Transfer sessions/tracks between mirror servers.
Dahong Chen
Brian Lee
Hello, Dahong.
Thank you for your question about moving sessions from one UCSC Genome Browser mirror to another.
There is not a way to move all your sessions in one go from genome-asia.ucsc.edu to genome.ucsc.edu. You will have to export the custom tracks and the session settings separately for each session on genome-asia.ucsc.edu. Then on genome.ucsc.edu, you can load the session settings from a file, then attach the custom tracks, then save the session on genome.ucsc.edu.
Below is an example of doing these steps from a session existing on genome-euro.ucsc.edu. First, you will transfer the session settings file (which will not include the custom tracks).
Here are some example steps moving the session file from the genome-euro mirror to the main genome.ucsc.edu site (without custom tracks).
1) Save/Load session on genome-euro:
http://genome-euro.ucsc.edu/s/brianlee/EUROSessionCT_hg19_mm102) With the session existing on genome-euro and loaded go to the session page (My Data -> My Sessions) scroll down to the "Save Settings" section and find the "Save current settings to a local file:" section and enter a name like "sessionSettingsEuro" after file and click the "submit" button. A file will now be downloaded called sessionSettingsEuro.
3) Go to the main site, genome.ucsc.edu, and navigate to the session page (My Data -> My Sessions) making sure you are logged-in so you can save new sessions. Scroll down to "Restore Settings" and click the "Choose File" button next to the "Use settings from a local file:" option.
4) Find the sessionSettingsEuro file and click the "submit" button. You will now have your settings transferred. Note that it mentions expired custom tracks, "the session has at least one expired custom track (in database hg19 and mm10)" this is because the settings do not include the text-based custom tracks.
5) Save this session, going to "Save Settings" and giving it a name like "RRSessionCT_hg19_mm10".
Now we will transfer the custom tracks from genome-euro to genome.ucsc.edu for this session.
On genome.euro.ucsc.edu return to the session:
1) Save/Load your session on genome-euro:
http://genome-euro.ucsc.edu/s/brianlee/EUROSessionCT_hg19_mm102) With the session existing on genome-euro and loaded go to the session page (My Data -> My Sessions) scroll down to the "Save Settings" section and find the "Save Custom Tracks:" section and click the "submit" next to "backup custom tracks to archive .tar.gz".
3) On the next screen you can see which databases have uploaded text-based custom tracks. Click the "create custom tracks backup archive" button.
4) Enter a name such as "transferTracks" after the "Download archive as local file:" and then click the "download backup archive" button.
5) On your computer find the transferTracks.tar.gz and double-click it to expand the file. Click into the created transferTracks folder and then to the mm10 directory. Note the custom track file. One also exists for hg19 for this session.
6) On genome.ucsc.edu with the previous RRSessionCT_hg19_mm10 session loaded go to the custom track page (My Data -> Custom Tracks) and click the "Choose file" button for "Or upload" a custom track. Go into the mm10 directory described above and select the custom track and click "submit."
7) Return the custom track page (My Data -> Custom Tracks) and find the "add custom tracks" button. Change the genome to "genome Human" and assembly "Feb. 2009 (GRCh37/hg19)" and click the "Choose File" button.
8) Navigate to the transferTracks folder and then to the hg19 directory. Select the hg19 custom track and click "submit."
9) Go to the Genome browser for hg19 and mm10 and see the custom tracks are now attached for this session.
10) Save this session, going to "Save Settings" and giving it the same name as in above "RRSessionCT_hg19_mm10"
Now the sessions should be the same between the original on genome-euro and the new one on the genome.ucsc.edu.
There are other ways to batch download and upload custom tracks described here under "Restore a Custom track": http://genome.ucsc.edu/goldenPath/help/hgSessionHelp.html#Create
There may be difficulties with transferring sessions with hubs. Each mirror has a unique identifier for the URL attached to a hub stored within a table called hubStatus. By reconnecting hubs to the new machine you can find the appropriate hub_identifer# and then use scripting approaches to correct the new identifier on the new mirror. What is happening is that the Browser gives a new internal number like hub_1235 to each URL, but these numbers are not shared between mirrors and a downloaded session file will have a number for the old mirror and on the new mirror it may be hub_1239. A "cartDump" http://genome-euro.ucsc.edu/cgi-bin/cartDump when the hub is attached lets one see the numbers on either mirror (it is also in the downloaded session file). To update the older session you could manually edit lines in the text session file from these older hub_##### (say hub_1235) to point to the new location mirror number (say hub_1239) so it will match the hubStatus table existing in the new mirror. Do note that any custom tracks saved on an assembly hub will have a special "hubUrl" file, but this likely does not apply in your session.
For users that have @mail.nih.gov addresses, they may be interested to know there is a mirror of the UCSC Genome browser run by the NIH Helix HPC central IT group. See https://helix.nih.gov/, David Hoover should be the admin there who can give NIH members accounts on this mirror. NIH members using this mirror should be able to load protected BAM files at this location because this NIH administered UCSC mirror is behind the NIH firewall.
All the best,
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Dahong Chen
Sent: Wednesday, December 23, 2020 17:41
To: Dahong Chen <cd...@hotmail.com>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Re: [genome] Transfer sessions/tracks between mirror servers.