# HG changeset patch
# User morinlab
# Date 1476208882 14400
# Node ID 6340da10d13460ee40eda7dddeedd709b96c62d5

planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/packages/package_sequenza_2_1_2 commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty

diff -r 000000000000 -r 6340da10d134 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Oct 11 14:01:22 2016 -0400
@@ -0,0 +1,43 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="R" version="3.2.1">
+    <repository changeset_revision="77d439695328" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="deseq2" version="1.10.0">
+    <repository changeset_revision="5d9def29ff0b" name="package_deseq2_1_10_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="pypy" version="5.4.1">
+    <repository changeset_revision="32b2ef0a02cd" name="package_pypy_5_4_1" owner="morinlab" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="sequenza" version="2.1.2">
+    <install version="1.0">
+      <actions>
+        <action type="setup_r_environment">
+          <repository changeset_revision="77d439695328" name="package_r_3_2_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+            <package name="R" version="3.1.2" />
+          </repository>
+          <package>https://depot.galaxyproject.org/package/noarch/iterators_1.0.8.tar.gz</package>
+          <package>https://depot.galaxyproject.org/package/noarch/foreach_1.4.3.tar.gz</package>
+          <package>https://github.com/marcoalbuquerque-sfu/bioconductor-galaxy-cancer-genomics-toolbox/raw/master/zlibbioc_1.16.0.tar.gz</package>
+          <package>https://depot.galaxyproject.org/package/noarch/bitops_1.0-6.tar.gz</package>
+          <package>https://github.com/marcoalbuquerque-sfu/bioconductor-galaxy-cancer-genomics-toolbox/raw/master/BiocGenerics_0.16.1.tar.gz</package>
+          <package>https://github.com/marcoalbuquerque-sfu/bioconductor-galaxy-cancer-genomics-toolbox/raw/master/S4Vectors_0.8.1.tar.gz</package>
+          <package>https://github.com/marcoalbuquerque-sfu/bioconductor-galaxy-cancer-genomics-toolbox/raw/master/IRanges_2.4.1.tar.gz</package>
+          <package>https://github.com/marcoalbuquerque-sfu/bioconductor-galaxy-cancer-genomics-toolbox/raw/master/GenomeInfoDb_1.6.1.tar.gz</package>
+          <package>https://github.com/marcoalbuquerque-sfu/bioconductor-galaxy-cancer-genomics-toolbox/raw/master/XVector_0.10.0.tar.gz</package>
+          <package>https://github.com/marcoalbuquerque-sfu/bioconductor-galaxy-cancer-genomics-toolbox/raw/master/GenomicRanges_1.22.1.tar.gz</package>            
+          <package>https://github.com/marcoalbuquerque-sfu/bioconductor-galaxy-cancer-genomics-toolbox/raw/master/Biobase_2.30.0.tar.gz</package>
+          <package>https://depot.galaxyproject.org/package/noarch/DBI_0.3.1.tar.gz</package>
+          <package>https://depot.galaxyproject.org/package/noarch/RSQLite_1.0.0.tar.gz</package>
+          <package>https://github.com/marcoalbuquerque-sfu/bioconductor-galaxy-cancer-genomics-toolbox/raw/master/AnnotationDbi_1.33.1.tar.gz</package>                                 
+          <package>https://github.com/marcoalbuquerque-sfu/bioconductor-galaxy-cancer-genomics-toolbox/raw/master/copynumber_1.10.0.tar.gz</package>
+          <package>https://cran.r-project.org/src/contrib/squash_1.0.7.tar.gz</package>
+          <package>https://github.com/marcoalbuquerque-sfu/bioconductor-galaxy-cancer-genomics-toolbox/raw/master/sequenza_2.1.2.tar.gz</package>
+        </action>
+        <action type="set_environment">
+          <environment_variable action="set_to" name="SEQUENZA_INSTALL_DIR">$INSTALL_DIR</environment_variable>
+        </action>
+      </actions>
+    </install> 
+  </package>
+</tool_dependency>