--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue May 12 15:04:12 2015 -0400
@@ -0,0 +1,40 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="hmmer3_1b1" version="3.1b1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">ftp://selab.janelia.org/pub/software/hmmer3/3.1b1/hmmer-3.1b1.tar.gz</action>
+                <action type="autoconf" />
+                <action type="change_directory">easel/miniapps/</action>
+                <action type="make_install" />
+                <action type="set_environment">
+                    <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable>
+                    <environment_variable name="HMMER31_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable>
+                    <environment_variable name="C_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable>
+                    <environment_variable name="CPLUS_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+HMMER is used for searching sequence databases for homologs of protein
+sequences, and for making protein sequence alignments. It implements methods
+using probabilistic models called profile hidden Markov models (profile HMMs).
+
+Compared to BLAST, FASTA, and other sequence alignment and database search
+tools based on older scoring methodology, HMMER aims to be significantly more
+accurate and more able to detect remote homologs because of the strength of its
+underlying mathematical models. In the past, this strength came at significant
+computational expense, but in the new HMMER3 project, HMMER is now essentially
+as fast as BLAST.
+
+As part of this evolution in the HMMER software, we are committed to making the
+software available to as many scientists as possible. Earlier releases of HMMER
+were restricted to command line use. To make the software more accessible to
+the wide scientific community, we now provide servers that allow sequence
+searches to be performed interactively via the Web.
+
+http://hmmer.janelia.org/
+
+        </readme>
+    </package>
+</tool_dependency>