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Update README.md
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koditaraszka authored Apr 5, 2018
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Expand Up @@ -103,10 +103,10 @@ If you don't have root access, remove the `sudo` part and instead use `--user`
* The `setup.py` script is supposed to install setuptools for you if you don't have it. This sometimes works and sometimes doesn't. If you get and error with a message like ` invalid command 'develop'`, it means that setuptools is not installed. To solve this issue, you can manually install [setup tools](https://pypi.python.org/pypi/setuptools#installation-instructions). For example, on Linux, you can run `curl https://bootstrap.pypa.io/ez_setup.py -o - | sudo python`
(but note there are other ways of installing setuptools as well).

6. Pasta now includes additional aligners for Linux users: mafft-ginsi, mafft-homologs, contralign (version 1), and probcons. In order to use mafft-homologs and contralign, the user must set the environment variable CONTRALIGN_DIR=/dir/to/sate-tools-linux.
6. Pasta now includes additional aligners for Linux and MAC users: mafft-ginsi, mafft-homologs, contralign (version 1), and probcons. In order to use mafft-homologs and contralign, the user must set the environment variable CONTRALIGN_DIR=/dir/to/sate-tools-linux.

A simple step-by-step for this is as following:
a. change your directory to sate-tools-linux, type `pwd` in the command line, and copying the output
a. change your directory to sate-tools-linux (or sate-tools-mac), type `pwd` in the command line, and copy the output
b. `vim ~/.bashrc`, press i and then type CONTRALIGN_DIR=(paste the copied output/directory) at the bottom of the text file, the press ESC followed by :wq
c. then in the command line type `source ~/.bashrc`

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