$ sudo pip install biopython pymongo pysam bx-python mongokit -U If you wish to install the pipeline dependencies on their own before the pipeline, you can do so using the following commands: $ sudo pip install numpy Cython anyjson -U Installing Python and Pip on Ubuntu 11.10: $ sudo apt-get install python python-dev python-pip The recommended way of installing the CaPSID pipeline is using pip, which will take care of the dependencies automatically.
You may need to source the file or restart before it will work: $ source /etc/environment
Make sure you version of Java is at least 1.7.0_91: $ java -version $ sudo update-java-alternatives -s java-1.7.0-openjdk-amd64 Installing OpenJDK Java package: $ sudo apt-get install icedtea-7-plugin openjdk-7-jre openjdk-7-jdk Installing Oracle JVM requires that it be downloaded directly from Oracle's site and installed as per their instructons: OpenJDK can be installed on Ubuntu using its package manager. Web Application Installing Java on Ubuntu 11.10ĬaPSID can be used with OpenJDK or Oracle VM. In order to complete the installation of the packages, you need to update the sources and then install the desired package $ sudo apt-get update It should be possible to import the key into apt's public keyring with a command like this: $ sudo apt-key adv -keyserver -recv 7F0CEB10Īdd this line verbatim to your /etc/apt/sources.list: $ deb dist 10gen MongoDB should be installed using the following set of instructions (see also mongodb installation):įirst add the 10gen GPG key, the public gpg key used for signing these packages. You will need to make sure that your username is on the sudo authorized list located at /etc/sudoers.