# HG changeset patch
# User iuc
# Date 1466889848 14400
# Node ID 51d4ab2c4dcf1065aebe68ab28198d3ea856afa8
# Parent  95cffefc0dfeffeca031d1625b42e6a0426e53f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393

diff -r 95cffefc0dfe -r 51d4ab2c4dcf tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jun 15 06:22:39 2016 -0400
+++ b/tool_dependencies.xml	Sat Jun 25 17:24:08 2016 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="c9bd782f5342" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="stacks" version="1.40">
         <install version="1.0">
@@ -9,12 +9,12 @@
                 <action sha256sum="bf2304ba4ec44991db327ea77eb0f8c58de6d665162abf72470f5cd9dfb71493" type="download_by_url">https://depot.galaxyproject.org/software/stacks/stacks_1.40_src_all.tar.gz</action>
 
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="c9bd782f5342" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                         <package name="samtools" version="0.1.19" />
                     </repository>
                 </action>
 
-                <action type="shell_command">./configure --prefix=$INSTALL_DIR --enable-bam --with-bam-include-path=${BAM_ROOT}/include/bam --with-bam-lib-path=${BAM_LIB_PATH}</action>
+                <action type="shell_command">./configure --prefix=$INSTALL_DIR --enable-bam --with-bam-include-path=${BAM_INCLUDE} --with-bam-lib-path=${BAM_LIB_PATH}</action>
                 <action type="shell_command">make</action>
                 <action type="shell_command">make install</action>
                 <!-- create env.sh -->