diff tool_dependencies.xml @ 1:643da63cb382 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/kinwalker commit 3103ebed1a420c7d3415b67ef532ea579edf9faa

--- a/tool_dependencies.xml	Thu Feb 26 12:40:03 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="vienna_rna" version="2.1">
-        <repository changeset_revision="3b53eda26527" name="package_vienna_rna_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="gnu_coreutils" version="8.22">
-        <repository changeset_revision="ac64dfe4b1fb" name="package_gnu_coreutils_8_22" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="kinwalker" version="1.0">
-        <install version="1.0">
-            <actions>
-                <action target_filename="kinwalker.tar.gz" type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/kinwalker/kinwalker-patched.tar.gz</action>
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="3b53eda26527" name="package_vienna_rna_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
-                        <package name="vienna_rna" version="2.1" />
-                    </repository>
-                </action> 
-                <action type="shell_command">make VRNA_INC="-I$ROOT_VIENNA_RNA_DIR/include/ViennaRNA" VRNA_LIB="-L$ROOT_VIENNA_RNA_DIR/lib -lRNA" LDFLAGS="-fopenmp"</action>
-                <action type="move_file">
-                    <source>kinwalker</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-
-The  Kinwalker  algorithm performs cotranscriptional folding of RNAs, 
-starting at a user a specified structure (default: open chain) and 
-ending at the minimum free energy structure. Folding events are 
-performed between transcription of additional bases and are regulated 
-by barrier heights between the source and target structure.
-
-        </readme>
-    </package>
-</tool_dependency>