# HG changeset patch
# User shirish
# Date 1401803404 14400
# Node ID 4a8cd798d083be6a4d73ae667a1fdc78e89225ac
# Parent  9b2a3a7b73bd0db89f318abbed3c5019b7fc6fee
Deleted selected files

diff -r 9b2a3a7b73bd -r 4a8cd798d083 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jun 03 08:05:16 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,83 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="samtools" version="0.1.18">
-        <install version="1.0">
-            <actions_group>
-                <actions os="linux" architecture="i386">
-                    <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.18-linux-i386.tgz</action>
-                    <action type="move_directory_files">
-                        <source_directory>.</source_directory>
-                        <destination_directory>$INSTALL_DIR</destination_directory>
-                    </action>
-                </actions>
-                <actions os="linux" architecture="x86_64">
-                    <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.18-linux-x86_64.tgz</action>
-                    <action type="move_directory_files">
-                        <source_directory>.</source_directory>
-                        <destination_directory>$INSTALL_DIR</destination_directory>
-                    </action>
-                </actions>
-                <actions os="darwin" architecture="i386">
-                    <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.18-Darwin-i386.tgz</action>
-                    <action type="move_directory_files">
-                        <source_directory>.</source_directory>
-                        <destination_directory>$INSTALL_DIR</destination_directory>
-                    </action>
-                </actions>
-                <actions os="darwin" architecture="x86_64">
-                    <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.18-Darwin-x86_64.tgz</action>
-                    <action type="move_directory_files">
-                        <source_directory>.</source_directory>
-                        <destination_directory>$INSTALL_DIR</destination_directory>
-                    </action>
-                </actions>
-                <actions>
-                    <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.18.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: 0.1.18 (r982:295)
-
-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>
\ No newline at end of file