Mercurial > repos > hyungrolee > mgescan_test

diff tool_dependencies.xml @ 5:088266bbf150 draft default tip

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Deleted selected files
author hyungrolee
date Mon, 15 Feb 2016 03:00:00 -0500
parents 33dfa472f8ef
children
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--- a/tool_dependencies.xml	Mon Feb 15 01:50:27 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="trf" version="4.0">
-        <repository changeset_revision="a2e1d1f25e35" name="tandem_repeats_finder" owner="urgi-team" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="mgescan" version="3">
-        <install version="1.0">
-            <actions_group>
-            	<!--
-                <actions architecture="x86_64" os="linux">
-			<action type="download_by_url">
-				https://github.com/MGEScan/mgescan/archive/1.0.tar.gz
-			</action>
-                    <action type="move_directory_files">
-                        <source_directory>.</source_directory>
-                        <destination_directory>$INSTALL_DIR</destination_directory>
-                    </action>
-                </actions>
-                -->
-                <actions>
-		<action type="download_by_url">
-				https://github.com/MGEScan/mgescan/archive/1.0.tar.gz
-                    </action>
-                    <action type="set_environment_for_install">
-                        <repository changeset_revision="a2e1d1f25e35" name="tandem_repeats_finder" owner="urgi-team" toolshed="https://toolshed.g2.bx.psu.edu">
-                            <package name="trf" version="4.0" />
-                        </repository>
-                    </action>
-                    <action type="shell_command">python setup.py install</action>
-                    <action type="move_file">
-                        <source>mgescan</source>
-                        <destination>$INSTALL_DIR/mgescan</destination>
-                    </action>
-                </actions>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/mgescan</environment_variable>
-                    <environment_variable action="set_to" name="MGESCAN_SRC">$INSTALL_DIR</environment_variable>
-                </action>
-            </actions_group>
-        </install>
-        <readme>
-Program: mgescan (Tools for identifying LTR &amp; nonLTR)
-Version: 3.0 
-
-Usage:
-    mgescan both &lt;genome_dir&gt; [--output=&lt;data_dir&gt;] [--mpi=&lt;num&gt;]
-    mgescan ltr &lt;genome_dir&gt; [--output=&lt;data_dir&gt;] [--mpi=&lt;num&gt;]
-    mgescan nonltr &lt;genome_dir&gt; [--output=&lt;data_dir&gt;] [--mpi=&lt;num&gt;]
-    mgescan (-h | --help)
-    mgescan --version
-
-        </readme>
-    </package>
-</tool_dependency>