# HG changeset patch
# User jjohnson
# Date 1378223310 14400
# Node ID 06697b4877f93d78863657b595293139d1f633a1

Uploaded

diff -r 000000000000 -r 06697b4877f9 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Sep 03 11:48:30 2013 -0400
@@ -0,0 +1,81 @@
+<?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="shell_command">chmod ugo+rx misc/*.p?</action>
+                <action type="shell_command">mkdir misc/bin</action>
+                <action type="shell_command">cp -p `find misc -type f -perm -555` misc/bin/</action>
+                <action type="move_file">
+                    <source>samtools</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>bcftools/bcftools</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>bcftools/vcfutils.pl</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_directory_files">
+                    <source_directory>misc/bin</source_directory>
+                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                </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
+
+This also installs bcftools and misc utility commands:
+        bcftools
+        vcfutils.pl
+        ace2sam
+        bamcheck
+        blast2sam.pl
+        bowtie2sam.pl
+        export2sam.pl
+        interpolate_sam.pl
+        maq2sam-long
+        maq2sam-short
+        md5fa
+        md5sum-lite
+        novo2sam.pl
+        psl2sam.pl
+        sam2vcf.pl
+        samtools.pl
+        soap2sam.pl
+        varfilter.py
+        wgsim
+        wgsim_eval.pl
+        zoom2sam.pl
+        </readme>
+    </package>
+</tool_dependency>