687d35acc65ff6e5dc22e80c749549ff7d8886ef max Tue Aug 21 13:36:58 2018 -0700 Revert "moving all config files in GBIB to the new .gi.ucsc.edu domain names" Apparently there is no plan to create hgdownload.gi.ucsc.edu. The previous commit was completely useless. This reverts commit e1b3625f3a40bfee5c483284fa7f6b23bf6bd47d. diff --git src/browserbox/README.txt src/browserbox/README.txt index 2648d62..26512ef 100644 --- src/browserbox/README.txt +++ src/browserbox/README.txt @@ -1,63 +1,39 @@ kent/browserbox/ This directory contains the config files that are needed for the Genome Browser in a box. It should be possible to convert a Ubuntu 14 installation into a Genome Browser in a box by copying all these -files into the root directory as sudo. (Redmine #11957) But we have -never done this, we have a running VM and don't need to rebuild it. - -The most important part of the GBIB setup is the update script, located in -this directory under kent/browserbox/root/updateBrowser. Making changes to GBIB -usually means changing this script as WE DO NOT MODIFY THE GBIB VM, we only -make changes to the update script, so all running GBIBs out there will still -work and they are all in sync. - -If you change the copy of the update script in this git repo, please be aware -that it will not automatically land on GBIBs to prevent accidentally breaking -them all. You change updateBrowser, copy it to hgwdev.gi.ucsc.edu/gbib, you -test it on your own GBIB with "updateBrowser hgwdev". If it works, you commit the -file into the git repo and request a push of the file from hgwdev.gi.ucsc.edu/gbib to -hgdownload.gi.ucsc.edu/gbib. This is all explained in the genomewiki page below. - -This update script rsyncs the directory hgdownload::gbib/push whenever it updates -into / so hg.conf updates, little binary tools or similar changes can also come -in through the push directory. Again, we do not make changes to the GBIB VM, -but only through the update script or possibly through the push directory. - -PLEASE READ the main gbib doc page and the pages linked from there: -http://genomewiki.ucsc.edu/genecats/index.php/Genome_Browser_in_a_Box_config - ---- +files into the root directory as sudo. (Redmine #11957) -The following information is only relevant is you're thinking about rebuilding -a GBIB-like system from this directory. +See also the main gbib doc page: +http://genomewiki.ucsc.edu/genecats/index.php/Genome_Browser_in_a_Box_config The following symlinks are not in git and have to be set manually : usr/local/apache/htdocs/folders -> /media usr/local/apache/trash -> /data/trash/ usr/local/apache/userdata -> /data/userdata/ var/lib/mysql -> /data/mysql Change ownerships of /data/gbdb, /data/trash and /data/userdata to www-data and /data/mysql to mysql -This tree here does not include the trash cleaner binaries as they are > 5MB. Ask +This tree does not include the trash cleaner binaries as they are > 5MB. Ask Hiram to install the trash cleaner if you need it fixed or changed. The directory clientInstall/ contains two small scripts that add the entry "genome.ucsc.local" to the local hosts file. One is written in VisualBasic for Windows, the other is in AppleScript for OSX. The AppleScript version also contains a firewall rule that redirects localhost:1234 to localhost:80, the only way to get a restricted port (<1024) to work with VirtualBox. (Redmine #12834) The Applescript can be packaged into an app with the AppleScript editor. The result can only be copied around as a zip file due to OSX special file attributes. the files packages-ubuntu*.txt are the lists of packages installed on the final gbib in ubuntu13 and ubuntu14. Various changes of the box are documented in root/changes.txt The red box clipart is from http://www.clker.com/clipart-14656.html