INSTALL_LINUX.txt

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.

### 1. INSTALLING ANACONDA
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

### 2. INSTALLING THE ACCESSORY SOFTWARE VIA CONDA
$ conda install -c cyclus java-jdk
$ conda install dendropy mafft blast hmmer iqtree
$ conda clean --all

### 3. INSTALLING SYSTEM TOOLS (gcc, make, git, R)
$ sudo apt-get update
$ sudo apt-get install build-essential
$ sudo apt-get install git
$ sudo apt-get r-base

### 4. INSTALLING NON-STANDARD PERL MODULES
$ sudo cpan install LWP::Simple
$ sudo cpan install List::Util

### 5. RETRIEVING PROTTRACE VIA GIT
git clone https://github.com/BIONF/protTrace.git

### 6. CONFIGURING PROTTRACE
cd protTrace
perl bin/create_conf.pl -name=prog.config -getOma -getPfam

### 7. TEST RUN OF PROTTRACE
move into the toy_examples directory
$ python ../bin/protTrace.py -i test.id -c ../prog.config