diff --git a/docs/index.rst b/docs/index.rst index 9f0cf1f56..a6a26ca19 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -13,7 +13,9 @@ Welcome to SPRAS's documentation! ================================= -SPRAS is a Python package that builds on Snakemake and Docker to provide a standardized, reproducible, and scalable framework for applying pathway reconstruction +SPRAS is a Python package that builds on `Snakemake `_ and +`Docker `_ to provide a standardized, +reproducible, and scalable framework for applying pathway reconstruction methods (PRMs) to omics data. .. image:: _static/spras-overview.png @@ -27,7 +29,12 @@ methods (PRMs) to omics data. about install - vignettes + usage + +.. toctree:: + :maxdepth: 1 + :caption: Manual + output .. toctree:: diff --git a/docs/output.rst b/docs/output.rst index 88bbab0cf..1d7da3a95 100644 --- a/docs/output.rst +++ b/docs/output.rst @@ -9,8 +9,8 @@ and rows providing attributes for each edge. The header row is ``Node1 Node2 Rank Direction``. Each row lists the two nodes that are connected with an edge, the rank for that edge, and a directionality column to indicate whether the edge is directed or -undirected. The directionality values are either a ‘U’ for an undirected -edge or a ‘D’ for a directed edge, where the direction is from Node1 to +undirected. The directionality values are either a 'U' for an undirected +edge or a 'D' for a directed edge, where the direction is from Node1 to Node2. Pathways that do not contain ranked edges can output all 1s in the Rank column. diff --git a/docs/usage.rst b/docs/usage.rst new file mode 100644 index 000000000..161b39675 --- /dev/null +++ b/docs/usage.rst @@ -0,0 +1,12 @@ +Using SPRAS +=========== + +SPRAS is run through `Snakemake `_, which comes +with the SPRAS conda environment. + +To run SPRAS, run the following command inside the ``spras`` directory, +specifying a ``config.yaml`` and the number of cores to run SPRAS with: + +.. code-block:: bash + + snakemake --cores 1 --configfile config.yaml diff --git a/docs/vignettes.rst b/docs/vignettes.rst deleted file mode 100644 index d5d18a8fa..000000000 --- a/docs/vignettes.rst +++ /dev/null @@ -1,5 +0,0 @@ -SPRAS Python Vignettes -====================== - -Here are some nice vignettes explaining how *you* can run SPRAS against your own datasets -to do your awesome and revolutionary science!