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griffithlab · Feb 20, 2017 · c6312fb · c6312fb
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diff --git a/docs/features.rst b/docs/features.rst
@@ -13,9 +13,19 @@ pVAC-Seq uses a single-sample VCF file as its input. This VCF file must be annot
 
 pVAC-Seq utilizes the IEDB RESTful web interface. This means that none of the underlying prediction software, like NetMHC, needs to be installed locally.
 
+.. warning::
+   The IEDB RESTful API URLs are currently broken. Until this issue if fixed,
+   you will need to use a local IEDB installation to run pVAC-Seq. IEDB has
+   been informed of this issue. For more information on how to run pVAC-Seq
+   with a local IEDB installation, please see the page on :ref:`run`.
+
 **Support for local installation of the IEDB Analysis Resources**
 
-pVAC-Seq provides the option of using a local installation of the IEDB MHC `class I <http://tools.iedb.org/mhci/download/>`_ and `class II <http://tools.iedb.org/mhcii/download/>`_ binding prediction tools.
+pVAC-Seq provides the option of using a local installation of the IEDB MHC
+`class I <http://tools.iedb.org/mhci/download/>`_ and `class II <http://tools.iedb.org/mhcii/download/>`_
+binding prediction tools. Using a local IEDB installation is recommended for
+larger datasets or when the making predictions on many
+alleles, epitope lengths, or prediction algorithms.
 
 **MHC Class I and Class II predictions**
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -25,6 +25,12 @@ New in version |version|
 
 This version updates the IEDB RESTful API URL to the new target announced in IEDB Analysis Resource v2.15.1.
 
+.. warning::
+   The IEDB RESTful API URLs are currently broken. Until this issue if fixed,
+   you will need to use a local IEDB installation to run pVAC-Seq. IEDB has
+   been informed of this issue. For more information on how to run pVAC-Seq
+   with a local IEDB installation, please see the page on :ref:`run`.
+
 This release introduces a change in how invalid alleles are handeled. Previously, the pipeline would throw a fatal error. The
 pipeline will now proceed but invalid alleles will be skipped.
 

diff --git a/docs/install.rst b/docs/install.rst
@@ -33,7 +33,7 @@ If you have an old version of pVAC-Seq installed you might want to consider upgr
 
    pip install pvacseq --upgrade
 
-Installing IEDB binding prediction tools (optional)
+Installing IEDB binding prediction tools (recommended)
 ---------------------------------------------------
 
 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.

diff --git a/docs/run.rst b/docs/run.rst
@@ -1,6 +1,13 @@
+.. _run:
+
 Usage
 ====================================
 
+.. warning::
+   The IEDB RESTful API URLs are currently broken. Until this issue if fixed,
+   you will need to use a local IEDB installation to run pVAC-Seq. IEDB has
+   been informed of this issue.
+
 .. argparse::
     :module: lib.main
     :func: define_parser