Install & Configure

Download rna-tools by clicking here https://github.com/mmagnus/rna-tools/archive/master.zip (~30 MB) or using git:

$ git clone https://github.com/mmagnus/rna-tools.git
$ cd rna-tools

git is better if you want to contribute to the package or/and you want to get pretty frequent updates.

The first step is “zero” because not all requirements are needed to start working with rna-tools.

To install the full set of requirements, use pip:

  1. pip install -r docs/requirements.txt

and setup the package itself in three steps:

  1. Add the path to the package to your PYTHONPATH (in ~/.bashrc or ~/.zshrc), e.g., export PYTHONPATH=$PYTHONPATH:/home/magnus/src/rna-tools/

  2. Add the path to the bin folder of the package to your PATH (in ~/.bashrc or ~/.zshrc), e.g., export PATH=$PATH:/home/magnus/src/rna-tools/bin/

  3. Add the path to the bin folder of the package to your PATH (in ~/.bashrc or ~/.zshrc), e.g., export RNA_TOOLS_PATH=/home/magnus/src/rna-tools/

  4. And run the installation script:

    ➜  rna-tools git:(master) ✗ ./install_links_bin.sh
    Installed in ./bin
    rmsd_calc_to_target.py
    

should be OK now :-)

To set you own configuration, please first:

cp rna_tools_config_local.py_sample rna_tools_config_local.py # in rna-tools/rna_tools

and then edit rna_tools_config_local.py as you need. In my case it is:

rna_tools git:(master) ✗ cat rna_tools_config_local.py
VARNA_PATH  = '/Users/magnus/skills/rnax/varna_tut/'
VARNA_JAR_NAME = 'VARNA.jar'