# HG changeset patch
# User yhoogstrate
# Date 1400591976 14400
# Node ID bc398d6bac85604db4965a36fae905116f1be3de
# Parent  6099ef001118270e5d59f718bea45ac8e6e80751
Uploaded

diff -r 6099ef001118 -r bc398d6bac85 samtools-parallel-mpileup.xml
--- a/samtools-parallel-mpileup.xml	Tue May 20 09:12:25 2014 -0400
+++ b/samtools-parallel-mpileup.xml	Tue May 20 09:19:36 2014 -0400
@@ -2,8 +2,7 @@
 <tool id="samtools_parallel_mpileup" name="Samtools parallel mpileup">
 	<description>Samtools mpileup (supporting parallelization)</description>
 	<requirements>
-		<requirement type="package" version="0.1.19">samtools-parallel-mpileup</requirement>
-		<!-- <requirement type="package" version="0.1.19">samtools</requirement> -->
+		<requirement type="package" version="0.1.19">samtools_parallel_mpileup</requirement>
 		<requirement type="package" version="0.1.19">package_samtools_0_1_19</requirement>
 	</requirements>
 	<command>
diff -r 6099ef001118 -r bc398d6bac85 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue May 20 09:12:25 2014 -0400
+++ b/tool_dependencies.xml	Tue May 20 09:19:36 2014 -0400
@@ -6,7 +6,7 @@
 	</package>
 	
 	<!-- Optimized samtools (for threaded mpileup) -->
-	<package name="samtools-parallel-mpileup" version="0.1.19">
+	<package name="samtools_parallel_mpileup" version="0.1.19">
 		<install version="1.0">
 			<actions>
 				<action type="set_environment_for_install">
diff -r 6099ef001118 -r bc398d6bac85 tool_dependencies_plain.xml
--- a/tool_dependencies_plain.xml	Tue May 20 09:12:25 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,161 +0,0 @@
-
-	<!-- Classical samtools (doesn't support threaded mpileup) --><!--
-	<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="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
-				<action type="shell_command">make</action>
-				<action type="shell_command">chmod ugo+rx misc/*.p?</action>
-				<action type="shell_command">mkdir misc/bin</action>
-				<action type="shell_command">cp -p `find misc -type f -perm -555` misc/bin/</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>$INSTALL_DIR/bin</destination>
-				</action>
-				<action type="move_directory_files">
-					<source_directory>misc/bin</source_directory>
-					<destination_directory>$INSTALL_DIR/bin</destination_directory>
-				</action>
-				<action type="set_environment">
-					<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-				</action>
-			</actions>
-		</install>
-		<readme>
-Program: samtools (Tools for alignments in the SAM format)
-Version: 0.1.19 
-
-Usage:   samtools &lt;command&gt; [options]
-
-Command: view        SAM&lt;-&gt;BAM conversion
-         sort        sort alignment file
-         mpileup     multi-way pileup
-         depth       compute the depth
-         faidx       index/extract FASTA
-         tview       text alignment viewer
-         index       index alignment
-         idxstats    BAM index stats (r595 or later)
-         fixmate     fix mate information
-         flagstat    simple stats
-         calmd       recalculate MD/NM tags and '=' bases
-         merge       merge sorted alignments
-         rmdup       remove PCR duplicates
-         reheader    replace BAM header
-         cat         concatenate BAMs
-         targetcut   cut fosmid regions (for fosmid pool only)
-         phase       phase heterozygotes
-
-This also installs bcftools and misc utility commands:
-        bcftools
-        vcfutils.pl
-        ace2sam
-        bamcheck
-        blast2sam.pl
-        bowtie2sam.pl
-        export2sam.pl
-        interpolate_sam.pl
-        maq2sam-long
-        maq2sam-short
-        md5fa
-        md5sum-lite
-        novo2sam.pl
-        psl2sam.pl
-        sam2vcf.pl
-        samtools.pl
-        soap2sam.pl
-        varfilter.py
-        wgsim
-        wgsim_eval.pl
-        zoom2sam.pl
-        </readme>
-    </package>
-	-->
-	
-	
-	
-		
-	<!--
-	<package name="VarScan" version="2.3.6">
-		<install version="1.0">
-			<actions>
-				<action type="download_by_url">http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar</action>
-				<action type="move_file">
-					<source>VarScan.v2.3.6.jar</source>
-					<destination>$INSTALL_DIR/jars</destination>
-				</action>
-				<action type="set_environment">
-					<environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
-				</action>
-			</actions>
-		</install>
-		<readme>
-			Downloads VarScan2.
-		</readme>
-	</package>
-</tool_dependency>
--->
-
-
-<!--
-< ? xml version="1.0" ? >
-<tool_dependency>
-    <package name="ncurses" version="5.9">
-        <repository changeset_revision="f62fa47b852d" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="samtools" version="0.1.19">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="f62fa47b852d" name="package_ncurses_5_9" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="ncurses" version="5.9" />
-                    </repository>
-                </action>
-                <action type="shell_command">sed -i 's/-lcurses/-lncurses/' Makefile</action>
-                <action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$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>
-        </install>
-        <readme>
-Program: samtools (Tools for alignments in the SAM format)
-Version: 0.1.19
-
-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
-
-Requirements: libncurses header files
-        </readme>
-    </package>
\ No newline at end of file
diff -r 6099ef001118 -r bc398d6bac85 varscan_mpileup2snp.xml
--- a/varscan_mpileup2snp.xml	Tue May 20 09:12:25 2014 -0400
+++ b/varscan_mpileup2snp.xml	Tue May 20 09:19:36 2014 -0400
@@ -2,7 +2,7 @@
 <tool id="varscan_mpileup2snp" name="VarScan2 Call SNPs from a mpileup file">
 	<description>VarScan2 SNP/SNV detection; directly from a *.mpileup file.</description>
 	<requirements>
-		<requirement type="package" version="2.3.6">VarScan</requirement>
+		<requirement type="package" version="2.3.6">varscan</requirement>
 	</requirements>
 	<command>
 		cat $mpileup_input | java
diff -r 6099ef001118 -r bc398d6bac85 varscan_mpileup2snp_from_bam.xml
--- a/varscan_mpileup2snp_from_bam.xml	Tue May 20 09:12:25 2014 -0400
+++ b/varscan_mpileup2snp_from_bam.xml	Tue May 20 09:19:36 2014 -0400
@@ -2,9 +2,8 @@
 <tool id="varscan_mpileup2snp_from_bam" name="VarScan2 Call SNPs from BAM">
 	<description>VarScan2 SNP/SNV detection; directly reading *.bam file(s) &amp; using parallel mpileup generation, to avoid unncessairy I/O overhead and increase performance.</description>
 	<requirements>
-		<requirement type="package" version="0.1.19">samtools-parallel-mpileup</requirement>
-		<requirement type="package" version="2.3.6">VarScan</requirement>
-		<!-- <requirement type="package" version="0.1.19">samtools</requirement> -->
+		<requirement type="package" version="0.1.19">samtools_parallel_mpileup</requirement>
+		<requirement type="package" version="2.3.6">varscan</requirement>
 		<requirement type="package" version="0.1.19">package_samtools_0_1_19</requirement>
 	</requirements>
 	<command>