Mercurial > repos > bgruening > antismash

changeset 13:9cfa2fb488b0 draft

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Uploaded
author bgruening
date Thu, 10 Oct 2013 04:00:26 -0400
parents 0d7484be1b6f
children 46fd61e9c310
files antismash.xml tool_dependencies.xml
diffstat 2 files changed, 8 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/antismash.xml	Wed Oct 09 17:33:23 2013 -0400
+++ b/antismash.xml	Thu Oct 10 04:00:26 2013 -0400
@@ -13,8 +13,8 @@
 
             --input $infile
             --cpus 4
-            #set $type_list = ','.join([$type for $type in $types])
-            --enable $type_list
+            ##set $type_list = ','.join([$type for $type in $types])
+            --enable $types
             --input-type nucl
             $smcogs
             $clusterblast
--- a/tool_dependencies.xml	Wed Oct 09 17:33:23 2013 -0400
+++ b/tool_dependencies.xml	Thu Oct 10 04:00:26 2013 -0400
@@ -36,6 +36,8 @@
                     <action type="chmod">
                         <file mode="750">$INSTALL_DIR/run_antismash.py</file>
                     </action>
+                    <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
+                    <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
                 </actions>
                 <!-- Download the binaries for MUSCLE compatible with 64-bit OSX. -->
                 <actions architecture="i386" os="darwin">
@@ -47,6 +49,8 @@
                     <action type="chmod">
                         <file mode="750">$INSTALL_DIR/run_antismash.py</file>
                     </action>
+                    <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
+                    <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
                 </actions>
                 <!-- Download the binaries for AntiSmash compatible with 64-bit Linux. -->
                 <actions architecture="x86_64" os="linux">
@@ -71,10 +75,8 @@
                     <action type="chmod">
                         <file mode="750">$INSTALL_DIR/run_antismash.py</file>
                     </action>
-                </actions>
-
-                <actions>
-
+                    <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>
+                    <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
                 </actions>
 
                 <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. -->