diff tool_dependencies.xml @ 6:3ad7ef0ba385 draft

Use <stdio> because prokka writes some warnings on stderr. Update Orione citation. Update Prokka citation. Support Prokka 1.10. Upgrade dependencies to package_minced_0_1_6, package_barrnap_0_5 and package_tbl2asn_23_7. Added --proteins option. Add <citations>.

--- a/tool_dependencies.xml	Thu Jan 09 16:49:50 2014 -0500
+++ b/tool_dependencies.xml	Mon Oct 27 06:45:52 2014 -0400
@@ -1,37 +1,37 @@
 <?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="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="23b9ba41ad00" name="package_blast_plus_2_2_28" 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="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="007c736bf7e8" name="package_hmmer_3_1" owner="lionelguy" 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="http://toolshed.g2.bx.psu.edu" />
+    <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="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="acf0e8b718c9" name="package_prodigal_2_60" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="tbl2asn" version="22.4">
-    <repository changeset_revision="55f52e5395cd" name="package_tbl2asn_22_4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+  <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>
   <package name="gnu_parallel" version="20131122">
-    <repository changeset_revision="0e1e79b3b7db" name="package_gnu_parallel_20131122" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="0e1e79b3b7db" name="package_gnu_parallel_20131122" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="barrnap" version="0.3">
-    <repository changeset_revision="60763b9e2026" name="package_barrnap_0_3" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+  <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>
   <package name="infernal" version="1.1">
-    <repository changeset_revision="b5c01b683dc9" name="package_infernal_1_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="b5c01b683dc9" name="package_infernal_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
-  <package name="minced" version="0.1.4">
-    <repository changeset_revision="0cf9719bfe4b" name="package_minced_0_1_4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+  <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="1.8">
+  <package name="prokka" version="1.10">
     <install version="1.0">
       <actions>
-        <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action>
-        <action target_filename="bin/prokka" type="download_file">http://www.vicbioinformatics.com/prokka-1.8</action>
+        <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.10.tar.gz</action>
+        <action type="shell_command">bin/prokka --setupdb</action>
         <action type="move_directory_files">
           <source_directory>.</source_directory>
           <destination_directory>$INSTALL_DIR</destination_directory>
@@ -42,7 +42,7 @@
       </actions>
     </install>
     <readme>
-Warning: Prokka includes custom databases and is thus about a 2.0 GB download!
+Warning: Prokka includes custom databases and is thus about a 340 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;