diff tool_dependencies.xml @ 5:d7efb5d5352a draft default tip

Uploaded
author jason-ellul
date Wed, 01 Jun 2016 02:40:16 -0400
parents 796653c6376b
children
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--- a/tool_dependencies.xml	Wed Jun 01 02:36:11 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,135 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-	<!-- Optimized samtools (for threaded mpileup)
-	<package name="samtools-parallel-mpileup" version="0.1.19">
-		<install version="1.0">
-			<actions>
-				<action type="shell_command">svn checkout https://github.com/yhoogstrate/parallel-mpileup/trunk samtools-parallel-mpileup &amp;&amp; cd samtools-parallel-mpileup &amp;&amp; cd $(ls |grep samtools-) &amp;&amp; make &amp;&amp; cp samtools ../samtools-parallel-mpileup</action>
-				<action type="move_file">
-					<source>samtools-parallel-mpileup</source>
-					<destination>$INSTALL_DIR/bin</destination>
-				</action>
-				<action type="set_environment">
-					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-					<environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>
-				</action>
-			</actions>
-		</install>
-		<readme>
-			Downloads and installs a modified version of samtools, able to paralellize the mpileup function.
-		</readme>
-	</package>
-	-->
-    <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>$INSTALL_DIR/bin</destination>
-                    </action>
-                    <action type="move_file">
-                        <source>bcftools/bcftools</source>
-                        <destination>$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>
-            </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>
-	<package name="VarScan" version="2.3.6">
-		<install version="1.0">
-			<actions>
-				<action type="download_by_url">http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar</action>
-				<action type="move_file">
-					<source>VarScan.v2.3.6.jar</source>
-					<destination>$INSTALL_DIR/jars</destination>
-				</action>
-				<action type="set_environment">
-					<environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
-				</action>
-			</actions>
-		</install>
-		<readme>
-			Downloads VarScan2.
-		</readme>
-	</package>
-	
-	<package name="VarScan" version="2.3.6">
-		<install version="1.0">
-			<actions>
-				<action type="download_by_url">http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar</action>
-				<action type="move_file">
-					<source>VarScan.v2.3.6.jar</source>
-					<destination>$INSTALL_DIR/jars</destination>
-				</action>
-				<action type="set_environment">
-					<environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
-				</action>
-			</actions>
-		</install>
-		<readme>
-			Downloads VarScan2.
-		</readme>
-	</package>
-</tool_dependency>
-