# HG changeset patch
# User nick
# Date 1448323266 18000
# Node ID e9f9b1d1c6fb6f68e4a82701d99a567ad0a70615
# Parent  9d46c9ca7cebc84edcb2de3e316d37650fdf5d8a
planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty

diff -r 9d46c9ca7ceb -r e9f9b1d1c6fb make_families.xml
--- a/make_families.xml	Mon Nov 23 18:46:22 2015 -0500
+++ b/make_families.xml	Mon Nov 23 19:01:06 2015 -0500
@@ -3,9 +3,9 @@
   <description>from duplex sequencing data</description>
   <requirements>
     <requirement type="package" version="0.1">duplex</requirement>
-    <!-- <requirement type="set_environment">DUPLEX_DIR</requirement> -->
+    <requirement type="set_environment">DUPLEX_DIR</requirement>
   </requirements>
-  <command>paste $fastq1 $fastq2
+  <command>echo "\$DUPLEX_DIR" &gt;&amp;2 &amp;&amp; paste $fastq1 $fastq2
     | paste - - - -
     | awk -f \$DUPLEX_DIR/make-barcodes.awk -v TAG_LEN=$taglen -v INVARIANT=$invariant
     | sort
diff -r 9d46c9ca7ceb -r e9f9b1d1c6fb tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Nov 23 18:46:22 2015 -0500
+++ b/tool_dependencies.xml	Mon Nov 23 19:01:06 2015 -0500
@@ -8,17 +8,9 @@
       <actions>
         <action type="download_by_url">https://github.com/makrutenko/duplex/archive/master.tar.gz</action>
         <action type="shell_command">make</action>
-        <action type="move_file">
-          <source>*.so</source>
-          <destination>$INSTALL_DIR</destination>
-        </action>
-        <action type="move_file">
-          <source>*.py</source>
-          <destination>$INSTALL_DIR</destination>
-        </action>
-        <action type="move_file">
-          <source>*.awk</source>
-          <destination>$INSTALL_DIR</destination>
+        <action type="move_directory_files">
+          <source_directory>.</source_directory>
+          <destination_directory>$INSTALL_DIR</destination_directory>
         </action>
         <action type="set_environment">
           <environment_variable action="set_to" name="DUPLEX_DIR">$INSTALL_DIR</environment_variable>