# HG changeset patch
# User iuc
# Date 1426523964 14400
# Node ID 6eea043630269482fcbc67db3d194a2ba88f16db

Uploaded

diff -r 000000000000 -r 6eea04363026 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Mar 16 12:39:24 2015 -0400
@@ -0,0 +1,81 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="samtools" version="1.2">
+        <install version="1.0">
+            <actions_group>
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-1.2-Linux-x86_64.tgz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>
+                </actions>
+                <actions>
+                    <package name="ncurses" version="5.9">
+                        <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+                    </package>
+                    <package name="zlib" version="1.2.8">
+                        <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+                    </package>
+                    <action type="download_by_url">https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2</action>
+                    <action type="set_environment_for_install">
+                        <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                            <package name="ncurses" version="5.9" />
+                        </repository>
+                        <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                            <package name="zlib" version="1.2.8" />
+                        </repository>
+                    </action>
+                    <action type="shell_command">sed -i.bak 's#/usr/local#$INSTALL_DIR#' Makefile</action>
+                    <action type="shell_command">sed -i -e 's/-lcurses/-lncurses/' Makefile</action>
+                    <action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action>
+                    <action type="shell_command">make</action>
+                    <action type="move_file">
+                        <source>samtools</source>
+                        <destination>$INSTALL_DIR/bin</destination>
+                    </action>
+                </actions>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="set_to" name="SAMTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme>
+Program: samtools (Tools for alignments in the SAM format)
+Version: 1.2
+
+Usage:   samtools &lt;command&gt; [options]
+
+Commands:
+  -- indexing
+         faidx       index/extract FASTA
+         index       index alignment
+  -- editing
+         calmd       recalculate MD/NM tags and '=' bases
+         fixmate     fix mate information
+         reheader    replace BAM header
+         rmdup       remove PCR duplicates
+         targetcut   cut fosmid regions (for fosmid pool only)
+  -- file operations
+         bamshuf     shuffle and group alignments by name
+         cat         concatenate BAMs
+         merge       merge sorted alignments
+         mpileup     multi-way pileup
+         sort        sort alignment file
+         split       splits a file by read group
+         bam2fq      converts a BAM to a FASTQ
+  -- stats
+         bedcov      read depth per BED region
+         depth       compute the depth
+         flagstat    simple stats
+         idxstats    BAM index stats
+         phase       phase heterozygotes
+         stats       generate stats (former bamcheck)
+  -- viewing
+         flags       explain BAM flags
+         tview       text alignment viewer
+         view        SAM&lt;-&gt;BAM&lt;-&gt;CRAM conversion
+        </readme>
+    </package>
+</tool_dependency>