Merge remote-tracking branch 'origin/master' into hotfix

griffithlab · Mar 1, 2017 · eabbf77 · eabbf77
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diff --git a/docs/features.rst b/docs/features.rst
@@ -13,9 +13,26 @@ 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::
+   We only recommend using the RESTful API for small requests. If you use the
+   RESTful API to process large VCFs or to make predictions for many alleles,
+   epitope lengths, or prediction algorithms, you might overload their system.
+   This can result in the blacklisting of your IP address by IEDB, causing
+   403 errors when trying to use the RESTful API. In that case please open
+   a ticket with `IEDB support <http://help.iedb.org/>`_ to have your IP
+   address removed from the IEDB blacklist.
+
 **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.
+
+.. 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.
 
 **MHC Class I and Class II predictions**
 

diff --git a/docs/install.rst b/docs/install.rst
@@ -33,9 +33,17 @@ 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)
+.. _iedb_install:
+
+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.
+
 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.
 
 .. note::

diff --git a/docs/run.rst b/docs/run.rst
@@ -1,6 +1,14 @@
+.. _run:
+
 Usage
 ====================================
 
+.. 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.
+
 .. argparse::
     :module: lib.main
     :func: define_parser