diff tools/spades_2_5/tool_dependencies.xml @ 1:0f8b2da62d7d draft

Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/spades_2_5/tool_dependencies.xml	Mon Aug 19 09:06:17 2013 -0400
@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <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>
+                <!-- 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 2.5.0.
+
+See manual here http://spades.bioinf.spbau.ru/release2.5.0/manual.html
+See also here http://bioinf.spbau.ru/en/spades
+        </readme>
+    </package>
+</tool_dependency>
+