# HG changeset patch
# User iuc
# Date 1424978475 18000
# Node ID 96aab723499fc1b8a210bc097c2c05e83fd25132
# Parent  923adc89c666340a00a3eae465c4b4580df3ade2
Uploaded

diff -r 923adc89c666 -r 96aab723499f tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jul 22 12:04:37 2014 -0400
+++ b/tool_dependencies.xml	Thu Feb 26 14:21:15 2015 -0500
@@ -1,38 +1,57 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="ncurses" version="5.9">
-        <repository changeset_revision="71e3f4bfd1a9" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="http://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="http://toolshed.g2.bx.psu.edu" />
-    </package>
     <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="set_environment_for_install">
-                    <repository changeset_revision="71e3f4bfd1a9" name="package_ncurses_5_9" owner="iuc" toolshed="http://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="http://toolshed.g2.bx.psu.edu">
-                        <package name="zlib" version="1.2.8" />
-                    </repository>
+            <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>$INSTALL_DIR/bin</destination>
+                    </action>
+                    <action type="move_file">
+                        <source>bcftools/bcftools</source>
+                        <destination>$INSTALL_DIR/bin</destination>
+                    </action>
+                    <action type="move_file">
+                        <source>bcftools/vcfutils.pl</source>
+                        <destination>$INSTALL_DIR/bin</destination>
+                    </action>
+                    <action type="move_file">
+                        <source>libbam.a</source>
+                        <destination>$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>
-                <action type="shell_command">sed -i '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>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
+            </actions_group>
         </install>
         <readme>
 Program: samtools (Tools for alignments in the SAM format)
-Version: 0.1.19
+Version: 0.1.19-44428cd
 
 Usage:   samtools &lt;command&gt; [options]
 
@@ -51,10 +70,10 @@
          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
-
-Requirements: libncurses header files
+         bamshuf     shuffle and group alignments by name
         </readme>
     </package>
 </tool_dependency>