Fixed documentation to reflect the removal of bioconda-recipes

birgorg · Apr 5, 2020 · 53945e5 · 53945e5
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diff --git a/docs/usage/installation.rst b/docs/usage/installation.rst
@@ -50,13 +50,7 @@ Install it with the setup.py and check if BiRG is installed correctly by running
 Dependencies
 ++++++++++++
 
-BiRG needs the bioconda-recipe repo which should also be cloned from git:
-
-.. code-block:: console
-
-    $ git clone https://github.com/bioconda/bioconda-recipes.git
-
-To run BiRG you also need to have Docker installed and working. We use Docker to ensure that the
+To run BiRG you also to have Docker installed and working. We use Docker to ensure that the
 environment, which we are building and testing in is clean an reproducible.
 
 We recommend that you follow the Docker installation guide which can be found at the following link:

diff --git a/docs/usage/tutorial.rst b/docs/usage/tutorial.rst
@@ -104,7 +104,7 @@ We will also edit the the `build.sh`, as netReg requires us to set some flags fo
 Recipe Build
 ++++++++++++
 
-We are now ready to give our inital recipe as input to BiRG. The build command takes three required arguments as shown below:
+We are now ready to give our inital recipe as input to BiRG. The build command takes two required arguments as shown below:
 
 .. code-block:: console
     
@@ -114,8 +114,6 @@ We are now ready to give our inital recipe as input to BiRG. The build command t
                                      {cmake,python2,python3}
 
     positional arguments:
-      bioconda_recipe_path  Path to your local copy of the bioconda-recipe
-                              repository
       recipe_path           Path to folder with meta.yaml and build.sh templates
       {cmake,python2,python3}
                             The ? that you used when creating the template with
@@ -127,17 +125,15 @@ We are now ready to give our inital recipe as input to BiRG. The build command t
                             This creates an debug.log file that contains all debug
                             prints
 
-bioconda_recipe_path: Is the path to you local version of the bioconda-recipes repository, which can be found `here <https://github.com/bioconda/bioconda-recipes>`_ .
-
 recipe_path: Is the path to the recipe directory which was created by running `bioconda-recipe-gen init`.
 
 Strategy: Here you must tell BiRG which building strategy to use, we currently supports three strategies cmake, python2 or python3.
 
-Here is an example on how BiRG is called for building fuma:
+Here is an example on how BiRG is called for building netreg:
 
 .. code-block:: console
     
-    $ bioconda-recipe-gen build bioconda-recipes/ netreg/ cmake
+    $ bioconda-recipe-gen build netreg/ cmake
 
 When BiRG is running it will print out a lot of text, this is the output from it's building process.
 BiRG will also some times ask for your help, to determine which version of a dependency it should use.