problems with track hub upload
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Zi Peng Fan
Jul 17, 2015, 12:31:01 PM7/17/15
to gen...@soe.ucsc.edu, abr...@wi.mit.edu
Dear UCSC genome browser IT manger,
I am writing to ask for assistance to upload track hub to UCSC. I created a track hub (http://tak.wi.mit.edu/young_bams/wiggles/mm9/mESC.SMC1.ChIA-PET.hub/hub.txt) and ran the UCSC debug tool “hubCheck” with no error message. However, I was not able to upload the track to UCSC genome browser via http://genome.ucsc.edu/cgi-bin/hgHubConnect. I got the following error messages below. You can find the items in my track hub at http://tak.wi.mit.edu/young_bams/wiggles/mm9/mESC.SMC1.ChIA-PET.hub/. Could you let me know how could I fix this problem? Thank you.
“ERROR: No Content-Length: returned in header for http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&hubUrl=http://tak.wi.mit.edu/young_bams/wiggles/mm9/mESC.SMC1.ChIA-PET.hub/hub.txt, can't proceed, sorry Debug Help”
"ERROR: Error in TCP non-blocking connect() 111 - Connection refused Couldn't open http://tak.wi.mit.edu/young_bams/wiggles/mm9/mESC.SMC1.ChIA-PET.hub/hub.txt Debug Help"
Best,
Zi
Matthew Speir
Jul 17, 2015, 1:15:26 PM7/17/15
to Zi Peng Fan, gen...@soe.ucsc.edu, abr...@wi.mit.edu
Hi Zi,
Thank you for your question about uploading a track hub to the UCSC Genome Browser. Tracks hubs must be placed in publicly-accessible locations to be loaded into the Genome Browser. When trying to access your track hub from my web browser, I am met with the following error:
This webpage is not available
ERR_CONNECTION_REFUSED
This indicates to me that your track hub is not in a publicly-accessible location. You will need to talk your university or department IT staff to allow access to your track hub from external sources. At the very least, they will need to allow access to your track hub from genome.ucsc.edu.
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
Thank you for your question about uploading a track hub to the UCSC Genome Browser. Tracks hubs must be placed in publicly-accessible locations to be loaded into the Genome Browser. When trying to access your track hub from my web browser, I am met with the following error:
This webpage is not available
ERR_CONNECTION_REFUSED
This indicates to me that your track hub is not in a publicly-accessible location. You will need to talk your university or department IT staff to allow access to your track hub from external sources. At the very least, they will need to allow access to your track hub from genome.ucsc.edu.
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
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Zi Peng Fan
Jul 24, 2015, 11:20:35 AM7/24/15
to gen...@soe.ucsc.edu, Matthew Speir
Dear UCSC genome browser IT manager,
I am a computational biologist from Dr. Rick Young’s lab at Whitehead Institute/MIT. Dr. David Haussler suggested us to put our chromatin interaction datasets in a public hub at UCSC genome browser for public viewing. I have tested the data hub I created for the dataset with Matt’s help. I have now put the hub at our lab website (http://younglab.wi.mit.edu/mESC_ChIAPET_hub/hub.txt). Could you help us to test the data hub and let us know what else we need to do to create a public data hub? What is the best way to transfer the data over to UCSC genome browser so that they can be permanently host there?
Thanks.
Zi
Matthew Speir
Jul 24, 2015, 12:37:46 PM7/24/15
to Zi Peng Fan, gen...@soe.ucsc.edu
Hi Zi,
Thank you for your interest in registering a public track hub with the UCSC Genome Browser. Our engineering and quality assurance teams will review it to confirm that it meets our requirements. We will be in contact with you during this process. In the meantime, please have a look at our guidelines for public hubs: http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines. At the minimum, we require that each track has an associated description page that contains your contact information.
Thank you for your interest in registering a public track hub with the UCSC Genome Browser. Our engineering and quality assurance teams will review it to confirm that it meets our requirements. We will be in contact with you during this process. In the meantime, please have a look at our guidelines for public hubs: http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines. At the minimum, we require that each track has an associated description page that contains your contact information.
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
Zi Peng Fan
Aug 28, 2015, 3:20:44 PM8/28/15
to Matthew Speir, gen...@soe.ucsc.edu
Hi Matthew,
I am writing to see whether you have any updates for creating a public hub. Thanks.
Zi
Matthew Speir
Aug 28, 2015, 5:45:03 PM8/28/15
to Zi Peng Fan, gen...@soe.ucsc.edu
Hi Zi,
Your hub is currently in our queue and awaiting review by one of our QA engineers. In the meantime, there are some steps you can take to improve your hub. The first would be to review the guidelines available at http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines and then ensure that your hub meets all of these guidelines.
After a quick look at your hub, I can recommend at least one improvement to your hub. The tracks in your hub are missing an associated HTML description page that describes the data and provides basic contact information. You can look at the description pages from other public hubs, such as the "PhyloCSF" hub or the "Porcine DNA methylation and gene transcription" hubs, for examples to follow.
Your hub is currently in our queue and awaiting review by one of our QA engineers. In the meantime, there are some steps you can take to improve your hub. The first would be to review the guidelines available at http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines and then ensure that your hub meets all of these guidelines.
After a quick look at your hub, I can recommend at least one improvement to your hub. The tracks in your hub are missing an associated HTML description page that describes the data and provides basic contact information. You can look at the description pages from other public hubs, such as the "PhyloCSF" hub or the "Porcine DNA methylation and gene transcription" hubs, for examples to follow.
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
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