Mercurial > repos > bgruening > antismash

changeset 16:e2df6fe8b447 draft

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Uploaded
author bgruening
date Fri, 11 Oct 2013 16:46:08 -0400
parents 9a099b9b6857
children 213d82f33fc2
files antismash.xml tool_dependencies.xml
diffstat 2 files changed, 22 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/antismash.xml	Fri Oct 11 16:06:28 2013 -0400
+++ b/antismash.xml	Fri Oct 11 16:46:08 2013 -0400
@@ -41,29 +41,29 @@
         ## shuffling files to create the correct outputs for Galaxy
         
         ## html output
-        #if 'html' in $outputs:
+        #if 'html' in str($outputs).split(','):
             cp #echo os.path.join($outputfolder, 'index.html')# $html;
         #end if
         
         ## gene clusters
-        #if 'geneclusterprots_tabular' in $outputs:
+        #if 'geneclusterprots_tabular' in str($outputs).split(','):
             cp #echo os.path.join($outputfolder, 'geneclusters.txt')# $geneclusterprots;
         #end if
 
         ##SVG images
-        #if 'archive_svgs' in $outputs:
+        #if 'archive_svgs' in str($outputs).split(','):
             cd #echo os.path.join($outputfolder, 'svg')#;
-            tar cfz $archive_svgs *_all.svg genecluster*;
+            tar cfz $archive_svgs *_all.svg genecluster*;   
         #end if
 
         ##all files in a archive
-        #if 'archive' in $outputs:
+        #if 'archive' in str($outputs).split(','):
             cd $outputfolder;
             tar cf $archive *.zip;
         #end if
 
         ## genbank
-        #if 'gb' in $outputs:
+        #if 'gb' in str($outputs).split(','):
             #for $gb_file in glob.glob( os.path.join($outputfolder, '*.gbk') ):
                 cat $gb_file >> $genbank;
             #end for
--- a/tool_dependencies.xml	Fri Oct 11 16:06:28 2013 -0400
+++ b/tool_dependencies.xml	Fri Oct 11 16:46:08 2013 -0400
@@ -33,6 +33,11 @@
                     <action type="chmod">
                         <file mode="750">$INSTALL_DIR/run_antismash.py</file>
                     </action>
+                    <!-- AntiSmash has a prerequirement check that is not useful for us, because we
+                        do not offer the option for genprediction and do not install glimmer and Co.
+                        For that reason deactivate the check.
+                    -->
+                    <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/True/g' $INSTALL_DIR/run_antismash.py</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 $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
                 </actions>
@@ -46,6 +51,11 @@
                     <action type="chmod">
                         <file mode="750">$INSTALL_DIR/run_antismash.py</file>
                     </action>
+                    <!-- AntiSmash has a prerequirement check that is not useful for us, because we
+                        do not offer the option for genprediction and do not install glimmer and Co.
+                        For that reason deactivate the check.
+                    -->
+                    <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/True/g' $INSTALL_DIR/run_antismash.py</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>
@@ -63,7 +73,7 @@
                         do not offer the option for genprediction and do not install glimmer and Co.
                         For that reason deactivate the check.
                     -->
-                    <action type="shell_command">sed -i s/check_prereqs(plugins, options) > 0/True/</action>
+                    <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/True/g' $INSTALL_DIR/run_antismash.py</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 $INSTALL_DIR/antismash/generic_modules/clusterblast</action>
                 </actions>
@@ -77,6 +87,11 @@
                     <action type="chmod">
                         <file mode="750">$INSTALL_DIR/run_antismash.py</file>
                     </action>
+                    <!-- AntiSmash has a prerequirement check that is not useful for us, because we
+                        do not offer the option for genprediction and do not install glimmer and Co.
+                        For that reason deactivate the check.
+                    -->
+                    <action type="shell_command">sed -i 's/check_prereqs(plugins, options) &gt; 0/True/g' $INSTALL_DIR/run_antismash.py</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>