# HG changeset patch
# User yhoogstrate
# Date 1400591210 14400
# Node ID ef13be78c5fcb2d691dd81dcae0e6f253371ca50
# Parent  19360b35f760c6fec7dcea38dae20b95a799bced
Uploaded

diff -r 19360b35f760 -r ef13be78c5fc samtools-parallel-mpileup.xml
--- a/samtools-parallel-mpileup.xml	Wed Mar 05 11:08:26 2014 -0500
+++ b/samtools-parallel-mpileup.xml	Tue May 20 09:06:50 2014 -0400
@@ -3,7 +3,8 @@
 	<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</requirement> -->
+		<requirement type="package" version="0.1.19">package_samtools_0_1_19</requirement>
 	</requirements>
 	<command>
 		#if $reference_genome_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1
diff -r 19360b35f760 -r ef13be78c5fc tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Mar 05 11:08:26 2014 -0500
+++ b/tool_dependencies.xml	Tue May 20 09:06:50 2014 -0400
@@ -1,10 +1,23 @@
 <?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>
+	
 	<!-- 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 $(ls |grep samtools-) &amp;&amp; make &amp;&amp; cp samtools ../samtools-parallel-mpileup</action>
+				<action type="set_environment_for_install">
+					<repository changeset_revision="f62fa47b852d" name="package_ncurses_5_9" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+						<package name="ncurses" version="5.9" />
+					</repository>
+				</action>
+				<action type="shell_command">svn checkout https://github.com/yhoogstrate/parallel-mpileup/trunk samtools-parallel-mpileup &amp;&amp; cd samtools-parallel-mpileup</action>
+				<action type="shell_command">sed -i 's/-lcurses/-lncurses/' Makefile</action>
+				<action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action>
+				<action type="shell_command">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>
@@ -20,101 +33,11 @@
 		</readme>
 	</package>
 	
-	<!-- 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="package_samtools_0_1_19" version="0.1.19">
+		<repository changeset_revision="40250a414486" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+	</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 name="varscan" version="2.3.6">
+		<repository changeset_revision="f82940004c84" name="varscan_version_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
 	</package>
 </tool_dependency>
\ No newline at end of file
diff -r 19360b35f760 -r ef13be78c5fc varscan_mpileup2snp_from_bam.xml
--- a/varscan_mpileup2snp_from_bam.xml	Wed Mar 05 11:08:26 2014 -0500
+++ b/varscan_mpileup2snp_from_bam.xml	Tue May 20 09:06:50 2014 -0400
@@ -4,7 +4,8 @@
 	<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</requirement> -->
+		<requirement type="package" version="0.1.19">package_samtools_0_1_19</requirement>
 	</requirements>
 	<command>
 		#if $reference_genome_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1