Mercurial > repos > iuc > package_samtools_0_1_19

diff tool_dependencies.xml @ 7:c9bd782f5342 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_0_1_19 commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
author iuc
date Sat, 25 Jun 2016 17:21:35 -0400
parents 96aab723499f
children
line wrap: on
line diff
--- a/tool_dependencies.xml	Thu Feb 26 14:21:15 2015 -0500
+++ b/tool_dependencies.xml	Sat Jun 25 17:21:35 2016 -0400
@@ -3,22 +3,28 @@
     <package name="samtools" version="0.1.19">
         <install version="1.0">
             <actions_group>
-                <actions os="linux" architecture="x86_64">
-                    <action type="download_by_url" target_filename="samtools-0.1.19.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.19-Linux-x86_64.tgz</action>
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url" sha256sum="3cc457cd66e077b70887155435d8f563154371a61e7ac6714bc10b6aa19841bd" target_filename="samtools-0.1.19.tgz">https://depot.galaxyproject.org/software/samtools/samtools_0.1.19_linux_x64.tar.gz</action>
                     <action type="move_directory_files">
                         <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR</destination_directory>
                     </action>
+                    <action type="set_environment">
+                        <environment_variable name="BAM_INCLUDE" action="set_to">$INSTALL_DIR/include</environment_variable>
+                    </action>
                 </actions>
-                <actions os="darwin" architecture="x86_64">
-                    <action type="download_by_url" target_filename="samtools-0.1.19.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.19-Darwin-x86_64.tgz</action>
+                <actions architecture="x86_64" os="darwin">
+                    <action type="download_by_url" sha256sum="01e0a2cb38b1bcd433461cef43ff6555755a30dfbe83cb9c0a24cb028b104ac7" target_filename="samtools-0.1.19.tgz">https://depot.galaxyproject.org/software/samtools/samtools_0.1.19_darwin_x64.tar.gz</action>
                     <action type="move_directory_files">
                         <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR</destination_directory>
                     </action>
+                    <action type="set_environment">
+                        <environment_variable name="BAM_INCLUDE" action="set_to">$INSTALL_DIR/include</environment_variable>
+                    </action>
                 </actions>
                 <actions>
-                    <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.19.tar.bz2</action>
+                    <action type="download_by_url" sha256sum="d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4">https://depot.galaxyproject.org/software/samtools/samtools_0.1.19_src_all.tar.bz2</action>
                     <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
                     <action type="shell_command">make</action>
                     <action type="move_file">
@@ -41,6 +47,9 @@
                         <source_directory>.</source_directory>
                         <destination_directory>$INSTALL_DIR/include/bam</destination_directory>
                     </action>
+                    <action type="set_environment">
+                        <environment_variable name="BAM_INCLUDE" action="set_to">$INSTALL_DIR/include/bam</environment_variable>
+                    </action>
                 </actions>
                 <action type="set_environment">
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>