Mercurial > repos > peterjc > mummer

changeset 5:49d5b43e68a0 draft

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Uploaded v0.0.4 with explicit gnuplot dependency
author peterjc
date Wed, 29 Oct 2014 07:16:28 -0400
parents 17fc3d010ba0
children a773c7ddf2e5
files tools/mummer/README.rst tools/mummer/mummer.xml tools/mummer/tool_dependencies.xml
diffstat 3 files changed, 14 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/tools/mummer/README.rst	Tue Oct 28 09:42:53 2014 -0400
+++ b/tools/mummer/README.rst	Wed Oct 29 07:16:28 2014 -0400
@@ -18,18 +18,18 @@
 Automated Installation
 ======================
 
-This should be straightforward, Galaxy should automatically download and install
-the MUMmer files, and GhostScript which provides the ``ps2pdf`` binary.
-
-It also needs the tool ``gnuplot`` to be installed and on the system ``$PATH``.
+Automated installation from the Galaxy Tool Shed should be straightforward.
+In addition to the wrapper itself, Galaxy should automatically download and
+install the MUMmer files, gnuplot, and GhostScript which provides the
+``ps2pdf`` binary.
 
 
 Manual Installation
 ===================
 
 This expects MUMmer binaries (at least ``mummer``, ``nucmer``, ``promer``, and
-``mummerplot``) and the tools ``gnuplot`` and ``ps2pdf`` to be on the system
-``$PATH``.
+``mummerplot``) and the tools ``gnuplot`` and ``ps2pdf`` (from GhostScript) to
+be on the system ``$PATH``.
 
 To install the wrapper copy or move the following files under the Galaxy tools
 folder, e.g. in a ``tools/mummer`` folder:
@@ -61,6 +61,7 @@
 v0.0.2  - Correct typo in Tool identifier.
         - Include MUMmer citation in Galaxy XML markup.
 v0.0.3  - Install ``ps2pdf`` using Tool Shed's GhostScript package.
+v0.0.4  - Install ``gnuplot`` using Tool Shed's gnuplot package.
 ======= ======================================================================
 
 
--- a/tools/mummer/mummer.xml	Tue Oct 28 09:42:53 2014 -0400
+++ b/tools/mummer/mummer.xml	Wed Oct 29 07:16:28 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="mummerplot_wrapper" name="MUMmer dotplot" version="0.0.3">
+<tool id="mummerplot_wrapper" name="MUMmer dotplot" version="0.0.4">
     <description>Combine mummer/nucmer/promer with mummerplot</description>
     <requirements>
             <!-- Needs ps2pdf from ghostscript -->      
@@ -10,6 +10,9 @@
             <requirement type="binary">promer</requirement>
             <requirement type="binary">mummerplot</requirement>
             <requirement type="package" version="3.23">mummer</requirement>
+	    <!-- mummerplot needs the gnuplot binary -->
+            <requirement type="binary">gnuplot</requirement>
+            <requirement type="package" version="4.6">gnuplot</requirement>
     </requirements>
     <version_command interpreter="python">
 mummer.py --version
--- a/tools/mummer/tool_dependencies.xml	Tue Oct 28 09:42:53 2014 -0400
+++ b/tools/mummer/tool_dependencies.xml	Wed Oct 29 07:16:28 2014 -0400
@@ -6,4 +6,7 @@
     <package name="ghostscript" version="9.10">
         <repository changeset_revision="9345d2740f0c" name="package_ghostscript_9_10" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
+    <package name="gnuplot" version="4.6">
+        <repository changeset_revision="e1e78b23b0da" name="package_gnuplot_4_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
 </tool_dependency>