/bin/ucsc-to-json.pl --in source_loc --track gtexGene --out dest_loc
> 
> Please let me know if you require any other information. The source for each file is available here- https://docs.google.com/spreadsheets/d/1l_O-GYGqyU6Sk9hBSWFwp-ehjr0RAQndpylnYOrzmzA/edit?usp=sharing <https://docs.google.com/spreadsheets/d/1l_O-GYGqyU6Sk9hBSWFwp-ehjr0RAQndpylnYOrzmzA/edit?usp=sharing>
> 
> Regards,
> Shamika
> 
> On 16/11/2020 16:41, Nathan Dunn wrote:
>> 
>> I’d have to see the individual data and commands you were using for each.
>> 
>> More info can be found here https://jbrowse.org/docs/html_features.html <https://jbrowse.org/docs/html_features.html> and here https://jbrowse.org/docs/flatfile-to-json.pl.html <https://jbrowse.org/docs/flatfile-to-json.pl.html> 
>> 
>> That being said, it LOOKS like the filter you are running is for genes, where typically the top-level should be mRNA (for your working attachment), but that is just a guess. 
>> 
>> If you provide a snippet, command, and output I can provide some more direct feedback. 
>> 
>> Nathan
>> 
>> 
>> 
>>> On Nov 16, 2020, at 7:26 AM, Shamika Mohanan <sm...@eb... <mailto:sm...@eb...>> wrote:
>>> 
>>> Hello,
>>> 
>>> I am trying to load GFF/GTF/BED/BigBED/BAM/UCSC SQL files using the command line scripts available in Apollo-2.6.1/bin. 
>>> 
>>> Most files load properly and are available on Apollo as seen in attachment_1. There are few files that do load but do not display the data properly as seen in attachment_2. 
>>> 
>>> I have listed the files that show this problem here- https://docs.google.com/spreadsheets/d/1l_O-GYGqyU6Sk9hBSWFwp-ehjr0RAQndpylnYOrzmzA/edit?usp=sharing <https://docs.google.com/spreadsheets/d/1l_O-GYGqyU6Sk9hBSWFwp-ehjr0RAQndpylnYOrzmzA/edit?usp=sharing>
>>> 
>>> Should I set some option when running the scripts?
>>> 
>>> Regards,
>>> Shamika
>>> <attachment_2.png><attachment_1.png>

Re: [Gmod-ajax] JBrowse2 config.json

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

Sounds good! These are very valuable comments. Thanks!

On Tue, Nov 17, 2020 at 11:03 AM Colin <col...@gm...> wrote:

> In general we do allow and encourage putting multiple genome assemblies in
> a single config.json.for jbrowse 2. Then each track specifies which
> assembly each track belongs to (or for synteny tracks, which assemblies
> [plural] it belongs to)
>
>
>
> In Jbrowse 2 we allow ?config= so you could have multiple unrelated
> configs but we have not made the "include" system of jbrowse 1 that lets
> you merge multiple configs though.
>
> If this is seems important to separate things out, let us know but single
> config.json containing multiple assemblies is the current concept :)
>
> -Colin
>
> On Mon, Nov 16, 2020, 10:28 AM Ke Jiang <bio...@gm...> wrote:
>
>> Hi,
>>
>> I've been playing with JBrowse2 first release for a few days. In
>> JBorwse (1), I've been using a strategy to separate configuration and data
>> for multiple genomes by creating config.json for each genome (and pointing
>> data to the corresponding genomic data). It worked pretty well as it
>> reduced chances of messing up other genomes while making changes to one
>> genome. I noticed for JBrowse2, there is a master config.json sitting in
>> the JBrowe2 folder and we lay out multiple genomes and assemblies in it. Is
>> this the way to manage multiple genomes in JBrowse2 now? Because JBrowse2
>> has to consider the multiple genome view for synteny, so everything has to
>> be in one single config.json? Or more generally, what is the general idea
>> (or best practices?) of handling multiple organisms in JBrowse2?
>>
>> Thanks again for the development of JBrowse 2! It is truly exciting to
>> see it!
>>
>> Ke
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] JBrowse2 config.json

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

In general we do allow and encourage putting multiple genome assemblies in
a single config.json.for jbrowse 2. Then each track specifies which
assembly each track belongs to (or for synteny tracks, which assemblies
[plural] it belongs to)



In Jbrowse 2 we allow ?config= so you could have multiple unrelated configs
but we have not made the "include" system of jbrowse 1 that lets you merge
multiple configs though.

If this is seems important to separate things out, let us know but single
config.json containing multiple assemblies is the current concept :)

-Colin

On Mon, Nov 16, 2020, 10:28 AM Ke Jiang <bio...@gm...> wrote:

> Hi,
>
> I've been playing with JBrowse2 first release for a few days. In
> JBorwse (1), I've been using a strategy to separate configuration and data
> for multiple genomes by creating config.json for each genome (and pointing
> data to the corresponding genomic data). It worked pretty well as it
> reduced chances of messing up other genomes while making changes to one
> genome. I noticed for JBrowse2, there is a master config.json sitting in
> the JBrowe2 folder and we lay out multiple genomes and assemblies in it. Is
> this the way to manage multiple genomes in JBrowse2 now? Because JBrowse2
> has to consider the multiple genome view for synteny, so everything has to
> be in one single config.json? Or more generally, what is the general idea
> (or best practices?) of handling multiple organisms in JBrowse2?
>
> Thanks again for the development of JBrowse 2! It is truly exciting to see
> it!
>
> Ke
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] [apollo] Errors when running ucsc-to-json.pl script

[smm <sm...@eb...>]

Hello,

Thanks. I have increased ulimit as suggested. I will let you know if it 
worked. In the meantime, running these commands raise an error-

~/web-apollo-test-server/Apollo-2.6.1/bin/ucsc-to-json.pl --in 
source_loc --track mrna --out dest_loc

Cannot convert mrna track; this script is not capable of handling psl 
tracks.
  at 
/home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm 
line 7.
     Bio::JBrowse::ConfigurationManager::__ANON__("Cannot convert mrna 
track; this script is not capable of hand"...) called at 
/home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/bin/ucsc-to-json.pl 
line 202

~/web-apollo-test-server/Apollo-2.6.1/bin/ucsc-to-json.pl --in 
source_loc --track phyloP100way --out dest_loc

Cannot convert phyloP100way track; this script is not capable of 
handling wig tracks.
  at 
/home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm 
line 7.
     Bio::JBrowse::ConfigurationManager::__ANON__("Cannot convert 
phyloP100way track; this script is not capable"...) called at 
/home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/bin/ucsc-to-json.pl 
line 202

I have downloaded the .sql and .txt files from here- 
http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/. Please let me 
know if I should set some flag or if there is some other way to load 
UCSC MySQL database.

