Registering my TrackHub

[Benoit Ballester]

Dear UCSC Genome Browser developer, 

I would like to have our Track Hub registered with UCSC and share it in the Public listing. 

This hub is linked with a NAR Database submission for the 2018 issue (deadline 15th September). 

Here is the HUB link. 

http://tagc.univ-mrs.fr/remap/hubDirectory/trackhub/hub.txt 

I hope we've done everything right, I used Daniel’s (Zerbino) HTML template as well. 

Please let me know if there is anything, 

Cheers, 

Ben

--
Benoît Ballester, PhD
Inserm U1090, TAGC
Campus de Luminy
13288 Marseille Cedex 9
France
+33 4 91 82 87 28
(1st)  benoit.b...@inserm.fr
(2nd) benoit.b...@univ-amu.fr 

[Christopher Lee]

Hi Ben,

Thank you for your request to add a public track hub. Your hub has
been added to our review queue, and our team will be reviewing your
hub to ensure that it meets our Public Hub standards. The timing on
when your hub review will be complete is unknown, though you will be
contacted either during the review process or upon completion.

If you haven't done so already, you can review the Public Hub
Guidelines page to get an idea of what suggestions may be needed:
http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines

From a quick look of the hub, it appears the bigDataUrl's have some
typos and refer to files that don't exist.

Please let us know if you have any further questions!

Thank you again for your inquiry and using the UCSC Genome Browser. If
you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a
publicly-accessible forum. If your question includes sensitive data,
you may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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[Benoit Ballester]

Hi Chris, 

The bigDataUrl’s  typos have been corrected. 

Ben

--
Benoît Ballester, PhD
Inserm U1090, TAGC
Campus de Luminy
13288 Marseille Cedex 9
France
+33 4 91 82 87 28
(1st)  benoit.b...@inserm.fr
(2nd) benoit.b...@univ-amu.fr 

[Benoit Ballester]

Apologie for this, but unfortunately our server hosting the track hub is down (longer than expected maintenance) 

I will let you know as soon as our server restarted. 

--
Benoît Ballester, PhD
Inserm U1090, TAGC
Campus de Luminy
13288 Marseille Cedex 9
France
+33 4 91 82 87 28
(1st)  benoit.b...@inserm.fr
(2nd) benoit.b...@univ-amu.fr 

On 13 Sep 2017, at 20:18, Christopher Lee <chm...@ucsc.edu> wrote:

[Benoit Ballester]

Hi Christopher, 

By any chance, is there any news regarding the ReMap track hub registration I have sent in September. 

For information, this TrackHub will accompany our ReMap 2018 publication in the NAR DB issue, back-to-back with the JASPAR 2018 paper, which I have just seen, has a already its trackhub public. 

Please, let me know if there is anything I can to speed this process up. 

Cheers, 

Benoit

--
Benoît Ballester, PhD

INSERM U1090 TAGC

Aix-Marseille-Université
Parc Scientifique de Luminy

13288 Marseille Cedex 9
France
+33 4 91 82 87 28
(1st)  benoit.b...@inserm.fr
(2nd) benoit.b...@univ-amu.fr 

On 13 Sep 2017, at 20:18, Christopher Lee <chm...@ucsc.edu> wrote:

[Matthew Speir]

Hi Benoit,

I apologize for the delayed response and thank you for following up about your public track hub.

I think your public track hub looks excellent, though there is one minor issue that you should fix. Some of the characters on your track description page don't seem to be encoded properly and come out as a garbled mess when viewed in the Genome Browser. Here is an example of some of these garbled characters:

We retrieved the list of ENCODE data as FASTQ files from the ENCODE portal (https://www.encodeproject.org/) using the following filters: Assay: “ChIP-seq†, Organism: “Homo sapiens†, Target of assay: “transcription factor†, Available data: “fastq†on 2016 June 21st. Metadata information in JSON format and FASTQ files were retrieved using the Python requests module.

I believe you just need to change how you are encoding the double quotes ("") in your HTML files.

Since this is such a minor change, I have gone ahead and added your hub to our public list at http://genome.ucsc.edu/cgi-bin/hgHubConnect and sent an announcement to our announcement mailing list, https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-announce. I can also tweet about it if you have a twitter handle you'd like me to include (e.g. @benoit for a personal one or something for your lab).

