Merge pull request #520 from lucazpinheiro/patch-1

Changed proposed on issue #513

docs/install/manual_install.md

@@ -70,6 +70,7 @@ environment within anaconda to avoid conflicts with other applications.
   ```
   $ source setup/setup_conda.sh
   ```
+  IMPORTANT: this script works for MacOSX and Ubuntu based Linux distributions, the OS must be specified on the command with one of two choices: ```Linux-x86_64``` or ```MacOSX-x86_64```. The final command would be this ```source setup/setup_conda.sh Linux-x86_64``` or this ```source setup/setup_conda.sh MacOSX-x86_64```.
 
 - Setup the `emission` environment.
 
@@ -96,7 +97,7 @@ environment within anaconda to avoid conflicts with other applications.
   root                     /..../anaconda
   ```
 
-- If you have setup the environment already and just need to switch to it, you can also use `source activate emission` to switch to the emission environment. To switch out of the emission environment, or to manipulate it in other ways, read the conda documentation on environments https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html Note that depending on the version of conda that you have installed, you may use `conda activate` or `source activate`
+- If you have setup the environment already and just need to switch to it, you can also use `conda activate emission` to switch to the emission environment. To switch out of the emission environment, or to manipulate it in other ways, read the conda documentation on environments https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html
 
 - Remember to re-run the setup script every time you pull from the main repository because the dependencies may have changed.
 
@@ -124,6 +125,13 @@ Tip: Run "bower install" instead if you are prompted password for 'https://githu
 ## Run ##
 ---------
 
+IMPORTANT: If you have used the ```setup_conda.sh``` script, you will need to run the command 
+  ```
+  $HOME/miniconda/etc/profile.d/conda.sh
+  ```
+  on every new terminal. This is due to the installation being made through a script, which doesn't modify the ```bashrc```                       with the correct path.
+
+
 1. On OSX, start the database  (Note: mongodb appears to be installed as a service on Windows devices and it starts automatically on reboot). 
 
         $ mongod