Mercurial > repos > iuc > package_transtermhp_2_09

changeset 0:0a21f73e2f15 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_transtermhp_2_09 commit 025696892784ba9fd07404ce4d21f3dca4ac1a1e-dirty
author iuc
date Fri, 17 Jul 2015 14:33:36 -0400
parents
children
files tool_dependencies.xml
diffstat 1 files changed, 59 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Jul 17 14:33:36 2015 -0400
@@ -0,0 +1,59 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="transtermhp" version="2.09">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://transterm.cbcb.umd.edu/transterm_hp_v2.09.zip</action>
+                <action type="shell_command">make</action>
+                <action type="move_file">
+                    <source>transterm</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>2ndscore</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>calibrate.sh</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>make_expterm.py</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>mfold_rna.sh</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>expterm.dat</source>
+                    <destination>$INSTALL_DIR/data</destination>
+                </action>
+                <action type="set_environment">
+                  <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable>
+                  <environment_variable action="set_to" name="TRANSTERM_EXPTERM_DAT">$INSTALL_DIR/data/expterm.dat</environment_variable>
+                  <environment_variable action="set_to" name="TRANSTERMHP_ROOT_PATH">$INSTALL_DIR/</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+TransTermHP v. 2.0 is a complete rewrite by Carl Kingsford of TransTerm v. 1.0,
+originally written by Maria D. Ermolaeva. The first TransTermHP was described in
+the paper:
+
+ [1] Maria D. Ermolaeva, Hanif G. Khalak, Owen White, Hamilton O. Smith and
+     Steven L. Salzberg. Prediction of Transcription Terminators in Bacterial
+     Genomes. J Mol Biol 301, (1), 27-33 (2000)
+
+TransTermHP v 2.0 is free software and is distributed under the GNU Public
+License. See the file LICENSE.txt included with TransTermHP for complete
+details.
+
+This package ships with the built-in experm.dat file which ships with
+transterm. In tools, this may be used as::
+
+    transterm -p \$TRANSTERM_EXPTERM_DAT
+
+        </readme>
+    </package>
+</tool_dependency>