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| == Release ==
| | This page is no longer maintained. |
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| The Gbib is a Ubuntu 13 VirtualBox VM with apache, mysql and the genome browser (see [[Preparing_VirtualBox_images]]).
| | Moved to [http://genomewiki.ucsc.edu/genecats/index.php/Genome_Browser_in_a_Box_config] |
| It has a special hg.conf, uses the tableList tables in all organism DBs and loads most files from hgdownload on the fly.
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| For QA release instructions, see [[Gbib release]]
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| Development for the Gbib is a different business and described in [[Gbib development]].
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| == Updating a box ==
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| the script /root/updateBrowser.sh does the whole update. By default, it updates the box to "release" state, which is the one on hgdownload, but can also update to "devbox", "alpha", or "beta" states, these can be prepared by developers or QA during testing, see [[Gbib release]]
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| The script updates various directories on the box:
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| - cgi-bin: from hgdownload (or from hgwdev, if alpha/beta/devbox state)
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| - htdocs: from hgdownload (or from hgwdev, if alpha/beta/devbox state)
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| - mysql: always from hgdownload
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| - additional files: e.g. additional icons and the tableListAdd.*.tab files in /root. Depending on state, from hgdownload or hgwdev
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| - html patches: Remove menu items, change some text. Static.
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| - some mysql tables (via hgMirror): remove some tracks from search, hide some tracks, load /root/tableListAdd.* etc. Calls hgMirror for this.
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| Protected tracks have no state and are not updated.
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| == Protected tracks ==
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| protected tracks are tracks that are not on hgdownload but are available from the box. Currently these are OMIM and hgmd, but will hopefully include LOVD and decipher one day.
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| These tracks are missing from the tableList table in hg19, so their tableList info is in /root/tableListAdd.hg19.tab and is added to tableList after each rsync. This is done by hgMirror, (is called from updateBrowser.sh), because hgMirror includes all post-rsync code now.
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| The track tables are added manually to the box once and are not updated with normal auto updates.
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| OMIM are just the normal tables, in a copy form hgwbeta from Apr 2014.
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| The HGMD table is just a pointer to a bigbed file on hgdownload. Our binaries include code to add a password when this file is loaded via https.
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| == Auto updates ==
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| The updateBrowser.sh script is called by cron every five minutes. This can be changed with autoUpdatesOff and autoUpdatesOn as user "browser" (see ~browser/.bashrc).
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| The updateBrowser.sh script checks if a flagfile on hgdownload has changed relative to a local file. If it has not been changed, then the script just stops.
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| == Pushing files into the box ==
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| If a CGI release requires other files, outside the cgi-bin directory, or special software on the box, these files have to be pushed into the box.
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| To push a file into the box, on hgwdev, copy it into /usr/local/apache/gbib/push/ in many cases you will have to create the right subdirectory. Note that /usr/local/apache/gbib/push/ is the "root" of the box. After each update, the box will rsync from /usr/local/apache/gbib/push/ into /.
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| You can test if this works by running
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| updateBrowser beta
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| on the box which will use the files from hgwdev.
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| If it works, tell the pushers to push the push directory onto hgdownload. On the next update of the box (usually Sunday), all boxes will pull the push directory into their root directory.
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| If an update requires an ubuntu package, you will have to add "apt-get install" commands to updateBrowser.sh.
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