Regards,
Shamika

On 16/11/2020 16:35, Nathan Dunn wrote:
> If you type in the
>
> ulimit -n
>
> command what do you see?
>
> My guess is that this needs to be upped.  Ulimit -n 10000 e.g.,
>
> http://gmod.827538.n3.nabble.com/Gmod-ajax-restrict-zoom-level-tp4042205p4043034.html
>
>
>
> Nathan
>
>
>> On Nov 16, 2020, at 7:47 AM, Shamika Mohanan <sm...@eb... 
>> <mailto:sm...@eb...>> wrote:
>>
>> Hello,
>>
>> When trying to load data from
>> http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/
>> using Apollo-2.6.1/bin/ucsc-to-json.pl script, I get errors like
>>
>> Cannot convert gwipsvizRiboseq track; this script is not capable of 
>> handling bigWig tracks.
>> (or)
>> Cannot convert phyloP100way track; this script is not capable of 
>> handling wig tracks.
>> (or)
>> Cannot convert mrna track; this script is not capable of handling psl 
>> tracks.
>> (or)
>> couldn't open /tmp/0FT2Jm8Ge5.sort: Too many open files
>>  at 
>> /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/bin/ucsc-to-json.pl 
>> line 286.
>>  at 
>> /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm 
>> line 7.
>> Bio::JBrowse::ConfigurationManager::__ANON__("couldn't open 
>> /tmp/0FT2Jm8Ge5.sort: Too many open files\x{a} at /"...) called at 
>> /usr/share/perl/5.22/Carp.pm line 166
>> Carp::croak("couldn't open /tmp/0FT2Jm8Ge5.sort: Too many open 
>> files\x{a}") called at 
>> /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/jbrowse/bin/../src/perl5/Bio/JBrowse/ExternalSorter.pm 
>> line 98
>> Bio::JBrowse::ExternalSorter::finish(Bio::JBrowse::ExternalSorter=HASH(0x2e4efe0)) 
>> called at 
>> /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/bin/ucsc-to-json.pl 
>> line 286
>>
>> The final error was seen when loading a large file. Is there a way to 
>> get past these errors?
>>
>> Regards,
>> Shamika
>

Re: [Gmod-ajax] [apollo] Issues with data visualisation on Apollo

[smm <sm...@eb...>]

Hello,

These are three example commands that I have run. None of them show any 
error. But the visualization is not ideal on Apollo.

1. GFF
~/web-apollo-test-server/Apollo-2.6.1/bin/flatfile-to-json.pl --gff 
GRCh38_latest_genomic.gff --trackLabel RefSeq_GRCh38 --out dest_loc

2. BigBED to BED
./bigBedToBed mane.0.9.bb mane.0.9.bed
~/web-apollo-test-server/Apollo-2.6.1/bin/flatfile-to-json.pl --bed 
mane.0.9.bed --trackLabel UCSC_MANE --out dest_loc

3. SQL
~/web-apollo-test-server/Apollo-2.6.1/bin/ucsc-to-json.pl --in 
source_loc --track gtexGene --out dest_loc

Please let me know if you require any other information. The source for 
each file is available here- 
https://docs.google.com/spreadsheets/d/1l_O-GYGqyU6Sk9hBSWFwp-ehjr0RAQndpylnYOrzmzA/edit?usp=sharing

Regards,
Shamika

On 16/11/2020 16:41, Nathan Dunn wrote:
>
> I’d have to see the individual data and commands you were using for each.
>
> More info can be found here 
> https://jbrowse.org/docs/html_features.html and here 
> https://jbrowse.org/docs/flatfile-to-json.pl.html
>
> That being said, it LOOKS like the filter you are running is for 
> genes, where typically the top-level should be mRNA (for your working 
> attachment), but that is just a guess.
>
> If you provide a snippet, command, and output I can provide some more 
> direct feedback.
>
> Nathan
>
>
>
>> On Nov 16, 2020, at 7:26 AM, Shamika Mohanan <sm...@eb... 
>> <mailto:sm...@eb...>> wrote:
>>
>> Hello,
>>
>> I am trying to load GFF/GTF/BED/BigBED/BAM/UCSC SQL files using the 
>> command line scripts available in Apollo-2.6.1/bin.
>>
>> Most files load properly and are available on Apollo as seen in 
>> attachment_1. There are few files that do load but do not display the 
>> data properly as seen in attachment_2.
>>
>> I have listed the files that show this problem here- 
>> https://docs.google.com/spreadsheets/d/1l_O-GYGqyU6Sk9hBSWFwp-ehjr0RAQndpylnYOrzmzA/edit?usp=sharing
>>
>> Should I set some option when running the scripts?
>>
>> Regards,
>> Shamika
>> <attachment_2.png><attachment_1.png>
>

Re: [Gmod-ajax] JBrowse2 config.json

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

Hi Ke,

There aren't any well-worn best practices yet with JBrowse 2, since it's so
new. JBrowse-web actually can be pointed at different configuration files
using a URL query param similar to how JBrowse 1 was, the form of that
looks like `https://my.jbrowse/?config=url/to/myconfig.json`

It doesn't support "include" in configuration files like JBrowse 1 did,
however.

Thanks for being one of the early users! We've got a team of developers
working on it every day, and you can very much influence how it develops.
We're always very interested to hear about what works well, doesn't work,
and how you end up using it!

Rob


On Mon, Nov 16, 2020 at 7:28 AM Ke Jiang <bio...@gm...> wrote:

> Hi,
>
> I've been playing with JBrowse2 first release for a few days. In
> JBorwse (1), I've been using a strategy to separate configuration and data
> for multiple genomes by creating config.json for each genome (and pointing
> data to the corresponding genomic data). It worked pretty well as it
> reduced chances of messing up other genomes while making changes to one
> genome. I noticed for JBrowse2, there is a master config.json sitting in
> the JBrowe2 folder and we lay out multiple genomes and assemblies in it. Is
> this the way to manage multiple genomes in JBrowse2 now? Because JBrowse2
> has to consider the multiple genome view for synteny, so everything has to
> be in one single config.json? Or more generally, what is the general idea
> (or best practices?) of handling multiple organisms in JBrowse2?
>
> Thanks again for the development of JBrowse 2! It is truly exciting to see
> it!
>
> Ke
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] [apollo] Issues with data visualisation on Apollo

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

I’d have to see the individual data and commands you were using for each.

