Mercurial > repos > iuc > package_samtools_1_2

diff tool_dependencies.xml @ 9:192f00129358 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit e6f0b88b7a59f0a10827fd55436b137b13cd1921
author iuc
date Fri, 09 Oct 2015 05:22:33 -0400
parents 9cd278d52bb6
children a55970300738
line wrap: on
line diff
--- a/tool_dependencies.xml	Tue Jul 07 06:21:42 2015 -0400
+++ b/tool_dependencies.xml	Fri Oct 09 05:22:33 2015 -0400
@@ -9,6 +9,13 @@
     <package name="samtools" version="1.2">
         <install version="1.0">
             <actions_group>
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-1.2-Linux-x86_64.tgz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>
+                </actions>
                 <actions>
                     <action type="download_by_url">https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2</action>
                     <action type="set_environment_for_install">
@@ -20,22 +27,13 @@
                         </repository>
                     </action>
                     <action type="shell_command">sed -i.bak 's#/usr/local#$INSTALL_DIR#' Makefile</action>
-                    <action type="shell_command">sed -i -e 's/-lcurses/-lncurses/' Makefile</action>
-                    <action type="shell_command">sed -i -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action>
+                    <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/' Makefile</action>
+                    <action type="shell_command">sed -i.bak -e "s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2 -I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH -L$NCURSES_LIB_PATH|g" Makefile</action>
                     <action type="shell_command">make</action>
                     <action type="move_file">
                         <source>samtools</source>
                         <destination>$INSTALL_DIR/bin</destination>
                     </action>
-                    <action type="shell_command">cd htslib-1.2.1 &amp;&amp; make bgzip tabix</action>
-                    <action type="move_file">
-                        <source>htslib-1.2.1/bgzip</source>
-                        <destination>$INSTALL_DIR/bin</destination>
-                    </action>
-                    <action type="move_file">
-                        <source>htslib-1.2.1/tabix</source>
-                        <destination>$INSTALL_DIR/bin</destination>
-                    </action>
                 </actions>
                 <action type="set_environment">
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>