Mercurial > repos > iuc > package_sailfish_0_7_6

changeset 0:04996d8b8587 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sailfish_0_7_6 commit da2c0649c11ed0d54c1de8d345be95882717bd1a-dirty
author iuc
date Fri, 16 Oct 2015 15:07:45 -0400
parents
children
files tool_dependencies.xml
diffstat 1 files changed, 58 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Oct 16 15:07:45 2015 -0400
@@ -0,0 +1,58 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="sailfish" version="0.7.6">
+        <install version="1.0">
+            <actions_group>
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url">https://github.com/kingsfordgroup/sailfish/releases/download/v0.7.6/SailfishBeta-0.7.6_Linux-x86-64.tar.gz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>
+                </actions>
+                <actions architecture="x86_64" os="darwin">
+                    <action type="download_by_url">https://github.com/kingsfordgroup/sailfish/releases/download/v0.7.6/SailfishBeta-0.7.6_OSX_10.10.tar.gz</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>
+                </actions>
+                <actions>
+                    <!-- first action is always downloading -->
+                    <action type="download_by_url">https://github.com/kingsfordgroup/sailfish/archive/v0.7.6.tar.gz</action>
+                    <package name="boost" version="1.57">
+                        <repository changeset_revision="a0dd39685fce" name="package_boost_1_57" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+                    </package>
+                    <package name="cmake" version="3.2.3">
+                        <repository changeset_revision="1aea698a1c63" name="package_cmake_3_2_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+                    </package>
+                    <!-- populate the environment variables from the dependend repos -->
+                    <action type="set_environment_for_install">
+                        <repository changeset_revision="a0dd39685fce" name="package_boost_1_57" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                            <package name="boost" version="1.57" />
+                        </repository>
+                        <repository changeset_revision="1aea698a1c63" name="package_cmake_3_2_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                            <package name="cmake" version="3.2.3" />
+                        </repository>
+                    </action>
+
+                    <!-- PYTHONPATH_NUMPY is set in the numpy package -->
+                    <action type="shell_command">
+                        mkdir build &amp;&amp;
+                        cd build &amp;&amp;
+                        cmake .. -DBOOST_ROOT=$BOOST_ROOT_DIR -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR</action>
+                    <action type="shell_command">cd ./build &amp;&amp; make </action>
+                    <action type="shell_command">cd ./build &amp;&amp; make install</action>
+                    <action type="set_environment">
+                        <environment_variable action="append_to" name="LD_LIBRARY_PATH">$ENV[BOOST_ROOT_DIR]/lib/</environment_variable>
+                    </action>
+                </actions>
+                <action type="set_environment">
+                    <environment_variable action="append_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib/</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme>Compiling sailfish requires a C++11 compiler (usually gcc).</readme>
+    </package>
+</tool_dependency>