Mercurial > repos > iuc > package_samtools_1_2

diff tool_dependencies.xml @ 1:f6ae3ba3f3c1 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_samtools_1_2 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
author iuc
date Fri, 17 Jul 2015 11:11:30 -0400
parents 6eea04363026
children
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--- a/tool_dependencies.xml	Mon Mar 16 12:39:24 2015 -0400
+++ b/tool_dependencies.xml	Fri Jul 17 11:11:30 2015 -0400
@@ -1,5 +1,11 @@
 <?xml version="1.0"?>
 <tool_dependency>
+    <package name="ncurses" version="5.9">
+        <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="zlib" version="1.2.8">
+        <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
     <package name="samtools" version="1.2">
         <install version="1.0">
             <actions_group>
@@ -11,12 +17,6 @@
                     </action>
                 </actions>
                 <actions>
-                    <package name="ncurses" version="5.9">
-                        <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-                    </package>
-                    <package name="zlib" version="1.2.8">
-                        <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
-                    </package>
                     <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">
                         <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
@@ -27,9 +27,9 @@
                         </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">make</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$NCURSES_LIB_PATH|g" Makefile</action>
+                    <action type="make_install" />
                     <action type="move_file">
                         <source>samtools</source>
                         <destination>$INSTALL_DIR/bin</destination>