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changeset 0:302d166cd10d draft default tip

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author hyungrolee
date Tue, 02 Feb 2016 01:51:30 -0500
parents
children
files tool_dependencies.xml
diffstat 1 files changed, 53 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Feb 02 01:51:30 2016 -0500
@@ -0,0 +1,53 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="tandem_repeats_finder" 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>$INSTALL_DIR</destination_directory>
+                    </action>
+                </actions>
+                <actions>
+		<action type="download_by_url">
+				https://github.com/MGEScan/mgescan/archive/1.0.tar.gz
+                    </action>
+                    <action type="set_environment_for_install">
+                        <repository changeset_revision="a2e1d1f25e35" name="tandem_repeats_finder" owner="urgi-team" toolshed="https://toolshed.g2.bx.psu.edu">
+                            <package name="trf" version="4.0" />
+                        </repository>
+                    </action>
+                    <action type="shell_command">cd mgescan-1.0</action>
+                    <action type="shell_command">python setup.py install</action>
+                    <action type="move_file">
+                        <source>mgescan</source>
+                        <destination>$INSTALL_DIR/bin</destination>
+                    </action>
+                </actions>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="set_to" name="SAMTOOLS_ROOT_PATH">$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>