--- a/tool_dependencies.xml	Thu Jul 12 08:24:21 2018 -0400
+++ b/tool_dependencies.xml	Thu Jul 12 08:27:08 2018 -0400
@@ -1,19 +1,27 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="R" version="3.1.2">
-    <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-  </package>
-  <package name="Perl" version="5.18">
-    <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-  </package>
-  <package>https://depot.galaxyproject.org/software/plotrix/plotrix_3.6_src_all.tar.gz</package>
-  <package>https://depot.galaxyproject.org/software/bioconductor-sushi/bioconductor-sushi_1.14.0_src_all.tar.gz</package>
-  <package>https://depot.galaxyproject.org/software/RColorBrewer/RColorBrewer_1.1-2_src_all.tar.gz</package>
-  <package>https://depot.galaxyproject.org/software/ggplot2/ggplot2_1.0.1_src_all.tar.gz</package>
-  <package name="Perl" version="5.18" />
-  <package>https://depot.galaxyproject.org/software/perl-statistics-r/perl-statistics-r_0.34_src_all.tar.gz</package>
-  <package>https://cpan.metacpan.org/authors/id/Y/YA/YANICK/Parallel-ForkManager-1.19.tar.gz</package>
-  <package>https://cpan.metacpan.org/authors/id/F/FA/FANGLY/Statistics-R-0.34.tar.gz</package>
-  <package>https://cpan.metacpan.org/authors/id/J/JV/JV/Getopt-Long-2.50.tar.gz</package>
-  <package>https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/String-Random-0.29.tar.gz</package>
-</tool_dependency>
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="bwa" version="0.7.12">
+    <repository changeset_revision="dcae4134cd62" name="package_bwa_0_7_12" owner="avowinkel" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="bedtools" version="2.24">
+    <repository changeset_revision="3416a1d4a582" name="package_bedtools_2_24" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="samtools" version="1.2">
+    <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="R" version="3.1.2">
+    <repository changeset_revision="d9f7d84125b7" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="Perl" version="5.18">
+    <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package>https://depot.galaxyproject.org/software/plotrix/plotrix_3.6_src_all.tar.gz</package>
+  <package>https://depot.galaxyproject.org/software/bioconductor-sushi/bioconductor-sushi_1.14.0_src_all.tar.gz</package>
+  <package>https://depot.galaxyproject.org/software/RColorBrewer/RColorBrewer_1.1-2_src_all.tar.gz</package>
+  <package>https://depot.galaxyproject.org/software/ggplot2/ggplot2_1.0.1_src_all.tar.gz</package>
+  <package>https://depot.galaxyproject.org/software/perl-statistics-r/perl-statistics-r_0.34_src_all.tar.gz</package>
+  <package>https://cpan.metacpan.org/authors/id/Y/YA/YANICK/Parallel-ForkManager-1.19.tar.gz</package>
+  <package>https://cpan.metacpan.org/authors/id/F/FA/FANGLY/Statistics-R-0.34.tar.gz</package>
+  <package>https://cpan.metacpan.org/authors/id/J/JV/JV/Getopt-Long-2.50.tar.gz</package>
+  <package>https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/String-Random-0.29.tar.gz</package>
+</tool_dependency>