# HG changeset patch
# User iuc
# Date 1455659825 18000
# Node ID f27d2f8761ae4917b067e0744256723b8d635c28
# Parent  0538fd6721193ccdf3fc4684c741112366b27bbd
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_atlas_3_10 commit 09872476567320942381c809c574e99d4b090bea-dirty

diff -r 0538fd672119 -r f27d2f8761ae tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jul 16 05:43:42 2015 -0400
+++ b/tool_dependencies.xml	Tue Feb 16 16:57:05 2016 -0500
@@ -1,9 +1,12 @@
+<?xml version="1.0"?>
 <tool_dependency>
     <package name="atlas" version="3.10.2">
         <install version="1.0">
             <actions_group>
                 <actions architecture="x86_64" os="linux">
-                    <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/atlas/atlas-3.10.2-Linux-x86_64.tar.gz</action>
+                    <action type="download_by_url" sha256sum="c36a9edf352aa3652ae2c3cccf752351e12291c1d018da842093f9dc70fa2da3">
+                        https://depot.galaxyproject.org/software/atlas/atlas_3.10.2_linux_x64.tar.gz
+                    </action>
                     <action type="move_directory_files">
                         <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR</destination_directory>
@@ -13,6 +16,7 @@
                         <environment_variable action="set_to" name="ATLAS_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable>
                         <environment_variable action="set_to" name="ATLAS_BLAS_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
                         <environment_variable action="set_to" name="ATLAS_LAPACK_LIB_DIR">$INSTALL_DIR/lib/atlas</environment_variable>
+                        <environment_variable action="set_to" name="ATLAS">$INSTALL_DIR</environment_variable>
                         <environment_variable action="set_to" name="ATLAS_ROOT_PATH">$INSTALL_DIR</environment_variable>
                         <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
                         <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/atlas</environment_variable>
@@ -36,12 +40,22 @@
                     <!-- NOOP: On OS X we will use Apple's vecLib -->
                 </actions>
                 <actions>
-                    <action type="download_file">http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2</action>
-                    <action type="download_file">http://www.netlib.org/lapack/lapack-3.5.0.tgz</action>
-                    <action type="download_file">https://depot.galaxyproject.org/patch/atlas/static_full_blas_lapack.diff</action>
-                    <action type="download_file">https://depot.galaxyproject.org/patch/atlas/shared_libraries.diff</action>
-                    <action type="download_file">https://depot.galaxyproject.org/patch/atlas/cpu-throttling-check.diff</action>
-                    <action type="shell_command">tar -jxvf atlas3.10.2.tar.bz2</action>
+                    <action type="download_file" sha256sum="3aab139b118bf3fcdb4956fbd71676158d713ab0d3bccb2ae1dc3769db22102f">
+                        https://depot.galaxyproject.org/software/atlas/atlas_3.10.2+gx0_src_all.tar.bz2
+                    </action>
+                    <action type="download_file" sha256sum="9ad8f0d3f3fb5521db49f2dd716463b8fb2b6bc9dc386a9956b8c6144f726352">
+                        https://depot.galaxyproject.org/software/lapack/lapack_3.5.0_src_all.tar.gz
+                    </action>
+                    <action type="download_file" sha256sum="adbe462b179a2d626cd229cddcb08e39ae2f2544eccf80ab617790b307667146">
+                        https://depot.galaxyproject.org/software/atlas/atlas_patch-blas-lapack-1.0_src_all.diff
+                    </action>
+                    <action type="download_file" sha256sum="95862478f7d276f948a58c583acd2935ada9ad3bb55944a303d94e161e202d89">
+                        https://depot.galaxyproject.org/software/atlas/atlas_patch-shared-lib-1.0_src_all.diff
+                    </action>
+                    <action type="download_file" sha256sum="f805600c46719f74752e9026e1461d084a385ba67838364a81c36cdfb69cad82">
+                        https://depot.galaxyproject.org/software/atlas/atlas_patch-cpu-throttle-1.0_src_all.diff
+                    </action>
+                    <action type="shell_command">tar -jxvf atlas_3.10.2+gx0_src_all.tar.bz2</action>
                     <!-- a 64-bit architecture is assumed for compilation -->
                     <action type="shell_command"><![CDATA[
                         cd ATLAS &&