#Sourcetree linux install
#Sourcetree linux password

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#Sourcetree linux install

Wget -O /usr/local/apache/cgi-bin/hg.confĭownload Hiram's install scripts to some place.

#Sourcetree linux password

# alternative: use the public mysql server and my configuration, should work if your root password is 'browser' Set the mysql connection to the public mysql server:ĬustomTracks.tmpdir=/usr/local/apache/trash/customTrash Mysql -u root -p (you chose the password during installation of the package) -e 'create database customTrash create database hgcentral # setup mysql, set the root password to 'browser'

Sudo chown $USER:$USER /usr/local/apache/cgi-bin Sudo chown www-data:www-data /usr/local/apache/trash/customTrash Sudo mkdir -p /usr/local/apache/trash/customTrash

# setup the custom trash dir in the same way # the cgis create links to images in /trash Sudo chown www-data:www-data /usr/local/apache/trash # apache needs to be able to create images This path does not conform to Ubuntu's specifications but has the advantage that we don't need to change any make variable in the UCSC tree. I prefer to place the CGIs in the same location where UCSC has them, that's /usr/local/apache. Run a genome browser mirror on your local machine, compiled from source You can mirror hg19 like this ('bash browserInstall.sh hg19'), but remember that it will take a lot of space, ~2.2 TB. This will be very slow unless you're in San Francisco. If you look into the /usr/local/apache/cgi-bin/hg.conf file, you can see that we use the public mysql server through the internet. Then connect with a firefox to localhost. Just tested this with ubuntu 14 LTS, centos 6, centos 7, fedora 20 and OSX 10.10 (on OSX, requires Xcode and macports): The fastest way ever to get a genome browser up and running on Ubuntu, Fedora, Centos, OSX # this does not seem to be necessary anymoreĪdd the parameter HG_WARN=-w to DIRS if you don't want the compilation to stop on error messages. # please not that these won't install the samtools library to handle bam filesĪpt-get install mysql-server-5.0 apache2 libmysqlclient15-dev libpng12-dev libssl-dev openssl mysql-client-5.5 mysql-client-core-5.5Įxport MYSQLINC=`mysql_config -include | sed -e 's/^-I//g'`ĭIRS='SCRIPTS=/usr/local/bin CGI_BIN=/usr/lib/cgi-bin DOCUMENTROOT=/var/www/genome BINDIR=/usr/local/bin' # install required packages from repository # we need to be root to install packages and put stuff into /usr/local In theory, once you have installed the samtools library, you can just copy-paste this script into a command line They will put all binaries in /usr/local, all cgi-bins in /usr/lib/cgi-bin and all html-like things into /var/www/genome. They have been tested on Debian Lenny (64 and 32bit), Ubuntu Maverick and Ubuntu 13.04. These commands compile the UCSC genome browser and all source tools. Please note the instructions and scripts in the source tree that can build the kent source tree on The installation is not easy, see below for a script that automates the process. The UCSC source tree includes tools for the command line and the CGIs for a local UCSC genome browser mirror.