diff --git a/docs/source/function/function.rst b/docs/source/function/function.rst new file mode 100644 index 00000000..71833d8f --- /dev/null +++ b/docs/source/function/function.rst @@ -0,0 +1,20 @@ +API +=== + + + +Function findOverlaps +##################### + +Joining datasets on ranges as key is frequently used in bioinformatics. Since dataset may consist of millions of elements a natural/brute-force solution is slow, inefficient and may not even + + +Using UDFs +########## + + +Additional parameteres +###################### + + + diff --git a/docs/source/implementation/implementation.rst b/docs/source/implementation/implementation.rst new file mode 100644 index 00000000..6a0b156b --- /dev/null +++ b/docs/source/implementation/implementation.rst @@ -0,0 +1,5 @@ +Implementation details +====================== + + + diff --git a/docs/source/index.rst b/docs/source/index.rst index 7aafa4ff..bb5e746e 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -3,18 +3,39 @@ You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -Welcome to bdg-spark-granges's documentation! -============================================= +SeQuiLa documentation +====================== .. toctree:: :maxdepth: 2 - :caption: Contents: + + quickstart/quickstart + +.. toctree:: + :maxdepth: 2 + + overview/overview + +.. toctree:: + :maxdepth: 3 + + usage/usage + +.. toctree:: + :maxdepth: 2 + + function/function + + + + + -Indices and tables -================== +.. Indices and tables +.. ================== -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` +.. * :ref:`genindex` +.. * :ref:`modindex` +.. * :ref:`search` diff --git a/docs/source/overview/overview.rst b/docs/source/overview/overview.rst new file mode 100644 index 00000000..e7788799 --- /dev/null +++ b/docs/source/overview/overview.rst @@ -0,0 +1,19 @@ +Overview +======== + + + + +Motivation +########### + +Joining datasets on ranges as key is frequently used in bioinformatics. Since dataset may consist of millions of elements a natural/brute-force solution is slow, inefficient and may not even + + +Solution overview +################# + + +Methods and algorithms (Implementation) +###################### + diff --git a/docs/source/quickstart/quickstart.rst b/docs/source/quickstart/quickstart.rst new file mode 100644 index 00000000..d71bec52 --- /dev/null +++ b/docs/source/quickstart/quickstart.rst @@ -0,0 +1,17 @@ +Quickstart +========== + + + + +Test run at local machine +######################### + +Prerequisities: Docker daemon installed and running. ``_ + +in your commandline invoke: +docker run --it -p 4040:4040 biodatageeks/bdg-toolset bdg-shell + + + + diff --git a/docs/source/usage/usage.rst b/docs/source/usage/usage.rst new file mode 100644 index 00000000..a2f08efd --- /dev/null +++ b/docs/source/usage/usage.rst @@ -0,0 +1,24 @@ +Usage +===== + +Playing within docker container +############################### +fsfds + + +Running at local machine +************************** +fsdfdsf + +Running at yarn +***************** +fsdfds + + +Running as Spark Thrift Server +############################## +fsdfsd + +Integrating granges with Spark application +########################################## +fsf