# HG changeset patch
# User iuc
# Date 1376947178 14400
# Node ID cb87eae7fc3e868e63349b7a73d0be08ba18f2bd

Uploaded

diff -r 000000000000 -r cb87eae7fc3e tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Aug 19 17:19:38 2013 -0400
@@ -0,0 +1,43 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="samtools" version="0.1.19">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
+                <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
+                <action type="shell_command">make</action>
+                <action type="move_file">
+                    <source>samtools</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+Program: samtools (Tools for alignments in the SAM format)
+Version: 0.1.19
+
+Usage:   samtools &lt;command&gt; [options]
+
+Command: view        SAM&lt;-&gt;BAM conversion
+         sort        sort alignment file
+         mpileup     multi-way pileup
+         depth       compute the depth
+         faidx       index/extract FASTA
+         tview       text alignment viewer
+         index       index alignment
+         idxstats    BAM index stats (r595 or later)
+         fixmate     fix mate information
+         flagstat    simple stats
+         calmd       recalculate MD/NM tags and '=' bases
+         merge       merge sorted alignments
+         rmdup       remove PCR duplicates
+         reheader    replace BAM header
+         cat         concatenate BAMs
+         targetcut   cut fosmid regions (for fosmid pool only)
+         phase       phase heterozygotes
+        </readme>
+    </package>
+</tool_dependency>