More info can be found here https://jbrowse.org/docs/html_features.html <https://jbrowse.org/docs/html_features.html> and here https://jbrowse.org/docs/flatfile-to-json.pl.html <https://jbrowse.org/docs/flatfile-to-json.pl.html> 

That being said, it LOOKS like the filter you are running is for genes, where typically the top-level should be mRNA (for your working attachment), but that is just a guess. 

If you provide a snippet, command, and output I can provide some more direct feedback. 

Nathan



> On Nov 16, 2020, at 7:26 AM, Shamika Mohanan <sm...@eb...> wrote:
> 
> Hello,
> 
> I am trying to load GFF/GTF/BED/BigBED/BAM/UCSC SQL files using the command line scripts available in Apollo-2.6.1/bin. 
> 
> Most files load properly and are available on Apollo as seen in attachment_1. There are few files that do load but do not display the data properly as seen in attachment_2. 
> 
> I have listed the files that show this problem here- https://docs.google.com/spreadsheets/d/1l_O-GYGqyU6Sk9hBSWFwp-ehjr0RAQndpylnYOrzmzA/edit?usp=sharing
> 
> Should I set some option when running the scripts?
> 
> Regards,
> Shamika
> <attachment_2.png><attachment_1.png>

Re: [Gmod-ajax] [apollo] Scripts get killed

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

Going cross-post to the JBrowse list for questions 1 and 2 and answer what I can in-line.

In general, there may be issues with the way the perl libraries are included.  

It might work better using the jbrowse/bin instead or just downloading JBrowse separately to run the commands http://github.com/GMOD/jbrowse <http://github.com/GMOD/jbrowse> after running the setup script (should be identical in the Apollo-2.6.1/jbrowse/bin directory) , but I am just guessing. 

Nathan


> On Nov 16, 2020, at 7:49 AM, Shamika Mohanan <sm...@eb...> wrote:
> 
> Hello,
> 
> 1. Is there a nice way to handle loading really large data files? When trying to load ftp://ftp.ensembl.org/pub/release-101/regulation/homo_sapiens/MotifFeatures/Homo_sapiens.GRCh38.motif_features.gff.gz
> the process gets killed. 

Are you talking about using flatfile-to-json.pl. ? 

Can you post the command you ran and the output and any other relevant details?  

> 
> 2. When running Apollo-2.6.1/bin/generate-names.pl, the process gets killed. The script used to work earlier but now it gets killed. Is this because size of data it now has to process? 

Same as above.  This is a jbrowse command.


> 3. When running Apollo-2.6.1/tools/data/add_features_from_gff3_to_annotations.pl, the process gets killed. This script has never worked. Is there a specific reason the process would be killed?

Not sure.  My guess is that it has to do with Perl libraries.   I’ve run these using docker on the Mac as getting perl to function properly there is such a pain. 

That being said, I’ve mostly been working in PIP.  You might try loading GFF3 from here instead as we’ve been more actively maintaining that:

https://pypi.org/project/apollo/ <https://pypi.org/project/apollo/>

Nathan

> 
> Regards,
> Shamika
> 

Re: [Gmod-ajax] [apollo] Errors when running ucsc-to-json.pl script

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

If you type in the 

ulimit -n

command what do you see? 

My guess is that this needs to be upped.  Ulimit -n 10000 e.g., 

http://gmod.827538.n3.nabble.com/Gmod-ajax-restrict-zoom-level-tp4042205p4043034.html <http://gmod.827538.n3.nabble.com/Gmod-ajax-restrict-zoom-level-tp4042205p4043034.html>



Nathan


> On Nov 16, 2020, at 7:47 AM, Shamika Mohanan <sm...@eb...> wrote:
> 
> Hello,
> 
> When trying to load data from 
> http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/ 
> using Apollo-2.6.1/bin/ucsc-to-json.pl script, I get errors like 
> 
> Cannot convert gwipsvizRiboseq track; this script is not capable of handling bigWig tracks.
> (or)
> Cannot convert phyloP100way track; this script is not capable of handling wig tracks.
> (or)
> Cannot convert mrna track; this script is not capable of handling psl tracks.
> (or)
> couldn't open /tmp/0FT2Jm8Ge5.sort: Too many open files
>  at /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/bin/ucsc-to-json.pl line 286.
>  at /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 7.
> 	Bio::JBrowse::ConfigurationManager::__ANON__("couldn't open /tmp/0FT2Jm8Ge5.sort: Too many open files\x{a} at /"...) called at /usr/share/perl/5.22/Carp.pm line 166
> 	Carp::croak("couldn't open /tmp/0FT2Jm8Ge5.sort: Too many open files\x{a}") called at /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/jbrowse/bin/../src/perl5/Bio/JBrowse/ExternalSorter.pm line 98
> 	Bio::JBrowse::ExternalSorter::finish(Bio::JBrowse::ExternalSorter=HASH(0x2e4efe0)) called at /home/web-apollo-test-server/web-apollo-test-server/Apollo-2.6.1/bin/ucsc-to-json.pl line 286
> 
> The final error was seen when loading a large file. Is there a way to get past these errors?
> 
> Regards,
> Shamika

[Gmod-ajax] JBrowse2 config.json

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

Hi,

I've been playing with JBrowse2 first release for a few days. In
JBorwse (1), I've been using a strategy to separate configuration and data
for multiple genomes by creating config.json for each genome (and pointing
data to the corresponding genomic data). It worked pretty well as it
reduced chances of messing up other genomes while making changes to one
genome. I noticed for JBrowse2, there is a master config.json sitting in
the JBrowe2 folder and we lay out multiple genomes and assemblies in it. Is
this the way to manage multiple genomes in JBrowse2 now? Because JBrowse2
has to consider the multiple genome view for synteny, so everything has to
be in one single config.json? Or more generally, what is the general idea
(or best practices?) of handling multiple organisms in JBrowse2?

Thanks again for the development of JBrowse 2! It is truly exciting to see
it!

Ke

[Gmod-ajax] JBrowse 2 release

[Garrett S. <ste...@gm...>]

We are pleased to announce the first public release of JBrowse 2!

JBrowse 2 is the successor to JBrowse, but is a completely new
application written with modern web standards and frameworks.

Some of the features new to JBrowse 2 include:

   - New types of views, including circular, synteny, and dotplot views
   - Graphical configuration editing
   - Connections to resources such as UCSC Track Hubs

You can see some demos of JBrowse 2 in action here
<https://jbrowse.org/jb2/demos>. To get started using JBrowse 2, visit our
quickstart guide here <https://jbrowse.org/jb2/docs/quickstart_web>.

We'd love to hear what you think! You can find information about how to
contact us here <https://jbrowse.org/jb2/contact/>.

[image: jbrowse_logo.png] <https://jbrowse.org/jb2/>

The JBrowse Team

Re: [Gmod-ajax] JBrowse 2 guide

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

Sounds great! Thanks!

