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griffithlab · Feb 21, 2017 · b326522 · b326522
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diff --git a/docs/features.rst b/docs/features.rst
@@ -14,19 +14,25 @@ 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 is 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`.
+   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. Using a local IEDB installation is recommended for
-larger datasets or when the making predictions on 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.
+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/index.rst b/docs/index.rst
@@ -25,12 +25,6 @@ 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 is 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
@@ -35,9 +35,15 @@ If you have an old version of pVAC-Seq installed you might want to consider upgr
 
 .. _iedb_install:
 
-Installing IEDB binding prediction tools (recommended)
+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
@@ -4,9 +4,10 @@ Usage
 ====================================
 
 .. warning::
-   The IEDB RESTful API URLs are currently broken. Until this issue is fixed,
-   you will need to use a local IEDB installation to run pVAC-Seq. IEDB has
-   been informed of this issue.
+   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