Author: Michael R. Crusoe <michael.crusoe@gmail.com>
Description: Update docs to reflect a local install
--- toil.orig/docs/index.rst
+++ toil/docs/index.rst
@@ -31,7 +31,6 @@
    :caption: Getting Started
    :maxdepth: 2
 
-   gettingStarted/install
    gettingStarted/quickStart
 
 .. toctree::
--- toil.orig/docs/gettingStarted/quickStart.rst
+++ toil/docs/gettingStarted/quickStart.rst
@@ -8,11 +8,9 @@
 Running a basic workflow
 ------------------------
 
-A Toil workflow can be run with just three steps:
+A Toil workflow can be run with just two steps:
 
-1. Install Toil (see :ref:`installation-ref`)
-
-2. Copy and paste the following code block into a new file called ``helloWorld.py``:
+1. Copy and paste the following code block into a new file called ``helloWorld.py``:
 
    .. code-block:: python
 
@@ -30,14 +28,9 @@
           print output
 
 
-3. Specify the name of the :ref:`job store <jobStoreOverview>` and run the workflow::
-
-       (venv) $ python helloWorld.py file:my-job-store
+2. Specify the name of the :ref:`job store <jobStoreOverview>` and run the workflow::
 
-.. note::
-
-   Don't actually type ``(venv) $`` in at the beginning of each command. This is intended only to remind the user that
-   they should have their :ref:`virtual environment <venvPrep>` running.
+       python helloWorld.py file:my-job-store
 
 Congratulations! You've run your first Toil workflow using the default :ref:`Batch System <batchsysteminterface>`, ``singleMachine``,
 using the ``file`` job store.
@@ -64,13 +57,6 @@
 workflows that are portable across multiple workflow engines and platforms.
 Running CWL workflows using Toil is easy.
 
-#. First ensure that Toil is installed with the
-   ``cwl`` extra (see :ref:`extras`)::
-
-       (venv) $ pip install 'toil[cwl]'
-
-   This installs the ``toil-cwl-runner`` and ``cwltoil`` executables.
-
 #. Copy and paste the following code block into ``example.cwl``:
 
    .. code-block:: yaml
@@ -96,11 +82,11 @@
 
 #. To run the workflow simply enter ::
 
-        (venv) $ toil-cwl-runner example.cwl example-job.yaml
+        $ toil-cwl-runner example.cwl example-job.yaml
 
    Your output will be in ``output.txt``::
 
-        (venv) $ cat output.txt
+        $ cat output.txt
         Hello world!
 
 To learn more about CWL, see the `CWL User Guide`_ (from where this example was
@@ -110,7 +96,7 @@
 
 For information on using CWL with Toil see the section :ref:`cwl`
 
-.. _CWL User Guide: http://www.commonwl.org/v1.0/UserGuide.html
+.. _CWL User Guide: https://www.commonwl.org/user_guide/
 
 Running a basic WDL workflow
 ----------------------------
@@ -118,13 +104,6 @@
 The `Workflow Description Language`_ (WDL) is another emerging language for writing workflows that are portable across multiple workflow engines and platforms.
 Running WDL workflows using Toil is still in alpha, and currently experimental.  Toil currently supports basic workflow syntax (see :ref:`wdlSupport` for more details and examples).  Here we go over running a basic WDL helloworld workflow.
 
-#. First ensure that Toil is installed with the
-   ``wdl`` extra (see :ref:`extras`)::
-
-        (venv) $ pip install 'toil[wdl]'
-
-   This installs the ``toil-wdl-runner`` executable.
-
 #. Copy and paste the following code block into ``wdl-helloworld.wdl``::
 
         workflow write_simple_file {
@@ -144,11 +123,11 @@
 
 #. To run the workflow simply enter ::
 
-        (venv) $ toil-wdl-runner wdl-helloworld.wdl wdl-helloworld.json
+        $ toil-wdl-runner wdl-helloworld.wdl wdl-helloworld.json
 
    Your output will be in ``wdl-helloworld-output.txt``::
 
-        (venv) $ cat wdl-helloworld-output.txt
+        $ cat wdl-helloworld-output.txt
         Hello world!
 
 To learn more about WDL, see the main `WDL website`_ .
@@ -175,7 +154,7 @@
 
 #. Run it with the default settings::
 
-      (venv) $ python sort.py file:jobStore
+      $ python sort.py file:jobStore
 
    The workflow created a file called ``sortedFile.txt`` in your current directory.
    Have a look at it and notice that it contains a whole lot of sorted lines!
@@ -192,7 +171,7 @@
 
 3. Run with custom options::
 
-      (venv) $ python sort.py file:jobStore --numLines=5000 --lineLength=10 --overwriteOutput=True --workDir=/tmp/
+      $ python sort.py file:jobStore --numLines=5000 --lineLength=10 --overwriteOutput=True --workDir=/tmp/
 
    Here we see that we can add our own options to a Toil script. As noted above, the first two
    options, ``--numLines`` and ``--lineLength``, determine the number of lines and how many characters are in each line.
@@ -308,7 +287,7 @@
 with the ``--logLevel`` flag. For example, to only log ``CRITICAL`` level
 messages to the screen::
 
-   (venv) $ python sort.py file:jobStore --logLevel=critical --overwriteOutput=True
+   $ python sort.py file:jobStore --logLevel=critical --overwriteOutput=True
 
 This hides most of the information we get from the Toil run. For more detail,
 we can run the pipeline with ``--logLevel=debug`` to see a comprehensive
@@ -332,7 +311,7 @@
 
 When we run the pipeline, Toil will show a detailed failure log with a traceback::
 
-   (venv) $ python sort.py file:jobStore
+   $ python sort.py file:jobStore
    ...
    ---TOIL WORKER OUTPUT LOG---
    ...
@@ -354,11 +333,11 @@
 failure, the job store is preserved so that the workflow can be restarted,
 starting from the previously failed jobs. We can restart the pipeline by running ::
 
-   (venv) $ python sort.py file:jobStore --restart --overwriteOutput=True
+   $ python sort.py file:jobStore --restart --overwriteOutput=True
 
 We can also change the number of times Toil will attempt to retry a failed job::
 
-   (venv) $ python sort.py --retryCount 2 --restart --overwriteOutput=True
+   $ python sort.py --retryCount 2 --restart --overwriteOutput=True
 
 You'll now see Toil attempt to rerun the failed job until it runs out of tries.
 ``--retryCount`` is useful for non-systemic errors, like downloading a file that
@@ -369,7 +348,7 @@
 
 ::
 
-    (venv) $ python sort.py --restart --overwriteOutput=True
+    $ python sort.py --restart --overwriteOutput=True
 
 The pipeline will run successfully, and the job store will be removed on the
 pipeline's completion.
@@ -428,7 +407,7 @@
 
 #. Use the :ref:`destroyCluster` command to destroy the cluster::
 
-        (venv) $ toil destroy-cluster --zone us-west-2a <cluster-name>
+        $ toil destroy-cluster --zone us-west-2a <cluster-name>
 
    Note that this command will destroy the cluster leader
    node and any resources created to run the job, including the S3 bucket.
