diff tool_dependencies.xml @ 21:f509cd1d5a78 draft

planemo upload for repository https://github.com/galaxyproject/dunovo commit b'fd1625359a101d8a6b0b8d97028cc8be509398f2\n'-dirty

--- a/tool_dependencies.xml	Fri Nov 10 09:30:51 2017 -0500
+++ b/tool_dependencies.xml	Thu Jan 04 23:55:06 2018 -0500
@@ -1,10 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="bowtie2" version="2.2.5">
-    <repository changeset_revision="f5582ac5ba3c" name="package_bowtie_2_2_5" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-  </package>
-  <package name="samtools" version="0.1.18">
-    <repository changeset_revision="f499719dad6e" name="package_samtools_0_1_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+  <package name="bowtie" version="1.1.2">
+    <repository changeset_revision="8584a4574ab1" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
   </package>
   <package name="mafft" version="7.221">
     <repository changeset_revision="dd4a533a0e3c" name="mafft" owner="rnateam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
@@ -12,10 +9,37 @@
   <package name="networkx" version="1.10">
     <repository changeset_revision="3469a6858fd4" name="package_networkx_1_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
   </package>
-  <package name="dunovo" version="2.0.9">
+  <package name="dunovo" version="2.0.10">
     <install version="1.0">
       <actions>
-        <action sha256sum="6f5295b8eae0e161ee3bd28829ca140657743c695624ffc7f467f13eab2c547c" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.0.9.tar.gz</action>
+        <!-- download the main dunovo package files -->
+        <action sha256sum="81ef826b54746f4335f400b0ec5580bf04b5edfd8051682a684717fb32246227" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.0.10.tar.gz</action>
+        <!-- download the utillib submodule -->
+        <action type="download_file">https://github.com/NickSto/utillib/archive/v0.1.0.tar.gz</action>
+        <action type="shell_command">tar -zxvpf v0.1.0.tar.gz</action>
+        <action type="shell_command">rm v0.1.0.tar.gz</action>
+        <action type="move_file">
+          <source>utillib-0.1.0</source>
+          <destination>utillib</destination>
+        </action>
+        <!-- download the kalign submodule -->
+        <action type="download_file">https://github.com/makrutenko/kalign-dunovo/archive/v0.2.0.tar.gz</action>
+        <action type="shell_command">tar -zxvpf v0.2.0.tar.gz</action>
+        <action type="shell_command">rm v0.2.0.tar.gz</action>
+        <action type="move_file">
+          <source>kalign-dunovo-0.2.0</source>
+          <destination>kalign</destination>
+        </action>
+        <!-- download the ET submodule -->
+        <action type="download_file">https://github.com/NickSto/ET/archive/v0.2.2.tar.gz</action>
+        <action type="shell_command">tar -zxvpf v0.2.2.tar.gz</action>
+        <action type="shell_command">rm v0.2.2.tar.gz</action>
+        <action type="move_file">
+          <source>ET-0.2.2</source>
+          <destination>ET</destination>
+        </action>
+        <!-- make and install -->
+        <action type="shell_command">make clean</action>
         <action type="shell_command">make</action>
         <action type="move_directory_files">
           <source_directory>.</source_directory>
@@ -24,8 +48,6 @@
         <action type="set_environment">
           <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
         </action>
-        <!-- Note: This does not install the submodules.
-        Functionality they provide will not be available. -->
       </actions>
     </install>
   </package>