diff tool_dependencies.xml @ 0:cb66f1d643e4 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Feb 26 12:40:03 2015 -0500
@@ -0,0 +1,38 @@
+<?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>