diff tool_dependencies.xml @ 0:8d1cf7ce65cd draft

planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit d583ac16a6c6942730ea536eb59cc37941816030-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu May 18 17:25:33 2017 -0400
@@ -0,0 +1,101 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="samtools" version="1.2">
+        <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+
+    <package name="numpy" version="1.9">
+        <repository changeset_revision="1e2b7e63dec2" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+
+    <package name="biopython" version="1.68">
+        <readme>
+This package is based on package_biopython_1_67 owned by biopython. 
+https://toolshed.g2.bx.psu.edu/repository?user_id=fd5c6d0f82f315d8
+
+This Galaxy Tool Shed package installs Biopython from source, having
+first installed NumPy which is a build time depencency. This requires
+and assumes a standard C compiler is already installed, along with
+the Python header files.
+
+Development of this dependency definition is being done here on GitHub:
+https://github.com/biopython/galaxy_packages
+
+The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON.
+        </readme>
+         <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://biopython.org/DIST/biopython-1.68.tar.gz</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="1e2b7e63dec2" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="numpy" version="1.9" />
+                    </repository>
+                </action>
+                <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                <action type="shell_command">
+                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
+                    export PATH=$PATH:$PATH_NUMPY &amp;&amp; 
+                    export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp; 
+                    python setup.py install --install-lib $INSTALL_DIR/lib/python
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
+                    <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable>
+                </action>
+            </actions>
+        </install>
+    </package>
+    
+     <package name="ucsc_tools_340" version="1.0">
+        <install version="1.0">
+            <actions_group>
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/ucsc_tools_340.tar.gz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>                       
+                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                    </action>    
+                </actions>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions_group>
+         </install>
+         <readme>The well known UCSC tools from Jim Kent.</readme>
+    </package>
+    <package name="jbrowse_tools" version="1.12.1">
+        <install version="1.0">
+            <actions_group>
+                <action type="setup_perl_environment">
+                    <repository name="package_perl_5_18" owner="iuc">
+                        <package name="perl" version="5.18.1" />
+                    </repository>
+                <package>XML::Parser</package>
+                <package>http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz</package>
+                </action>
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url">http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=105</action>
+                    <action type="make_directory">$INSTALL_DIR/jbrowse</action>
+                    <action type="shell_command">
+                        ./setup.sh
+                    </action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>                       
+                        <destination_directory>$INSTALL_DIR/jbrowse</destination_directory>
+                    </action>    
+                    <action type="set_environment">
+                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse</environment_variable>
+                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/bin</environment_variable>
+                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/src</environment_variable>
+                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/extlib</environment_variable>
+                    </action>
+                </actions>
+            </actions_group>
+         </install>
+         <readme>The perl scripts for converting flat files to json.</readme>
+    </package>
+
+    
+</tool_dependency>