On Mon, Nov 9, 2020 at 12:02 PM Colin <col...@gm...> wrote:

> Really glad to hear the interest in JBrowse 2!
> This is actually a great question and could deserve a tutorial on our
> website just for this
>
> Our current docs on this include
> - User guide https://jbrowse.org/jb2/docs/user_guide
> - SV inspector section of the user guide
> https://jbrowse.org/jb2/docs/user_guide#sv-inspector
>
> The SV inspector is currently designed for TRA and BND type events in the
> VCF, so any SV caller that outputs TRA (sniffles for example) or breakends
> aka BND (pbsv, manta, etc). The SV inspector currently accepts a plain text
> VCF instead of gzipped just FYI
>
> Note that you mention the direct visualization of inversion/deletion,
> which is shown in our demos. This feature specifically linking of the
> supplementary alignments is still on a branch
> https://github.com/GMOD/jbrowse-components/pull/1231
>
> Once that branch is merged it will be much better at the "direct
> visualization of deletions/inversions" etc.
>
> Let me know if that helps
>
> -Colin
>
> On Mon, Nov 9, 2020 at 10:17 AM Ke Jiang <bio...@gm...> wrote:
>
>> Hi,
>>
>> I just gave my first try of JBrowse 2, and it works great for most of the
>> basic tracks and data types! I'm very interested in the structural variant
>> features shown in the demo, such as direct visualization of deletions,
>> inversions and translocations. Is there a more detailed guide or
>> documentation for these? Do we need a specific variant caller or specific
>> format of VCF to work with the BAMs, etc?
>>
>> Thanks for a great step forward for JBrowse!
>>
>> Ke
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] JBrowse 2 guide

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

Really glad to hear the interest in JBrowse 2!
This is actually a great question and could deserve a tutorial on our
website just for this

Our current docs on this include
- User guide https://jbrowse.org/jb2/docs/user_guide
- SV inspector section of the user guide
https://jbrowse.org/jb2/docs/user_guide#sv-inspector

The SV inspector is currently designed for TRA and BND type events in the
VCF, so any SV caller that outputs TRA (sniffles for example) or breakends
aka BND (pbsv, manta, etc). The SV inspector currently accepts a plain text
VCF instead of gzipped just FYI

Note that you mention the direct visualization of inversion/deletion, which
is shown in our demos. This feature specifically linking of the
supplementary alignments is still on a branch
https://github.com/GMOD/jbrowse-components/pull/1231

Once that branch is merged it will be much better at the "direct
visualization of deletions/inversions" etc.

Let me know if that helps

-Colin

On Mon, Nov 9, 2020 at 10:17 AM Ke Jiang <bio...@gm...> wrote:

> Hi,
>
> I just gave my first try of JBrowse 2, and it works great for most of the
> basic tracks and data types! I'm very interested in the structural variant
> features shown in the demo, such as direct visualization of deletions,
> inversions and translocations. Is there a more detailed guide or
> documentation for these? Do we need a specific variant caller or specific
> format of VCF to work with the BAMs, etc?
>
> Thanks for a great step forward for JBrowse!
>
> Ke
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] JBrowse 2 guide

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

Hi,

I just gave my first try of JBrowse 2, and it works great for most of the
basic tracks and data types! I'm very interested in the structural variant
features shown in the demo, such as direct visualization of deletions,
inversions and translocations. Is there a more detailed guide or
documentation for these? Do we need a specific variant caller or specific
format of VCF to work with the BAMs, etc?

Thanks for a great step forward for JBrowse!

Ke

Re: [Gmod-ajax] JBrowse Issue

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

Here is a FAQ link for this issue
https://jbrowse.org/docs/faq.html#what-webserver-is-needed-for-jbrowse :)

To start a quick server for testing

npm install -g http-server
http-server
# then navigate to http://localhost:8080 in the browser


-Colin


On Mon, Oct 19, 2020 at 3:16 PM Scott Cain <sc...@sc...> wrote:

> Hi Alex,
>
> You have to access JBrowse through a web server because it makes extensive
> use of asynchronous javascript, so using file:/// won't work.  There are
> multiple ways of going about setting up a web server, but if you'd like
> guidance for that, please let us know.
>
> Scott
>
>
> On Mon, Oct 19, 2020 at 12:06 PM Alex Mathew <ama...@gm...> wrote:
>
>> Hello,
>>
>> My name is Alexander Mathew and I am an undergraduate Computer Science
>> student at the University of Nevada, Reno. I need to use JBrowse for an on
>> campus job I have, and I am having difficulty in the installation process.
>> I followed the tutorial and ran setup.sh. The Volvox data was said to have
>> been formatted correctly, but I still get an error message. I have attached
>> pictures for reference. I look forward to hearing from you.
>>
>> Thank you,
>> Alexander Mathew
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] JBrowse Issue

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

Hi Alex,

You have to access JBrowse through a web server because it makes extensive
use of asynchronous javascript, so using file:/// won't work.  There are
multiple ways of going about setting up a web server, but if you'd like
guidance for that, please let us know.

Scott


On Mon, Oct 19, 2020 at 12:06 PM Alex Mathew <ama...@gm...> wrote:

> Hello,
>
> My name is Alexander Mathew and I am an undergraduate Computer Science
> student at the University of Nevada, Reno. I need to use JBrowse for an on
> campus job I have, and I am having difficulty in the installation process.
> I followed the tutorial and ran setup.sh. The Volvox data was said to have
> been formatted correctly, but I still get an error message. I have attached
> pictures for reference. I look forward to hearing from you.
>
> Thank you,
> Alexander Mathew
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-ajax] JBrowse Issue

[Alex M. <ama...@gm...>]

Hello,

My name is Alexander Mathew and I am an undergraduate Computer Science
student at the University of Nevada, Reno. I need to use JBrowse for an on
campus job I have, and I am having difficulty in the installation process.
I followed the tutorial and ran setup.sh. The Volvox data was said to have
been formatted correctly, but I still get an error message. I have attached
pictures for reference. I look forward to hearing from you.

Thank you,
Alexander Mathew

Re: [Gmod-ajax] Trying to test jbrowse-web

[Daniel R. P. <dr...@it...>]

Plus, just to keep you posted. I am trying to embed the JBrowse React component in an Angular web application. I am using the following method https://medium.com/@zacky_14189/embedding-react-components-in-angular-the-easy-way-60f796b68aef , and I have gotten a React navbar to work in Angular. There are a few more methods to test. It is only to know if you are interested in knowing more about it and maybe to give punctual supports in case it is needed.