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/81F2D620-09DD-43A3-8378-F50C4DBEEAD1%40inserm.fr.

[Benoit Ballester]

Hi Matthew, 

Excellent news ! 

Yes I’ll fix the weird characters asap on monday morning. 

It would be great if you tweet about it, my tweeter account is @BenoitBallester

Cheers, 

Ben

--
Benoît Ballester, PhD

INSERM U1090 TAGC

Aix-Marseille-Université
Parc Scientifique de Luminy
13288 Marseille Cedex 9
France
+33 4 91 82 87 28
(1st)  benoit.b...@inserm.fr
(2nd) benoit.b...@univ-amu.fr 

[Benoit Ballester]

Hi Mathew, Christopher, 

How can I track access and data usage of the ReMAp Track hub ? 

I have a Google Analytics account on the ReMap website tracking the different pages. 

However I am not sure how to track the direct track hub access. 

Would you have any hints/info ? 

Cheers, 

Benoit 

--
Benoît Ballester, PhD

INSERM U1090 TAGC

Aix-Marseille-Université
Parc Scientifique de Luminy
13288 Marseille Cedex 9
France
+33 4 91 82 87 28
(1st)  benoit.b...@inserm.fr
(2nd) benoit.b...@univ-amu.fr 

[Matthew Speir]

Hi Benoit,

Thank you for your question about tracking usage of your ReMap hub.

We can generate these usage metrics for your hub upon request, although in the past we've only generated them when the hub has been available for at least a few months. In the future, we have plans to make this hub usage information available through a URL, though we don't really have an estimate of when that will be available. We'll be sure to let you and the other public hub providers know when this is available.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

[Benoit Ballester]

Dear Matthew, Christopher, 

Our server hosting the track crashed a couple of days ago, hence we have changed our URL for the trackHub. 

Could you please update the URL in the Public Hub for ReMap ?

http://pedagogix-tagc.univ-mrs.fr/remap/hubDirectory/trackhub/hub.txt 

Thanks,, 

Benoit

--
Benoît Ballester, PhD

Inserm U1090, TAGC
Campus de Luminy
13288 Marseille Cedex 9
France
+33 4 91 82 87 28
(1st)  benoit.b...@inserm.fr
(2nd) benoit.b...@univ-amu.fr 

ReMap2018: http://remap.cisreg.eu  

[Matthew Speir]

Hello, Benoit.

Thank you for providing us with an updated URL for your hub. I have updated the URL in our system and it should be working properly on our site. 

Also, to follow-up on your earlier question about track hub usage information. Since your hub has been available for a few months now, I can look into generating these usage stats and then pass them along to you in another email.

If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir

UCSC Genome Bioinformatics Group

(2nd) benoit.ballester@univ-amu.fr 

On 8 Oct 2017, at 18:44, Benoit Ballester <benoit.b...@inserm.fr> wrote:

Hi Matthew, 

Excellent news ! 

Yes I’ll fix the weird characters asap on monday morning. 

It would be great if you tweet about it, my tweeter account is @BenoitBallester

Cheers, 

Ben

--
Benoît Ballester, PhD

INSERM U1090 TAGC

Aix-Marseille-Université
Parc Scientifique de Luminy
13288 Marseille Cedex 9
France
+33 4 91 82 87 28
(1st)  benoit.b...@inserm.fr

(2nd) benoit.ballester@univ-amu.fr 

(2nd) benoit.ballester@univ-amu.fr 

[Benoit Ballester]

On 30 Apr 2018, at 17:07, Matthew Speir <msp...@soe.ucsc.edu> wrote:

Hello, Benoit.

Thank you for providing us with an updated URL for your hub. I have updated the URL in our system and it should be working properly on our site. 

Also, to follow-up on your earlier question about track hub usage information. Since your hub has been available for a few months now, I can look into generating these usage stats and then pass them along to you in another email.

This would be great thanks !

--
Benoît Ballester, PhD

INSERM U1090 TAGC

Aix-Marseille-Université
Parc Scientifique de Luminy
13288 Marseille Cedex 9
France
+33 4 91 82 87 28
(1st)  benoit.b...@inserm.fr

(2nd) benoit.b...@univ-amu.fr