Genome-preview machine: Difference between revisions
| Line 42: | Line 42: | ||
-y | --noprompt : Just do it, don't ask me. | -y | --noprompt : Just do it, don't ask me. | ||
</pre> | </pre> | ||
'''From your hgwdev kent repository the below steps to update CGIs/js/style take place.''' | |||
'''Note: you'll first need to update''' the ''js files for preview'' at: | '''Note: you'll first need to update''' the ''js files for preview'' at: | ||
ls -l /usr/local/apache/htdocs/js/preview/ | ls -l /usr/local/apache/htdocs/js/preview/ | ||
<pre> | <pre> | ||
cd ~/kent/src/hg/js | |||
git pull | git pull | ||
make USER=preview | make USER=preview | ||
</pre> | </pre> | ||
'''Note: you'll first need to update''' the ''style files'' for hgwdev at: | '''Note: you'll first need to update''' the ''style files'' for hgwdev at: | ||
ls -l /src/hg/htdocs/style | ls -l /src/hg/htdocs/style | ||
<pre> | <pre> | ||
cd ~/kent/src/hg/htdocs/style | |||
git pull | git pull | ||
make alpha | make alpha | ||
</pre> | </pre> | ||
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'''Note: you'll first need to update''' ''the CGIs for preview'' at: ls -lrt /usr/local/apache/cgi-bin-preview/ | '''Note: you'll first need to update''' ''the CGIs for preview'' at: ls -lrt /usr/local/apache/cgi-bin-preview/ | ||
<pre> | <pre> | ||
cd ~/kent/src | |||
git pull | git pull | ||
USER=preview make cgi | |||
</pre> | </pre> | ||
There are some redundant git pulls here, they exist to | There are some redundant git pulls here, they exist to drive home the message to be sure your branch is current. Once all your files are updated, you should run the command with the -c --check option to see what will be updated: '''pushDevToPreview -c''' and remember to have accessed the qateam identity '''ssh qateam@hgwdev''' | ||
If things look pretty good, then you are ready to run the command, with the -i interactive mode so you can see what commands are being run: | If things look pretty good, then you are ready to run the command, with the -i interactive mode so you can see what commands are being run: | ||
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</pre> | </pre> | ||
Finally you'll check on genome-preview if the changes are updated. | |||
[[Category:Browser QA]][[Category:Browser Development]] | [[Category:Browser QA]][[Category:Browser Development]] | ||
Revision as of 22:32, 30 April 2019
In early 2011, we created a new machine called genome-preview, which is a mirror of our development machine: genome-test.
It is here: http://genome-preview.soe.ucsc.edu/
It has these warnings on the home page:
WARNING: This is our preview site. This website is a weekly mirror of our internal development server for public access. Data and tools here are under construction, have not been quality reviewed, and are subject to change at any time. We provide this site for early access, with the warning that it is less available and stable than our public site. For high-quality reviewed annotations on our production server, visit http://genome.ucsc.edu.
In general, we do not push updates/files/tables/patches to this machine by hand. It is generally understood that it will sometimes be out of commission, as it is a mirror of a development machine.
The impetus behind this machine was to allow early access to the ENCODE data by ENCODE consortia members.
Automated Updates
The genome-preview machine is updated on a weekly basis like so:
On Friday nights (11:33 pm), the following stuff is copied from hgwdev:
- mysql tables (excluding mysql, customTrash, and other things)
- hgcentraltest tables (excluding userDb, sessionDb, namedSessionDb and hubStatus)
- CGIs
- htdocs
Most of the stuff on /gbdb comes from backups of the /hive/data and /hive/groups.
- /hive/data is backed up on Fridays at 5:22 am
- /hive/groups is backed up on Wednesdays at 5:22 am.
Note that this may cause some inconsistencies if new data is added on Thursday to /hive/groups and accessed by new CGIs, since the data will not be available on the backups until the following Wednesday.
Updating Genome-Preview with pushDevToPreview
If there is a need to sync the CGIs on hgwdev to genome-preview the pushDevToPreview script will do it (from the qateam@hgwdev identity).
pushDevToPreview -h Usage: pushDevToPreview [-chiqvy] -c | --check : Don't do the push, just say what would be pushed. -h | --help : Print this message. -i : Interactive mode. Ask me before doing any command. -q | --quiet : Quiet mode. Don't print anything unless necessary. -v | --verbose : Increase verbosity. -y | --noprompt : Just do it, don't ask me.
From your hgwdev kent repository the below steps to update CGIs/js/style take place.
Note: you'll first need to update the js files for preview at:
ls -l /usr/local/apache/htdocs/js/preview/
cd ~/kent/src/hg/js git pull make USER=preview
Note: you'll first need to update the style files for hgwdev at: ls -l /src/hg/htdocs/style
cd ~/kent/src/hg/htdocs/style git pull make alpha
Note: you'll first need to update the CGIs for preview at: ls -lrt /usr/local/apache/cgi-bin-preview/
cd ~/kent/src git pull USER=preview make cgi
There are some redundant git pulls here, they exist to drive home the message to be sure your branch is current. Once all your files are updated, you should run the command with the -c --check option to see what will be updated: pushDevToPreview -c and remember to have accessed the qateam identity ssh qateam@hgwdev
If things look pretty good, then you are ready to run the command, with the -i interactive mode so you can see what commands are being run:
pushDevToPreview -i Pushing files from hgwdev to genome-preview Do you wish to proceed? (y/[n]): y Doing directory /usr/local/apache/cgi-bin-preview/ between hgwdev and genome-preview The command to be executed is /usr/bin/rsync -rlptDi --delete --chown=qateam:protein --exclude=hg.conf* /usr/local/apache/cgi-bin-preview/ genome-preview:/usr/local/apache/cgi-bin-preview/ ... ...
Finally you'll check on genome-preview if the changes are updated.