Best regards,

Daniel Reyes
________________________________
De: Daniel Reyes Parrilla
Enviado: jueves, 15 de octubre de 2020 8:29
Para: Colin
CC: gmo...@li...; Rafael Nebot Medina
Asunto: Re: [Gmod-ajax] Trying to test jbrowse-web

It worked! Thank you very much :)
________________________________
De: Colin [col...@gm...]
Enviado: miércoles, 14 de octubre de 2020 16:24
Para: Daniel Reyes Parrilla
CC: gmo...@li...; Rafael Nebot Medina
Asunto: Re: [Gmod-ajax] Trying to test jbrowse-web

Forgot to mention to run `samtools faidx yourfile.fa`, but the https://jbrowse.org/jb2/docs/quickstart_web guide should detail further :)


-Colin

On Wed, Oct 14, 2020 at 11:05 AM Colin <col...@gm...<mailto:col...@gm...>> wrote:
Hi Daniel!

There are two ways you can approach this

1) Approach it as a "developer" and use our github quickstart guide https://github.com/gmod/jbrowse-components#quick-start

This basically involves the following commands basically (must use yarn, not npm)

git clone https://github.com/GMOD/jbrowse-components
cd jbrowse-components
yarn
cd products/jbrowse/web
yarn start

This should automatically launch a JBrowse 2 instance with demo data that you can browse. Further work at setting up your own data will involve using steps from (2) below

2) Approach it as a "user" that downloads a pre-built bundle https://jbrowse.org/jb2/docs/quickstart_web and then, as a user, you can then follow steps to use the JBrowse CLI tool


The main gist of this is to run the following commands

npm install -g @jbrowse/cli
jbrowse create /var/www/html/jbrowse2
cd /var/www/html/jbrowse2
jbrowse add-assembly ~/yourfile.fa --load copy # this will copy the yourfile.fa to /var/www/html/jbrowse2 and create a config entry for this genome
samtools index ~/yourfile.bam
jbrowse add-track ~/yourfile.bam --load copy # this will copy yourfile.fa to /var/www/html/jbrowse2 and create a track entry for this genome

I hope this helps clarify!



-Colin

On Wed, Oct 14, 2020 at 10:57 AM Daniel Reyes Parrilla <dr...@it...<mailto:dr...@it...>> wrote:
Hello,

I have been trying for some hours to use and test the jbrowse-web (0.0.1-beta.26) product of JBrowse2 (https://github.com/GMOD/jbrowse-components/tree/master/products/jbrowse-web ).I do not know where I am failing and I would like you to do me a favor to help me. I have realized that there are a list of packages that have not been already published to npm.

  *   "@jbrowse/plugin-breakpoint-split-view": "^0.0.1-beta.15",
  *   "@jbrowse/plugin-circular-view": "^0.0.1-beta.15",
  *   "@jbrowse/plugin-dotplot-view": "^0.0.1-beta.15",
  *   "@jbrowse/plugin-hic": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-legacy-jbrowse": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-linear-comparative-view": "^0.0.1-beta.15",
  *   "@jbrowse/plugin-lollipop": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-menus": "^0.0.1-beta.14",
  *   "@jbrowse/plugin-rdf": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-spreadsheet-view": "^0.0.1-beta.19",
  *   "@jbrowse/plugin-sv-inspector": "^0.0.1-beta.14",
  *   "@jbrowse/plugin-trackhub-registry": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-filtering": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-hic": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-legacy-jbrowse": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-linear-comparative-view": "^0.0.1-beta.15",
  *   "@jbrowse/plugin-lollipop": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-menus": "^0.0.1-beta.14",
  *   "@jbrowse/plugin-rdf": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-spreadsheet-view": "^0.0.1-beta.19",
  *   "@jbrowse/plugin-sv-inspector": "^0.0.1-beta.14",
  *   "@jbrowse/plugin-trackhub-registry": "^0.0.1-beta.13"

Even though I have deleted them from the package.json file and the corePlugins.ts list. With this I suppose that it would work fine.

After that, when I executed npm start it didn't recognize rescripts, so I added "@rescripts/cli": "0.0.14",  "@rescripts/rescript-env": "0.0.12" and "@rescripts/utilities": "0.0.7", to the package.json but it still gives me the following error:

> rescripts --max-http-header-size=100000 start

internal/modules/cjs/loader.js:638
    throw err;
    ^

Error: Cannot find module 'react-scripts/config/paths'
    at Function.Module._resolveFilename (internal/modules/cjs/loader.js:636:15)
    at Function.Module._load (internal/modules/cjs/loader.js:562:25)
    at Module.require (internal/modules/cjs/loader.js:692:17)
    at require (internal/modules/cjs/helpers.js:25:18)
    at Object.<anonymous> (/home/daniel/Documentos/jbrowse-web/node_modules/@rescripts/utilities/paths.js:2:27)
    at Module._compile (internal/modules/cjs/loader.js:778:30)
    at Object.Module._extensions..js (internal/modules/cjs/loader.js:789:10)
    at Module.load (internal/modules/cjs/loader.js:653:32)
    at tryModuleLoad (internal/modules/cjs/loader.js:593:12)
    at Function.Module._load (internal/modules/cjs/loader.js:585:3)

Best regards,

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

Re: [Gmod-ajax] Trying to test jbrowse-web

[Daniel R. P. <dr...@it...>]

It worked! Thank you very much :)
________________________________
De: Colin [col...@gm...]
Enviado: miércoles, 14 de octubre de 2020 16:24
Para: Daniel Reyes Parrilla
CC: gmo...@li...; Rafael Nebot Medina
Asunto: Re: [Gmod-ajax] Trying to test jbrowse-web

Forgot to mention to run `samtools faidx yourfile.fa`, but the https://jbrowse.org/jb2/docs/quickstart_web guide should detail further :)


-Colin

On Wed, Oct 14, 2020 at 11:05 AM Colin <col...@gm...<mailto:col...@gm...>> wrote:
Hi Daniel!

There are two ways you can approach this

1) Approach it as a "developer" and use our github quickstart guide https://github.com/gmod/jbrowse-components#quick-start

This basically involves the following commands basically (must use yarn, not npm)

git clone https://github.com/GMOD/jbrowse-components
cd jbrowse-components
yarn
cd products/jbrowse/web
yarn start

This should automatically launch a JBrowse 2 instance with demo data that you can browse. Further work at setting up your own data will involve using steps from (2) below

2) Approach it as a "user" that downloads a pre-built bundle https://jbrowse.org/jb2/docs/quickstart_web and then, as a user, you can then follow steps to use the JBrowse CLI tool


The main gist of this is to run the following commands

npm install -g @jbrowse/cli
jbrowse create /var/www/html/jbrowse2
cd /var/www/html/jbrowse2
jbrowse add-assembly ~/yourfile.fa --load copy # this will copy the yourfile.fa to /var/www/html/jbrowse2 and create a config entry for this genome
samtools index ~/yourfile.bam
jbrowse add-track ~/yourfile.bam --load copy # this will copy yourfile.fa to /var/www/html/jbrowse2 and create a track entry for this genome

I hope this helps clarify!



