# HG changeset patch
# User yhoogstrate
# Date 1394021704 18000
# Node ID b4185ce77360e096ae72d3ed8f301cd8eedf06f9
# Parent  ff87ad6669eb8fbe602cc8cb24680384295b292f
Uploaded

diff -r ff87ad6669eb -r b4185ce77360 tool-data/all_fasta.loc.sample
--- a/tool-data/all_fasta.loc.sample	Wed Mar 05 05:44:50 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-#This file lists the locations and dbkeys of all the fasta files
-#under the "genome" directory (a directory that contains a directory
-#for each build). The script extract_fasta.py will generate the file
-#all_fasta.loc. This file has the format (white space characters are
-#TAB characters):
-#
-#<unique_build_id>	<dbkey>	<display_name>	<file_path>
-#
-#So, all_fasta.loc could look something like this:
-#
-#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
-#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
-#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
-#
-#Your all_fasta.loc file should contain an entry for each individual
-#fasta file. So there will be multiple fasta files for each build,
-#such as with hg19 above.
-#
diff -r ff87ad6669eb -r b4185ce77360 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Wed Mar 05 05:44:50 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
-<tables>
-	<!-- Locations of all fasta files under genome directory -->
-	<table name="all_fasta" comment_char="#">
-		<columns>value, dbkey, name, path</columns>
-		<file path="tool-data/all_fasta.loc" /> 
-	</table>
-</tables>
\ No newline at end of file
diff -r ff87ad6669eb -r b4185ce77360 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Mar 05 05:44:50 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,120 +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>
-	
-	<!-- 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>
\ No newline at end of file