Mercurial > repos > lionelguy > prokka

changeset 8:6acf850bca99 draft

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Replaced the repository_dependencies by tool_dependencies
author lionelguy
date Fri, 06 Sep 2013 02:42:23 -0400
parents 39bc9c61c55b
children 37e2aeda27f4
files repository_dependencies.xml tool_dependencies.xml
diffstat 2 files changed, 41 insertions(+), 33 deletions(-) [+]
line wrap: on
line diff
--- a/repository_dependencies.xml	Thu Sep 05 07:42:05 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<repositories description="Prokka requires a suite of other tools">
-  <repository toolshed="http://toolshed.g2.bx.psu.edu" name="trna_prediction" owner="bgruening" changeset_revision="d34f31cbc9dd" />
-  <repository toolshed="http://toolshed.g2.bx.psu.edu" name="barrnap" owner="simon-gladman" changeset_revision="a41418a3bd38" />
-  <repository toolshed="http://toolshed.g2.bx.psu.edu" name="prodigal" owner="edward-kirton" changeset_revision="304c1a67bb7b" />
-  <!--<repository toolshed="http://toolshed.g2.bx.psu.edu" name="infernal" owner="" changeset_revision="" /> -->
-  <repository toolshed="http://toolshed.g2.bx.psu.edu" name="package_hmmer_3_1" owner="lionelguy" changeset_revision="007c736bf7e8" />
-  <repository toolshed="http://toolshed.g2.bx.psu.edu" name="ncbi_blast_plus" owner="devteam" changeset_revision="9dabbfd73c8a" />
-</repositories>
\ No newline at end of file
--- a/tool_dependencies.xml	Thu Sep 05 07:42:05 2013 -0400
+++ b/tool_dependencies.xml	Fri Sep 06 02:42:23 2013 -0400
@@ -1,36 +1,53 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="prokka" version="1.7">
-        <install version="1.0">
-            <actions>
+  <package name="hmmer" version="3.1b1">
+    <repository changeset_revision="007c736bf7e8" name="package_hmmer_3_1" owner="lionelguy" toolshed="http://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="blast+" version="2.2.26+">
+    <repository changeset_revision="40c69b76b46e" name="package_blast_plus_2_2_26" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="aragorn" version="1.2.36">
+    <repository changeset_revision="d34f31cbc9dd" name="trna_prediction" owner="bgruening" toolshed="http://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="prodigal" version="2.60">
+    <repository changeset_revision="304c1a67bb7b" name="prodigal" owner="edward-kirton" toolshed="http://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="package_barrnap_0_1" version="0.1">
+    <repository changeset_revision="a41418a3bd38" name="barrnap" owner="simon-gladman" toolshed="http://toolshed.g2.bx.psu.edu" />
+  </package>
+  <!--<package name="infernal" version="1.1rc4">
+    <repository name="package_infernal_1_1rc4" owner="iuc" />
+  </package> -->
+    <package name="prokka" version="1.7">
+      <install version="1.0">
+	<actions>
                 <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action>
                 <!-- Copying the whole bin, binaries, doc and db folders -->
-		<action type="make_directory">$INSTALL_DIR/bin</action>
-		<action type="make_directory">$INSTALL_DIR/binaries</action>
-		<action type="make_directory">$INSTALL_DIR/db</action>
-		<action type="make_directory">$INSTALL_DIR/doc</action>
-		<action type="move_directory_files">
-		  <source_directory>bin</source_directory>
-		  <destination_directory>$INSTALL_DIR/bin</destination_directory>
-		</action>
+                <action type="make_directory">$INSTALL_DIR/bin</action>
+                <action type="make_directory">$INSTALL_DIR/binaries</action>
+                <action type="make_directory">$INSTALL_DIR/db</action>
+                <action type="make_directory">$INSTALL_DIR/doc</action>
                 <action type="move_directory_files">
-		  <source_directory>binaries</source_directory>
-		  <destination_directory>$INSTALL_DIR/binaries</destination_directory>
-		</action>
-                <action type="move_directory_files">
-		  <source_directory>db</source_directory>
-		  <destination_directory>$INSTALL_DIR/db</destination_directory>
-		</action>
-                <action type="move_directory_files">
-		  <source_directory>doc</source_directory>
-		  <destination_directory>$INSTALL_DIR/doc</destination_directory>
-		</action>
+                  <source_directory>bin</source_directory>
+                  <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                </action>
+                        <action type="move_directory_files">
+                  <source_directory>binaries</source_directory>
+                  <destination_directory>$INSTALL_DIR/binaries</destination_directory>
+                </action>
+                        <action type="move_directory_files">
+                  <source_directory>db</source_directory>
+                  <destination_directory>$INSTALL_DIR/db</destination_directory>
+                </action>
+                        <action type="move_directory_files">
+                  <source_directory>doc</source_directory>
+                  <destination_directory>$INSTALL_DIR/doc</destination_directory>
+                </action>
                 <action type="set_environment">
-		  <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                 </action>
             </actions>
         </install>
-    
     <readme>
 This installs prokka 1.7
 Note: this is about a 2.0 GB download due to included custom databases.</readme>