-Colin

On Wed, Oct 14, 2020 at 10:57 AM Daniel Reyes Parrilla <dr...@it...<mailto:dr...@it...>> wrote:
Hello,

I have been trying for some hours to use and test the jbrowse-web (0.0.1-beta.26) product of JBrowse2 (https://github.com/GMOD/jbrowse-components/tree/master/products/jbrowse-web ).I do not know where I am failing and I would like you to do me a favor to help me. I have realized that there are a list of packages that have not been already published to npm.

  *   "@jbrowse/plugin-breakpoint-split-view": "^0.0.1-beta.15",
  *   "@jbrowse/plugin-circular-view": "^0.0.1-beta.15",
  *   "@jbrowse/plugin-dotplot-view": "^0.0.1-beta.15",
  *   "@jbrowse/plugin-hic": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-legacy-jbrowse": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-linear-comparative-view": "^0.0.1-beta.15",
  *   "@jbrowse/plugin-lollipop": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-menus": "^0.0.1-beta.14",
  *   "@jbrowse/plugin-rdf": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-spreadsheet-view": "^0.0.1-beta.19",
  *   "@jbrowse/plugin-sv-inspector": "^0.0.1-beta.14",
  *   "@jbrowse/plugin-trackhub-registry": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-filtering": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-hic": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-legacy-jbrowse": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-linear-comparative-view": "^0.0.1-beta.15",
  *   "@jbrowse/plugin-lollipop": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-menus": "^0.0.1-beta.14",
  *   "@jbrowse/plugin-rdf": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-spreadsheet-view": "^0.0.1-beta.19",
  *   "@jbrowse/plugin-sv-inspector": "^0.0.1-beta.14",
  *   "@jbrowse/plugin-trackhub-registry": "^0.0.1-beta.13"

Even though I have deleted them from the package.json file and the corePlugins.ts list. With this I suppose that it would work fine.

After that, when I executed npm start it didn't recognize rescripts, so I added "@rescripts/cli": "0.0.14",  "@rescripts/rescript-env": "0.0.12" and "@rescripts/utilities": "0.0.7", to the package.json but it still gives me the following error:

> rescripts --max-http-header-size=100000 start

internal/modules/cjs/loader.js:638
    throw err;
    ^

Error: Cannot find module 'react-scripts/config/paths'
    at Function.Module._resolveFilename (internal/modules/cjs/loader.js:636:15)
    at Function.Module._load (internal/modules/cjs/loader.js:562:25)
    at Module.require (internal/modules/cjs/loader.js:692:17)
    at require (internal/modules/cjs/helpers.js:25:18)
    at Object.<anonymous> (/home/daniel/Documentos/jbrowse-web/node_modules/@rescripts/utilities/paths.js:2:27)
    at Module._compile (internal/modules/cjs/loader.js:778:30)
    at Object.Module._extensions..js (internal/modules/cjs/loader.js:789:10)
    at Module.load (internal/modules/cjs/loader.js:653:32)
    at tryModuleLoad (internal/modules/cjs/loader.js:593:12)
    at Function.Module._load (internal/modules/cjs/loader.js:585:3)

Best regards,

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

Re: [Gmod-ajax] Trying to test jbrowse-web

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

Forgot to mention to run `samtools faidx yourfile.fa`, but the
https://jbrowse.org/jb2/docs/quickstart_web guide should detail further :)


-Colin

On Wed, Oct 14, 2020 at 11:05 AM Colin <col...@gm...> wrote:

> Hi Daniel!
>
> There are two ways you can approach this
>
> 1) Approach it as a "developer" and use our github quickstart guide
> https://github.com/gmod/jbrowse-components#quick-start
>
> This basically involves the following commands basically (must use yarn,
> not npm)
>
> git clone https://github.com/GMOD/jbrowse-components
> cd jbrowse-components
> yarn
> cd products/jbrowse/web
> yarn start
>
> This should automatically launch a JBrowse 2 instance with demo data that
> you can browse. Further work at setting up your own data will involve using
> steps from (2) below
>
> 2) Approach it as a "user" that downloads a pre-built bundle
> https://jbrowse.org/jb2/docs/quickstart_web and then, as a user, you can
> then follow steps to use the JBrowse CLI tool
>
>
> The main gist of this is to run the following commands
>
> npm install -g @jbrowse/cli
> jbrowse create /var/www/html/jbrowse2
> cd /var/www/html/jbrowse2
> jbrowse add-assembly ~/yourfile.fa --load copy # this will copy the
> yourfile.fa to /var/www/html/jbrowse2 and create a config entry for this
> genome
> samtools index ~/yourfile.bam
> jbrowse add-track ~/yourfile.bam --load copy # this will copy yourfile.fa
> to /var/www/html/jbrowse2 and create a track entry for this genome
>
> I hope this helps clarify!
>
>
>
> -Colin
>
> On Wed, Oct 14, 2020 at 10:57 AM Daniel Reyes Parrilla <
> dr...@it...> wrote:
>
>> Hello,
>>
>> I have been trying for some hours to use and test the jbrowse-web (
>> 0.0.1-beta.26) product of JBrowse2 (
>> https://github.com/GMOD/jbrowse-components/tree/master/products/jbrowse-web
>> ).I do not know where I am failing and I would like you to do me a favor to
>> help me. I have realized that there are a list of packages that have not
>> been already published to npm.
>>
>>    - "@jbrowse/plugin-breakpoint-split-view": "^0.0.1-beta.15",
>>    - "@jbrowse/plugin-circular-view": "^0.0.1-beta.15",
>>    - "@jbrowse/plugin-dotplot-view": "^0.0.1-beta.15",
>>    - "@jbrowse/plugin-hic": "^0.0.1-beta.13",
>>    - "@jbrowse/plugin-legacy-jbrowse": "^0.0.1-beta.13",
>>    - "@jbrowse/plugin-linear-comparative-view": "^0.0.1-beta.15",
>>    - "@jbrowse/plugin-lollipop": "^0.0.1-beta.13",
>>    - "@jbrowse/plugin-menus": "^0.0.1-beta.14",
>>    - "@jbrowse/plugin-rdf": "^0.0.1-beta.13",
>>    - "@jbrowse/plugin-spreadsheet-view": "^0.0.1-beta.19",
>>    - "@jbrowse/plugin-sv-inspector": "^0.0.1-beta.14",
>>    - "@jbrowse/plugin-trackhub-registry": "^0.0.1-beta.13",
>>    - "@jbrowse/plugin-filtering": "^0.0.1-beta.13",
>>    - "@jbrowse/plugin-hic": "^0.0.1-beta.13",
>>    - "@jbrowse/plugin-legacy-jbrowse": "^0.0.1-beta.13",
>>    - "@jbrowse/plugin-linear-comparative-view": "^0.0.1-beta.15",
>>    - "@jbrowse/plugin-lollipop": "^0.0.1-beta.13",
>>    - "@jbrowse/plugin-menus": "^0.0.1-beta.14",
>>    - "@jbrowse/plugin-rdf": "^0.0.1-beta.13",
>>    - "@jbrowse/plugin-spreadsheet-view": "^0.0.1-beta.19",
>>    - "@jbrowse/plugin-sv-inspector": "^0.0.1-beta.14",
>>    - "@jbrowse/plugin-trackhub-registry": "^0.0.1-beta.13"
>>
>> Even though I have deleted them from the package.json file and the
>> corePlugins.ts list. With this I suppose that it would work fine.
>>
>> After that, when I executed npm start it didn't recognize rescripts, so I
>> added "@rescripts/cli": "0.0.14",  "@rescripts/rescript-env": "0.0.12"
>> and "@rescripts/utilities": "0.0.7", to the package.json but it still
>> gives me the following error:
>>
>> > rescripts --max-http-header-size=100000 start
>>
>> internal/modules/cjs/loader.js:638
>>     throw err;
>>     ^
>>
>> Error: Cannot find module 'react-scripts/config/paths'
>>     at Function.Module._resolveFilename
>> (internal/modules/cjs/loader.js:636:15)
>>     at Function.Module._load (internal/modules/cjs/loader.js:562:25)
>>     at Module.require (internal/modules/cjs/loader.js:692:17)
>>     at require (internal/modules/cjs/helpers.js:25:18)
>>     at Object.<anonymous>
>> (/home/daniel/Documentos/jbrowse-web/node_modules/@rescripts/utilities/paths.js:2:27)
>>     at Module._compile (internal/modules/cjs/loader.js:778:30)
>>     at Object.Module._extensions..js
>> (internal/modules/cjs/loader.js:789:10)
>>     at Module.load (internal/modules/cjs/loader.js:653:32)
>>     at tryModuleLoad (internal/modules/cjs/loader.js:593:12)
>>     at Function.Module._load (internal/modules/cjs/loader.js:585:3)
>>
>> Best regards,
>>
>> Daniel Reyes
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] Trying to test jbrowse-web

