Dear Mike Gavrielides,
Thank you for your question about the UCSC Genome Browser. Unfortunately, we do not currently have a downloads server in Europe. We do offer UDR (UDT Enabled Rsync), https://github.com/LabAdvComp/UDR, a solution for slow download speeds. More information on UDR can be found on our downloads Page: http://hgdownload.soe.ucsc.edu/downloads.html, under the header "Source & Utilities Downloads."
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.
-Chris V
UCSC Genome Browser
--Hi all,
I am a software developer at Francis Crick Institute, London. I am writing with regards to a full mirror genome browser setup and more specifically about the hg19 data transfer.
We have put the /mysql/hg19 and /gbdb/hg19 to download (see rsync commands below). The data transfer process is quite slow as for the last four days it just got to 1.3TB which means it will take another ~18 days to download the complete 7.2TB set.
Rsync command to download the data:
rsync -avzP --delete --max-delete=20 rsync://hgdownload.cse.ucsc.edu/mysql/hg19 /camp/stp/aim/working/ucsc_gb_hg19/mysql
rsync -avzP --delete --max-delete=20 rsync://hgdownload.cse.ucsc.edu/gbdb/hg19 /camp/stp/aim/working/ucsc_gb_hg19/gbdb
I was wondering if there is an alternative method to get the data. Is there any other location closer to Europe that will speed up the transfer?
Kind regards,
Mike Gavrielides
Application Software Developer
Scientific Computing . AIM Team
The Francis Crick Institute
1 Midland Road
London
NW11AT
The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT
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Hi Mike,
Thank you for your question about getting human to show up in the species tree on your mirror. There are a few troubleshooting steps you can try to get to the bottom of what's going on.
1. What is the defaultDb for human?
- Please try this mysql command while connected to the hgcentral database:
select * from defaultDb where genome = "Human";
- If this returns hg38 like so:
+--------+------+ | genome | name | +--------+------+ | Human | hg38 | +--------+------+
update defaultDb set name = "hg19" where genome = "Human";
hgGateway.dbDbTaxonomy=/path/to/a/file
, and that the file pointed to by hgGateway.dbDbTaxonomy contains "Human":$ grep "hgGateway.dbDbTaxonomy" /usr/local/apache/cgi-bin/hg.conf hgGateway.dbDbTaxonomy=../js/dbDbTaxonomy.js $ grep "Human" /usr/local/apache/htdocs/js/dbDbTaxonomy.js [ ["Human", 9606, "Homo sapiens" ] ] ],
select * from dbDb where name='hg19'; +------+-------------------------+------------+----------+-----------------------------+--------+----------+--------+----------------+----------------------------------+----------+--------+-------------------------------------------------------------------------+-------+ | name | description | nibPath | organism | defaultPos | active | orderKey | genome | scientificName | htmlPath | hgNearOk | hgPbOk | sourceName | taxId | +------+-------------------------+------------+----------+-----------------------------+--------+----------+--------+----------------+----------------------------------+----------+--------+-------------------------------------------------------------------------+-------+ | hg19 | Feb. 2009 (GRCh37/hg19) | /gbdb/hg19 | Human | chr21:33,031,597-33,041,570 | 1 | 60 | Human | Homo sapiens | /gbdb/hg19/html/description.html | 1 | 0 | GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1) | 9606 | +------+-------------------------+------------+----------+-----------------------------+--------+----------+--------+----------------+----------------------------------+----------+--------+-------------------------------------------------------------------------+-------+
Please let us know if we can help you any further!
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
Hi,
Thank you for providing with the download information. I have it downloaded now, but I have a small issue.
I have installed the mysql database for hg19 on the genome browser instance we have, but there is no human selection available on the homepage. See screenshot attached.
I did exactly the same for S. cerevisiae (sacCer3) and it show on the home page and works fine.
Is there anything extra that needs to be done specifically for hg19?
Thank you in advance.
Kind regards,
Mike
. Mike Gavrielides
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/FEF6B752-3236-438B-966E-9BD89B8153AB%40crick.ac.uk.
Hi,
Thank you for providing with the download information. I have it downloaded now, but I have a small issue.
I have installed the mysql database for hg19 on the genome browser instance we have, but there is no human selection available on the homepage. See screenshot attached.
I did exactly the same for S. cerevisiae (sacCer3) and it show on the home page and works fine.
Is there anything extra that needs to be done specifically for hg19?
Thank you in advance.
Kind regards,
Mike
. Mike Gavrielides
Application Software Developer
Scientific Computing . AIM Team
The Francis Crick Institute
1 Midland Road
London
NW11AT
From: Chris Villarreal <cjvi...@ucsc.edu>
Date: Tuesday, 18 April 2017 at 21:06
To: Mike Gavrielides <mike.gav...@crick.ac.uk>
Cc: "gen...@soe.ucsc.edu" <gen...@soe.ucsc.edu>, "genome...@soe.ucsc.edu" <genome...@soe.ucsc.edu>, "m...@soe.ucsc.edu" <m...@soe.ucsc.edu>
Subject: Re: [genome] hd19 data download
Dear Mike Gavrielides,
Hi Christopher,
Thanks a lot for your help. It was the default human genome that needed to be setup so I updated it to hg19.
Thanks again. I appreciate it a lot.
All best,