Mercurial > repos > iuc > package_openms_2_0

changeset 4:78a0d41b76fb draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_openms_2_0 commit 97a064489364118d108b0dd2cfb4d9bc53080837
author iuc
date Thu, 19 Nov 2015 13:49:12 -0500
parents 1a16c401c5a4
children
files tool_dependencies.xml
diffstat 1 files changed, 12 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Wed Apr 29 22:40:28 2015 -0400
+++ b/tool_dependencies.xml	Thu Nov 19 13:49:12 2015 -0500
@@ -1,6 +1,4 @@
 <?xml version="1.0"?>
-<!-- ToDo can we get it easily without svn? Is this included in the final tarball? -->
-<!-- svn checkout http://svn.code.sf.net/p/open-ms/code/THIRDPARTY/SEARCHENGINES/Linux/64bit/ _searchengines -->
 <tool_dependency>
     <package name="openms" version="2.0">
         <install version="1.0">
@@ -24,28 +22,28 @@
                     <action type="download_by_url">https://github.com/OpenMS/contrib/archive/master.tar.gz</action>
                     <action type="shell_command">mv contrib-master ../contrib</action>
                     <package name="libtool" version="2.4">
-                        <repository name="package_libtool_2_4" owner="iuc" prior_installation_required="True" />
+                        <repository changeset_revision="5ccfb33b5622" name="package_libtool_2_4" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                     </package>
                     <package name="Qt" version="4.8">
-                        <repository name="package_qt_4_8" owner="iuc" prior_installation_required="True" />
+                        <repository changeset_revision="d05194d4dc93" name="package_qt_4_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                     </package>
                     <package name="zlib" version="1.2.8">
-                        <repository name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" />
+                        <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                     </package>
                     <package name="bzlib" version="1.0.6">
-                        <repository name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" />
+                        <repository changeset_revision="29f79feefc77" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                     </package>
                     <action type="set_environment_for_install">
-                        <repository name="package_libtool_2_4" owner="iuc">
+                        <repository changeset_revision="5ccfb33b5622" name="package_libtool_2_4" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                             <package name="libtool" version="2.4" />
                         </repository>
-                        <repository name="package_qt_4_8" owner="iuc">
+                        <repository changeset_revision="d05194d4dc93" name="package_qt_4_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                             <package name="Qt" version="4.8" />
                         </repository>
-                        <repository name="package_zlib_1_2_8" owner="iuc">
+                        <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                             <package name="zlib" version="1.2.8" />
                         </repository>
-                        <repository name="package_bzlib_1_0" owner="iuc">
+                        <repository changeset_revision="29f79feefc77" name="package_bzlib_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                             <package name="bzlib" version="1.0.6" />
                         </repository>
                     </action>
@@ -63,14 +61,13 @@
 
                     <action type="change_directory">..</action>
                     <action type="shell_command">cmake . -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DHAS_XSERVER=OFF -DENABLE_TUTORIALS=OFF -DENABLE_STYLE_TESTING=OFF -DENABLE_UNITYBUILD=OFF -DWITH_GUI=OFF</action>
-                    <action type="shell_command">make OpenMS TOPP UTILS</action>
-                    <action type="shell_command">make install</action>
+                    <action type="make_install">OpenMS TOPP UTILS</action>
                     <action type="set_environment">
                         <environment_variable action="set_to" name="OPENMS_ROOT_PATH">$INSTALL_DIR</environment_variable>
-                        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                         <environment_variable action="set_to" name="OPENMS_DATA_PATH">$INSTALL_DIR/share/OpenMS</environment_variable>
-                        <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable>
-                        <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$ENV[QT_ROOT_DIR]/lib/</environment_variable>
+                        <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
+                        <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[QT_ROOT_DIR]/lib/</environment_variable>
                     </action>
                 </actions>
             </actions_group>