diff --git a/docs/usage/getting_started.rst b/docs/usage/getting_started.rst index 58f9cc76..adb643bb 100644 --- a/docs/usage/getting_started.rst +++ b/docs/usage/getting_started.rst @@ -8,7 +8,6 @@ Installation #. Download the repo locally from github - ``git clone git@github.com:broadinstitute/ABC-Enhancer-Gene-Prediction.git`` - - Utilize the **dev** branch: ``git checkout dev`` #. Make sure you have conda & mamba installed - ``_ - Make sure you're not using strict channel priorities: ``conda config --set channel_priority flexible``. Otherwise, you may encounter package conflicts later when installing abc. @@ -54,7 +53,7 @@ Configuring ABC --------------- The primary configuration file for ABC is `config/config.yaml -`_ +`_ *First couple lines in config/config.yaml* @@ -87,7 +86,7 @@ The rule specific params are explained in the :ref:`ABC-methods` section. BiosampleTable Specifications ----------------------------- -`chr22 example `_ +`chr22 example `_ biosamples config is a tsv separated file with the following columns