# HG changeset patch
# User bebatut
# Date 1450445683 18000
# Node ID 2bf5fcf30e1f4c34e7b650c222087b358665d281
# Parent  c05e34aa939b1a166ce73c18c5585c0ef36843c4
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit e5b8f29dde45dddcda6ee283212dd1bdde487f87-dirty

diff -r c05e34aa939b -r 2bf5fcf30e1f humann2.xml
--- a/humann2.xml	Fri Dec 18 05:05:04 2015 -0500
+++ b/humann2.xml	Fri Dec 18 08:34:43 2015 -0500
@@ -4,7 +4,7 @@
     <requirements>
         <requirement type="package" version="2.2.5">bowtie2</requirement>
         <requirement type="package" version="2.0">metaphlan2</requirement>
-        <requirement type="package" version="0.6.13">diamond</requirement>
+        <requirement type="package" version="0.7.10">diamond</requirement>
         <requirement type="package" version="2.0">humann2</requirement>
     </requirements>
 
@@ -47,7 +47,7 @@
             --metaphlan \${METAPHLAN2_DIR}/
             --metaphlan-options "-t rel_ab"
             --bowtie2 \${PATH}
-            --diamond `which diamond`
+            --diamond \${PATH}
 
             --threads \${GALAXY_SLOTS:-4}
 
diff -r c05e34aa939b -r 2bf5fcf30e1f tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Dec 18 05:05:04 2015 -0500
+++ b/tool_dependencies.xml	Fri Dec 18 08:34:43 2015 -0500
@@ -13,7 +13,8 @@
         <install version="1.0">
             <actions>
                 <action type="download_by_url">https://bitbucket.org/biobakery/humann2/downloads/humann2_v0.5.0.tar.gz</action>
-                <action type="shell_command">python setup.py install --bypass-dependencies-install</action>
+                <action type="shell_command">export PYTHONPATH="$INSTALL_DIR/bin/lib/python/"</action>
+                <action type="shell_command">python setup.py install --home=$INSTALL_DIR/bin</action>
                 <action type="make_directory">$INSTALL_DIR/databases</action>
                 <action type="set_environment">
                     <environment_variable action="set_to" name="HUMANN2_DIR">$INSTALL_DIR/</environment_variable>