Install & Configure

Download rna-tools by clicking here https://github.com/mmagnus/rna-tools/archive/master.zip (~30 MB) and unpack the zip file, enter the folder:

$ cd rna-tools-master

OR use 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. If anything is missing you can install it later.

To install the full set of requirements, use pip:

  1. pip install -r docs/requirements.txt

  2. Setup the package paths by adding to your ~/.bashrc or ~/.zshrc following code:

    export RNA_TOOLS_PATH=<PATH TO YOUR RNA_TOOLS>
    export PYTHONPATH=$PYTHONPATH:$RNA_TOOLS_PATH
    export PATH=$PATH:$RNA_TOOLS_PATH'/bin/'
    

for example in my case it looks as:

export RNA_TOOLS_PATH=/home/magnus/work-src/rna-tools/
export PYTHONPATH=$PYTHONPATH:$RNA_TOOLS_PATH
export PATH=$PATH:$RNA_TOOLS_PATH'/bin/'
  1. And run the installation script:

    ➜  rna-tools git:(master) ✗ ./install_links_bin.sh
    Installed in ./bin
    rmsd_calc_to_target.py
    
  2. Run rna_tools_test_all.py to see if you got any errors, this should look like:

    (py37) [mm] rna-tools$ git:(master) rna_tools_test_all.py
    BlastPDB requires urllib3
    - Python: 3.7.4 (default, Aug 13 2019, 15:17:50) [Clang 4.0.1 (tags/RELEASE_401/final)]
    - rna-tools: b'py2-78-g3b3dd5f'
    - RNA_TOOLS_PATH set to  /home/magnus/work-src/rna-tools/
    - See full list of tools <https://github.com/mmagnus/rna-tools/blob/master/rna-tools-index.csv
    Seems OK
    

or for Python 2:

(base) [mm] rna-tools$ git:(master) rna_tools_test_all.py
- Python: 2.7.16 |Anaconda, Inc.| (default, Mar 14 2019, 16:24:02) [GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)]
- rna-tools: py2-78-g3b3dd5f
- RNA_TOOLS_PATH set to  /home/magnus/work-src/rna-tools/
- See full list of tools <https://github.com/mmagnus/rna-tools/blob/master/rna-tools-index.csv
Seems OK

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'