--- a/tool_dependencies.xml	Mon Oct 27 06:45:52 2014 -0400
+++ b/tool_dependencies.xml	Thu Oct 01 14:14:06 2015 -0400
@@ -1,25 +1,25 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="blast+" version="2.2.28">
-    <repository changeset_revision="23b9ba41ad00" name="package_blast_plus_2_2_28" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+  <package name="blast+" version="2.2.31">
+    <repository changeset_revision="16e1254ed634" name="package_blast_plus_2_2_31" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="hmmer" version="3.1b1">
-    <repository changeset_revision="007c736bf7e8" name="package_hmmer_3_1" owner="lionelguy" toolshed="https://toolshed.g2.bx.psu.edu" />
+  <package name="hmmer" version="3.1b2">
+    <repository changeset_revision="040ca41b61c1" name="package_hmmer_3_1b2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="aragorn" version="1.2.36">
     <repository changeset_revision="f09e2902e6ed" name="package_aragorn_1_2_36" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="prodigal" version="2.60">
-    <repository changeset_revision="acf0e8b718c9" name="package_prodigal_2_60" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="9ec3f1e9198e" name="package_prodigal_2_60" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="tbl2asn" version="23.7">
-    <repository changeset_revision="2271d52a8531" name="package_tbl2asn_23_7" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" />
+  <package name="tbl2asn" version="24.3">
+    <repository changeset_revision="41764d6a6a3c" name="package_tbl2asn_24_3" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="gnu_parallel" version="20131122">
     <repository changeset_revision="0e1e79b3b7db" name="package_gnu_parallel_20131122" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="barrnap" version="0.5">
-    <repository changeset_revision="ec528d56b01f" name="package_barrnap_0_5" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" />
+  <package name="barrnap" version="0.7">
+    <repository changeset_revision="c46ab932a19b" name="package_barrnap_0_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
   <package name="infernal" version="1.1">
     <repository changeset_revision="b5c01b683dc9" name="package_infernal_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
@@ -27,10 +27,10 @@
   <package name="minced" version="0.1.6">
     <repository changeset_revision="a135862cd007" name="package_minced_0_1_6" owner="takadonet" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="prokka" version="1.10">
+  <package name="prokka" version="1.11">
     <install version="1.0">
       <actions>
-        <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.10.tar.gz</action>
+        <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.11.tar.gz</action>
         <action type="shell_command">bin/prokka --setupdb</action>
         <action type="move_directory_files">
           <source_directory>.</source_directory>
@@ -42,13 +42,11 @@
       </actions>
     </install>
     <readme>
-Warning: Prokka includes custom databases and is thus about a 340 MB download!
+Warning: Prokka includes custom databases and is thus about a 360 MB download!
 
 Dependencies of Prokka which needs to be installed separately:
 - Perl core modules: File::Copy, FindBin, Getopt::Long, List::Util, Scalar::Util, Time::Piece, Time::Seconds;
 - Perl modules: Bio::SeqIO from BioPerl ( http://search.cpan.org/dist/BioPerl/ ) &gt;= 1.6.900, XML::Simple ( http://search.cpan.org/dist/XML-Simple/ ).
-
-Configuration: Previously (until Release 2), the PROKKA_SITE_OPTIONS variable in the installed env.sh file was used to adjust the number of CPUs to use (--cpus). This is not used anymore and may be removed.
     </readme>
   </package>
 </tool_dependency>