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

Hi Daniel!

There are two ways you can approach this

1) Approach it as a "developer" and use our github quickstart guide
https://github.com/gmod/jbrowse-components#quick-start

This basically involves the following commands basically (must use yarn,
not npm)

git clone https://github.com/GMOD/jbrowse-components
cd jbrowse-components
yarn
cd products/jbrowse/web
yarn start

This should automatically launch a JBrowse 2 instance with demo data that
you can browse. Further work at setting up your own data will involve using
steps from (2) below

2) Approach it as a "user" that downloads a pre-built bundle
https://jbrowse.org/jb2/docs/quickstart_web and then, as a user, you can
then follow steps to use the JBrowse CLI tool


The main gist of this is to run the following commands

npm install -g @jbrowse/cli
jbrowse create /var/www/html/jbrowse2
cd /var/www/html/jbrowse2
jbrowse add-assembly ~/yourfile.fa --load copy # this will copy the
yourfile.fa to /var/www/html/jbrowse2 and create a config entry for this
genome
samtools index ~/yourfile.bam
jbrowse add-track ~/yourfile.bam --load copy # this will copy yourfile.fa
to /var/www/html/jbrowse2 and create a track entry for this genome

I hope this helps clarify!



-Colin

On Wed, Oct 14, 2020 at 10:57 AM Daniel Reyes Parrilla <
dr...@it...> wrote:

> Hello,
>
> I have been trying for some hours to use and test the jbrowse-web (
> 0.0.1-beta.26) product of JBrowse2 (
> https://github.com/GMOD/jbrowse-components/tree/master/products/jbrowse-web
> ).I do not know where I am failing and I would like you to do me a favor to
> help me. I have realized that there are a list of packages that have not
> been already published to npm.
>
>    - "@jbrowse/plugin-breakpoint-split-view": "^0.0.1-beta.15",
>    - "@jbrowse/plugin-circular-view": "^0.0.1-beta.15",
>    - "@jbrowse/plugin-dotplot-view": "^0.0.1-beta.15",
>    - "@jbrowse/plugin-hic": "^0.0.1-beta.13",
>    - "@jbrowse/plugin-legacy-jbrowse": "^0.0.1-beta.13",
>    - "@jbrowse/plugin-linear-comparative-view": "^0.0.1-beta.15",
>    - "@jbrowse/plugin-lollipop": "^0.0.1-beta.13",
>    - "@jbrowse/plugin-menus": "^0.0.1-beta.14",
>    - "@jbrowse/plugin-rdf": "^0.0.1-beta.13",
>    - "@jbrowse/plugin-spreadsheet-view": "^0.0.1-beta.19",
>    - "@jbrowse/plugin-sv-inspector": "^0.0.1-beta.14",
>    - "@jbrowse/plugin-trackhub-registry": "^0.0.1-beta.13",
>    - "@jbrowse/plugin-filtering": "^0.0.1-beta.13",
>    - "@jbrowse/plugin-hic": "^0.0.1-beta.13",
>    - "@jbrowse/plugin-legacy-jbrowse": "^0.0.1-beta.13",
>    - "@jbrowse/plugin-linear-comparative-view": "^0.0.1-beta.15",
>    - "@jbrowse/plugin-lollipop": "^0.0.1-beta.13",
>    - "@jbrowse/plugin-menus": "^0.0.1-beta.14",
>    - "@jbrowse/plugin-rdf": "^0.0.1-beta.13",
>    - "@jbrowse/plugin-spreadsheet-view": "^0.0.1-beta.19",
>    - "@jbrowse/plugin-sv-inspector": "^0.0.1-beta.14",
>    - "@jbrowse/plugin-trackhub-registry": "^0.0.1-beta.13"
>
> Even though I have deleted them from the package.json file and the
> corePlugins.ts list. With this I suppose that it would work fine.
>
> After that, when I executed npm start it didn't recognize rescripts, so I
> added "@rescripts/cli": "0.0.14",  "@rescripts/rescript-env": "0.0.12" and
> "@rescripts/utilities": "0.0.7", to the package.json but it still gives me
> the following error:
>
> > rescripts --max-http-header-size=100000 start
>
> internal/modules/cjs/loader.js:638
>     throw err;
>     ^
>
> Error: Cannot find module 'react-scripts/config/paths'
>     at Function.Module._resolveFilename
> (internal/modules/cjs/loader.js:636:15)
>     at Function.Module._load (internal/modules/cjs/loader.js:562:25)
>     at Module.require (internal/modules/cjs/loader.js:692:17)
>     at require (internal/modules/cjs/helpers.js:25:18)
>     at Object.<anonymous>
> (/home/daniel/Documentos/jbrowse-web/node_modules/@rescripts/utilities/paths.js:2:27)
>     at Module._compile (internal/modules/cjs/loader.js:778:30)
>     at Object.Module._extensions..js
> (internal/modules/cjs/loader.js:789:10)
>     at Module.load (internal/modules/cjs/loader.js:653:32)
>     at tryModuleLoad (internal/modules/cjs/loader.js:593:12)
>     at Function.Module._load (internal/modules/cjs/loader.js:585:3)
>
> Best regards,
>
> Daniel Reyes
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] Trying to test jbrowse-web

