# HG changeset patch
# User peterjc
# Date 1372053555 14400
# Node ID d00a3cda08d80cb25f1113ffa0ab8e142bf6cb5e
# Parent  16a1a5ae98e9cd13223c66ba9c4a64142b43325d
Uploaded v0.0.4, auto-install Biopython

diff -r 16a1a5ae98e9 -r d00a3cda08d8 tools/filters/repository_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/filters/repository_dependencies.xml	Mon Jun 24 01:59:15 2013 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<repositories description="This requires Biopython as a dependency.">
+<!-- Leave out the tool shed and revision to get the current
+     tool shed and latest revision at the time of upload -->
+<repository changeset_revision="627c7b41b970" name="package_biopython_1_61" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+</repositories>
diff -r 16a1a5ae98e9 -r d00a3cda08d8 tools/filters/seq_rename.tar.gz
Binary file tools/filters/seq_rename.tar.gz has changed
diff -r 16a1a5ae98e9 -r d00a3cda08d8 tools/filters/seq_rename.txt
--- a/tools/filters/seq_rename.txt	Wed May 08 13:25:12 2013 -0400
+++ b/tools/filters/seq_rename.txt	Mon Jun 24 01:59:15 2013 -0400
@@ -23,14 +23,15 @@
 Automated Installation
 ======================
 
-This should be straightforward, provided you have installed Biopython 1.54 or later.
-Galaxy should automatically install the Python script, and run the unit tests.
+This should be straightforward using the Galaxy Tool Shed, which should be
+able to automatically install the dependency on Biopython, and then install
+this tool and run its unit tests.
 
 
 Manual Installation
 ===================
 
-There are just two files to install:
+There are just two files to install to use this tool from within Galaxy:
 
 * seq_rename.py (the Python script)
 * seq_rename.xml (the Galaxy tool definition)
@@ -59,6 +60,7 @@
        - Add unit test.
        - Check for errors using Python script's return code.
 v0.0.3 - Link to Tool Shed added to help text and this documentation.
+v0.0.4 - Automated installation of Biopython dependency.
 
 
 Developers
@@ -70,7 +72,7 @@
 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
 the following command from the Galaxy root folder:
 
-$ tar -czf seq_rename.tar.gz tools/filters/seq_rename.* test-data/four_human_proteins.fasta test-data/four_human_proteins.rename.tabular test-data/four_human_proteins.rename.fasta
+$ tar -czf seq_rename.tar.gz tools/filters/seq_rename.* tools/filters/repository_dependencies.xml test-data/four_human_proteins.fasta test-data/four_human_proteins.rename.tabular test-data/four_human_proteins.rename.fasta
 
 Check this worked:
 
diff -r 16a1a5ae98e9 -r d00a3cda08d8 tools/filters/seq_rename.xml
--- a/tools/filters/seq_rename.xml	Wed May 08 13:25:12 2013 -0400
+++ b/tools/filters/seq_rename.xml	Mon Jun 24 01:59:15 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="seq_rename" name="Rename sequences" version="0.0.3">
+<tool id="seq_rename" name="Rename sequences" version="0.0.4">
 	<description>with ID mapping from a tabular file</description>
 	<version_commmand interpreter="python">seq_rename.py --version</version_commmand>
 	<command interpreter="python">