# HG changeset patch
# User iuc
# Date 1465927280 14400
# Node ID 5eac5e2d91e211d38e709562c49b1ef28048f13c

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty

diff -r 000000000000 -r 5eac5e2d91e2 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Jun 14 14:01:20 2016 -0400
@@ -0,0 +1,24 @@
+<?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" />
+    </package>
+    <package name="stacks" version="1.40">
+        <install version="1.0">
+            <actions>
+                <action sha256sum="bf2304ba4ec44991db327ea77eb0f8c58de6d665162abf72470f5cd9dfb71493" type="download_by_url">https://depot.galaxyproject.org/software/stacks/stacks-1.40_src_all.tar.gz</action>
+                <action type="shell_command">./configure --prefix=$INSTALL_DIR --enable-bam --with-bam-include-path=${BAM_ROOT}/include/bam --with-bam-lib-path=${BAM_LIB_PATH}</action>
+                <action type="shell_command">make</action>
+                <action type="shell_command">make install</action>
+                <!-- create env.sh -->
+                <action type="set_environment">
+                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable>
+                        <environment_variable action="set_to" name="STACKS_ROOT_DIR">$INSTALL_DIR/</environment_variable>
+                </action>
+           </actions>
+        </install>
+        <readme>
+            This package installs STACKS from the sources available. Based on Cyril Monjeuad version
+        </readme>
+    </package>
+</tool_dependency>