[Daniel R. P. <dr...@it...>]

Hello,

I have been trying for some hours to use and test the jbrowse-web (0.0.1-beta.26) product of JBrowse2 (https://github.com/GMOD/jbrowse-components/tree/master/products/jbrowse-web ).I do not know where I am failing and I would like you to do me a favor to help me. I have realized that there are a list of packages that have not been already published to npm.

  *   "@jbrowse/plugin-breakpoint-split-view": "^0.0.1-beta.15",
  *   "@jbrowse/plugin-circular-view": "^0.0.1-beta.15",
  *   "@jbrowse/plugin-dotplot-view": "^0.0.1-beta.15",
  *   "@jbrowse/plugin-hic": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-legacy-jbrowse": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-linear-comparative-view": "^0.0.1-beta.15",
  *   "@jbrowse/plugin-lollipop": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-menus": "^0.0.1-beta.14",
  *   "@jbrowse/plugin-rdf": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-spreadsheet-view": "^0.0.1-beta.19",
  *   "@jbrowse/plugin-sv-inspector": "^0.0.1-beta.14",
  *   "@jbrowse/plugin-trackhub-registry": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-filtering": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-hic": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-legacy-jbrowse": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-linear-comparative-view": "^0.0.1-beta.15",
  *   "@jbrowse/plugin-lollipop": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-menus": "^0.0.1-beta.14",
  *   "@jbrowse/plugin-rdf": "^0.0.1-beta.13",
  *   "@jbrowse/plugin-spreadsheet-view": "^0.0.1-beta.19",
  *   "@jbrowse/plugin-sv-inspector": "^0.0.1-beta.14",
  *   "@jbrowse/plugin-trackhub-registry": "^0.0.1-beta.13"

Even though I have deleted them from the package.json file and the corePlugins.ts list. With this I suppose that it would work fine.

After that, when I executed npm start it didn't recognize rescripts, so I added "@rescripts/cli": "0.0.14",  "@rescripts/rescript-env": "0.0.12" and "@rescripts/utilities": "0.0.7", to the package.json but it still gives me the following error:

> rescripts --max-http-header-size=100000 start

internal/modules/cjs/loader.js:638
    throw err;
    ^

Error: Cannot find module 'react-scripts/config/paths'
    at Function.Module._resolveFilename (internal/modules/cjs/loader.js:636:15)
    at Function.Module._load (internal/modules/cjs/loader.js:562:25)
    at Module.require (internal/modules/cjs/loader.js:692:17)
    at require (internal/modules/cjs/helpers.js:25:18)
    at Object.<anonymous> (/home/daniel/Documentos/jbrowse-web/node_modules/@rescripts/utilities/paths.js:2:27)
    at Module._compile (internal/modules/cjs/loader.js:778:30)
    at Object.Module._extensions..js (internal/modules/cjs/loader.js:789:10)
    at Module.load (internal/modules/cjs/loader.js:653:32)
    at tryModuleLoad (internal/modules/cjs/loader.js:593:12)
    at Function.Module._load (internal/modules/cjs/loader.js:585:3)

Best regards,

Daniel Reyes

Re: [Gmod-ajax] Collapsing categories

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

I wanted to see if a solution could be made quickly, if you want to test
out a development branch you can try this

https://github.com/GMOD/jbrowse/tree/starcollapse


Tested using

[trackSelector]
collapsedCategories=Quantitative*

In  jbrowse.conf
On the volvox sample data

Let me know if how it works, very quickly drafted :)

-Colin


On Tue, Sep 29, 2020 at 1:13 PM Vaneet Lotay <van...@uc...>
wrote:

> Well currently you can collapse parent category as well as all
> subcategories if you specify each subcategory and parent category in the
> ‘collapsedCategories’ field.  I was looking for a shortcut to collapse all
> subcategories under a parent subcategory with maybe a wildcard character or
> some alternative that would work in your development.  It would be great if
> something to this effect could be added in a future release, because I am
> working with a lot of nested subcategories sometimes across 3-4 levels.
> Essentially having a collapse all function from a higher level in the
> configuration would be nice.
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
> *From:* Colin <col...@gm...>
> *Sent:* Monday, September 28, 2020 4:33 PM
> *To:* Vaneet Lotay <van...@uc...>
> *Cc:* gmod-ajax <gmo...@li...>
> *Subject:* Re: [Gmod-ajax] Collapsing categories
>
>
>
> [△EXTERNAL]
>
>
>
> That is interesting. I don't think anything like this exists. I guess
> currently the idea would be to collapse the parent category. rather than
> collapse all subcategories, but I guess if there is a mix of tracks and
> categories at one level you want to collapse all the categories at that
> level rather than the parent?
>
>
>
> -Colin
>
>
>
> On Mon, Sep 28, 2020 at 1:27 PM Vaneet Lotay <van...@uc...>
> wrote:
>
> Hello,
>
>
>
> I was wondering is there a way to collapse subcategories within a main
> category without having to specify every single subcategory separately
> within this field:
>
>
>
> trackSelector→collapsedCategories
>
>
>
> If not, it would be nice for this feature to be added to JBrowse somehow
> using a special wildcard character like perhaps this for example:
>
>
>
> collapsedCategories : “Category1/*,Category2/Subcategory1/*’
>
>
>
> If it’s not a feature please let me know if I should add a request to
> GitHub, as I think it would be very helpful when dealing with a lot of
> categories and subcategories which is the case in my scenario.
>
>
>
> 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
>
>