Mercurial > repos > lionelguy > spades

diff tools/spades_2_5/tool_dependencies.xml @ 3:d82f18c76309 draft

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Uploaded spades wrapper 0.6. Supports spades 2.5.1. Also removes the need for the hack at installation time, by fixing the problem with input files. Shows the license for the tool as well.
author lionelguy
date Thu, 12 Sep 2013 07:46:54 -0400
parents 0f8b2da62d7d
children 1b1af74a54ae
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line diff
--- a/tools/spades_2_5/tool_dependencies.xml	Thu Sep 05 07:43:48 2013 -0400
+++ b/tools/spades_2_5/tool_dependencies.xml	Thu Sep 12 07:46:54 2013 -0400
@@ -3,7 +3,7 @@
     <package name="spades" version="2.5.0">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">http://spades.bioinf.spbau.ru/release2.5.0/SPAdes-2.5.0-Linux.tar.gz</action>
+                <action type="download_by_url">http://spades.bioinf.spbau.ru/release2.5.1/SPAdes-2.5.1-Linux.tar.gz</action>
                 <!-- Copying the whole bin folder -->
 		<action type="make_directory">$INSTALL_DIR/bin</action>
 		<action type="make_directory">$INSTALL_DIR/share</action>
@@ -16,16 +16,16 @@
 		  <destination_directory>$INSTALL_DIR/share</destination_directory>
 		</action>
 		<!-- This is required to have spades accept .dat files -->
-		<action type="shell_command">sed -i -e "s/\('\.fa', '\.fasta', '\.fq', '\.fastq', '\.gz'\)/\\1, '.dat'/" $INSTALL_DIR/share/spades/spades_pipeline/support.py</action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
+		<!-- <action type="shell_command">sed -i -e "s/\('\.fa', '\.fasta', '\.fq', '\.fastq', '\.gz'\)/\\1, '.dat'/" $INSTALL_DIR/share/spades/spades_pipeline/support.py</action> -->
+                <!-- <action type="set_environment"> -->
+                <!--     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> -->
+                <!-- </action> -->
             </actions>
         </install>
         <readme>
-This installs SPAdes 2.5.0.
+This installs SPAdes 2.5.1.
 
-See manual here http://spades.bioinf.spbau.ru/release2.5.0/manual.html
+See manual here http://spades.bioinf.spbau.ru/release2.5.1/manual.html
 See also here http://bioinf.spbau.ru/en/spades
         </readme>
     </package>