diff tools/spades_3_0/tool_dependencies.xml @ 8:ff058438080a draft

Version 0.8, supports SPAdes 3.0.0

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/spades_3_0/tool_dependencies.xml	Wed Feb 05 05:19:03 2014 -0500
@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="spades" version="2.5.1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://spades.bioinf.spbau.ru/release3.0.0/SPAdes-3.0.0-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>
+		<action type="move_directory_files">
+		  <source_directory>bin</source_directory>
+		  <destination_directory>$INSTALL_DIR/bin</destination_directory>
+		</action>
+                <action type="move_directory_files">
+		  <source_directory>share</source_directory>
+		  <destination_directory>$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> -->
+            </actions>
+        </install>
+        <readme>
+This installs SPAdes 3.0.0.
+
+See manual here http://spades.bioinf.spbau.ru/release3.0.0/manual.html
+See also here http://bioinf.spbau.ru/en/spades
+        </readme>
+    </package>
+</tool_dependency>
+