# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1410201377 18000
# Node ID 0cd177bc347d02d4a7ed6a1a7e681d860180b686
# Parent  cec60c540546f660753590d8b0c04af844957799
Update tool dependencies

diff -r cec60c540546 -r 0cd177bc347d peptide_to_gff.xml
--- a/peptide_to_gff.xml	Wed Jun 26 15:56:16 2013 -0400
+++ b/peptide_to_gff.xml	Mon Sep 08 13:36:17 2014 -0500
@@ -1,8 +1,10 @@
 <tool id="peptide_to_gff" name="Peptide to GFF" version="1.0">
   <description>Map peptide to reference genome</description>
   <requirements>
-    <requirement type="package">kent_tools</requirement>
-    <requirement type="package" version="master">peptide_to_gff</requirement>
+    <requirement type="package" version="35x1">blat</requirement>
+    <requirement type="package" version="1.61">biopython</requirement>
+    <requirement type="package" version="0.1">bcbb_gff</requirement>
+    <requirement type="package" version="0.1">peptide_to_gff</requirement>
   </requirements>
   <command>peptide_to_gff
     #if $peptide_src.inputFormat == 'protein_pilot' or $peptide_src.inputFormat == 'tabular':
diff -r cec60c540546 -r 0cd177bc347d repository_dependencies.xml
--- a/repository_dependencies.xml	Wed Jun 26 15:56:16 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-hg clone ssh://hg@bitbucket.org/galaxyp/galaxyp-toolshed-peptides-to-gff
diff -r cec60c540546 -r 0cd177bc347d requirements.txt
--- a/requirements.txt	Wed Jun 26 15:56:16 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-numpy
-biopython==1.61
-bcbio-gff
diff -r cec60c540546 -r 0cd177bc347d tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jun 26 15:56:16 2013 -0400
+++ b/tool_dependencies.xml	Mon Sep 08 13:36:17 2014 -0500
@@ -1,14 +1,15 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="peptide_to_gff" version="master">
-        <install version="1.0">
-            <actions>
-              <action type="download_by_url">https://bitbucket.org/galaxyp/peptide_to_gff/get/5f32b86.tar.gz</action>
-              <action type="setup_virtualenv" />
-            </actions>
-        </install>
-        <readme>
-          Sets up a virtualenv for peptides-to-gff.
-        </readme>
+    <package name="biopython" version="1.61">
+        <repository name="package_biopython_1_61" owner="biopython" changeset_revision="ae9dda584395" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bcbb_gff" version="0.1">
+        <repository name="bcbb_gff_0_1" owner="galaxyp" changeset_revision="886eb2f99232" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="peptide_to_gff" version="0.1">
+        <repository name="package_peptides_to_gff_0_1" owner="galaxyp" changeset_revision="986d1d024720" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="blat" version="35x1">
+        <repository name="package_blat_35x1" owner="iuc" changeset_revision="cc0f4b49b6f1" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>