Mercurial > repos > iuc > package_snpeff_3_5

changeset 0:04d2a4f81413 draft default tip

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author iuc
date Mon, 24 Mar 2014 10:01:52 -0400
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files tool_dependencies.xml
diffstat 1 files changed, 41 insertions(+), 0 deletions(-) [+]
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+++ b/tool_dependencies.xml	Mon Mar 24 10:01:52 2014 -0400
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+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="snpEff" version="3.5">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://sourceforge.net/projects/snpeff/files/snpEff_v3_5_core.zip</action>
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="SNPEFF_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+
+SnpEff ( http://snpeff.sourceforge.net/ )
+
+"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
+
+This repository contains a tool_dependencies.xml file that downloads and installs SnpEff and SnpSift (SnpEff.jar and SnpSift.jar)
+
+The install create an environment variable: SNPEFF_JAR_PATH that contains the path to the jar files.   Tools using this can generate a command line:
+java -Xmx6G -jar \$SNPEFF_JAR_PATH/snpEff.jar eff -c \$SNPEFF_JAR_PATH/snpEff.config   ...
+
+The snpEff.config file is also installed, which specifies the default location for installed SnpEff genome databases:
+data_dir = ~/snpEff/data/
+
+The location of a genome database can be set via the commandline option -dataDir.  
+
+Another way to change the location of data_dir would be to create a symbolic link in the galaxy HOME directory:
+ln -s genome_data_path/snpEff ~/snpEff
+
+        </readme>
+    </package>
+</tool_dependency>
+