changeset 0:1ef76f8d8e52 draft

Uploaded tool dependency definition.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Mar 27 14:13:44 2014 -0400
@@ -0,0 +1,71 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="samtools" version="0.1.19">
+        <install version="1.0">
+            <actions_group>
+                <actions os="linux" architecture="x86_64">
+                    <action type="download_by_url" target_filename="samtools-0.1.19.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.19-Linux-x86_64.tgz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>
+                </actions>
+                <actions os="darwin" architecture="x86_64">
+                    <action type="download_by_url" target_filename="samtools-0.1.19.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.19-Darwin-x86_64.tgz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>
+                </actions>
+                <actions>
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/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>$INSTALL_DIR/bin</destination>
+                    </action>
+                    <action type="move_file">
+                        <source>libbam.a</source>
+                        <destination>$INSTALL_DIR/lib</destination>
+                    </action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR/include/bam</destination_directory>
+                    </action>
+                </actions>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable>
+                    <environment_variable name="BAM_ROOT" action="set_to">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme>
+Program: samtools (Tools for alignments in the SAM format)
+Version: 0.1.19-44428cd
+
+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
+         bedcov      read depth per BED region
+         targetcut   cut fosmid regions (for fosmid pool only)
+         phase       phase heterozygotes
+         bamshuf     shuffle and group alignments by name
+        </readme>
+    </package>
+</tool_dependency>
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