Update example data

docs/additional_commands.rst

@@ -3,6 +3,8 @@ Additional Commands
 
 To make using pVAC-Seq easier several convenience methods are included in the package.
 
+.. _example_data:
+
 Download Example Data
 ---------------------
 

docs/contact.rst

@@ -1,4 +1,4 @@
 Contact
 =======
 
-Bug reports or feature requests can be submitted on the `pVAC-Seq Github page <https://github.com/griffithlab/pVAC-Seq/issues>`_. You may also contact us by email at pvacseq-support@genome.wustl.edu.
+Bug reports or feature requests can be submitted on the `pVAC-Seq Github page <https://github.com/griffithlab/pVAC-Seq/issues>`_. You may also contact us by email at pvacseq-support@gowustl.onmicrosoft.com.

docs/index.rst

@@ -23,11 +23,28 @@ pVAC-Seq is a cancer immunotherapy pipeline for the identification of **p**\ ers
 New in version |version|
 ------------------------
 
-This is a hotfix release. It fixes an error introduced in a previous version
-that would occur when using a local installation of the IEDB tools and is
-related to some filtering we do on the output from the IEDB tools. More
-information can be found on `GitHub issue 278
-<https://github.com/griffithlab/pVAC-Seq/issues/278>`_.
+This release adds handling for DNPs and MNPs missense mutations.
+
+This version adds a new option ``--additonal-report-columns`` to the ``pvacseq
+run`` command which can be use
+to append additional columns of data to the report. Right now the only value
+supported for this option is ``sample_name`` which appends a column with the
+sample name to the final report.
+
+We updated the logic that determines whether or not a corresponding wildtype
+epitope for a mutant epitope is included in the report. Previously, we would only
+include the corresponding wildtype epitope if the number of **consecutive**
+matching amino acids between mutant and wildtype epitope was larger then half
+of the total number of amino acids in the epitope. We now use the **total** number of
+matching amino acids between the mutant epitope and the corespondig wildtype epitope
+across the whole length of the epitope to make that determination. The total
+number of matching amino acids needs to be larger than half of the length of
+the epitope. Otherwise the corresponding wildtype epitope is reported as "NA".
+
+With this release any execution of ``pvacseq run`` will create a log file of the
+inputs used. This log file is then used when executing another run
+with the same output directory. This ensures that you can only write to the same
+output directory if identical parameters are used.
 
 Citation
 --------

docs/install.rst

@@ -41,8 +41,10 @@ Installing IEDB binding prediction tools (strongly recommended)
 .. warning::
    Using a local IEDB installation is strongly recommended for larger datasets
    or when the making predictions for many alleles, epitope lengths, or
-   prediction algorithms. More information on how to install IEDB locally can
-   be found on the :ref:`Installation <iedb_install>` page.
+   prediction algorithms.
+
+.. warning::
+   The IEDB binding prediction tools are only compatible with Linux.
 
 You may create a local install of the IEDB binding prediction tools by first downloading the archives for `class I <http://tools.iedb.org/mhci/download/>`_ and `class II <http://tools.iedb.org/mhcii/download/>`_ from the IEDB website. If using both the Class I and the Class II tools, they both need to be installed into the same parent directory.
 
@@ -86,3 +88,24 @@ ____________
 .. note::
 
    Running the ``configure`` script requires a Python 2 environment. If you are currently emulating a Python 3 environment with Conda you will need to run ``source deactivate`` before executing the ``configure`` script.
+
+Getting Started
+---------------
+
+pVAC-Seq provides a set of example data to show the expected input and output files. You can download the data set by running the ``pvacseq download_example_data`` :ref:`command <example_data>`.
+
+The example data output can be reproduced by running the following command:
+
+.. code-block:: none
+
+   pvacseq run \
+   <example_data_dir>/input.vcf \
+   Test \
+   HLA-G*01:09,HLA-E*01:01,H2-IAb \
+   NetMHC PickPocket NNalign <output_dir> \
+   -e 9,10 \
+   -i <example_data_dir>/additional_input_file_list.yaml --tdna-vaf 20 \
+   --net-chop-method cterm --netmhc-stab \
+   --top-score-metric=lowest -d full --keep-tmp-files
+
+A detailed description of all command options can be found on the :ref:`Usage <run>` page.