# HG changeset patch
# User sanbi-uwc
# Date 1504775085 14400
# Node ID 0c43a89b5ca9499ee8716993d8e61372daa07676

planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/packages/package_lofreq_2_1_2 commit bae33ff4832e61fd4f4f9c3c52116d320299625a

diff -r 000000000000 -r 0c43a89b5ca9 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Sep 07 05:04:45 2017 -0400
@@ -0,0 +1,34 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="lofreq" version="2.1.2">
+        <install version="1.0">
+            <actions_group>
+                <actions os="linux" architecture="x86_64">
+                    <action type="download_by_url" md5sum="0e52d47ab0dcf8a16e732b0260a7565f" target_filename="lofreq_star-2.1.2_linux-x86-64.tgz">
+                        https://sourceforge.net/projects/lofreq/files/lofreq_star-2.1.2_linux-x86-64.tgz
+                    </action>
+                    <action type="shell_command">tar -zxvf lofreq_star-2.1.2_linux-x86-64.tgz -C $INSTALL_DIR</action>
+                </actions>
+                <actions os="darwin" architecture="x86_64">
+                    <action type="download_by_url" md5sum="d688ba34a4161d9690e264648aae2def" target_filename="lofreq_star-2.1.2_macosx.tgz">
+                        https://sourceforge.net/projects/lofreq/files/lofreq_star-2.1.2_macosx.tgz
+                    </action>
+                    <action type="shell_command">tar -zxvf lofreq_star-2.1.2_macosx.tgz -C $INSTALL_DIR</action>
+                </actions>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/lofreq_star-2.1.2/bin</environment_variable>
+                    <environment_variable action="set_to" name="LOFREQ_ROOT_DIR" >$INSTALL_DIR</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme>
+            <![CDATA[
+This installation recipe installs the LoFreq version 2.1.2. LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs 
+and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing 
+(e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.
+http://csb5.github.io/lofreq/.
+
+            ]]>
+        </readme>
+    </package>
+</tool_dependency>
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