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SystemBasicSetup
To install protTrace with all its dependencies, you will require a number of basic software such as the programs make, gcc, and wget. If these programs are not available on your system, it is considerably straightforward to install them using the following commands. Note, you will need to have root privileges on your system. If this is not the case, then please ask your systems administrator for help.
To install protTrace including all dependencies on a freshly set up 64 bit linux system follow the steps below. We assume that you have root privileges on your system.
Download anaconda version 2.7 from https://www.anaconda.com/download Install anaconda by running the the installer script. Move to the directory to which you downloaded the anaconda distribution
$ bash Anaconda2-5.3.1-Linux-x86_64.sh
$ conda config --add channels bioconda
$ source ~/.bashrc
$ conda install -c cyclus java-jdk
$ conda install dendropy mafft blast hmmer iqtree
$ conda clean --all
The steps outlined below require sudo privileges.
$ sudo apt-get update
$ sudo apt-get install build-essential
$ sudo apt-get install git
$ sudo apt-get r-base
Use cpan to install the required perl modules.
$ sudo cpan install LWP::Simple
$ sudo cpan install List::Util
$ git clone https://github.com/BIONF/protTrace.git
Once this step has been accomplished, you can continue configuring protTrace
All programs should be distributed with the Xcode package
Use the the command cpan for this purpose (see above)