# HG changeset patch
# User yhoogstrate
# Date 1469715912 14400
# Node ID f448376f428f5a2993227fd2f1e5790c47d28e63

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 00690c63c51a7f7563f2428c313d7fa75f2657e5-dirty

diff -r 000000000000 -r f448376f428f tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Jul 28 10:25:12 2016 -0400
@@ -0,0 +1,119 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <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>
+    
+    <package name="python" version="2.7.10">
+        <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="numpy" version="1.9">
+        <repository changeset_revision="f24fc0b630fc" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="pysam" version="0.8.2.1">
+        <repository changeset_revision="f8fecf1f6eba" name="package_pysam_0_8_2" owner="yhoogstrate" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="htseq" version="0.6.1">
+        <repository changeset_revision="fbb72996807d" name="package_htseq_0_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    
+    <package name="setuptools" version="19.0">
+        <repository changeset_revision="cb689698d484" name="package_setuptools_19_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    
+    <package name="segmentation-fold" version="1.6.5">
+        <install version="1.0">
+            <actions>
+                <action sha256sum="3a882b687f0977d1f25ef225992499fdc0d5ace687f104a9b557415aa1e7ab13" type="download_by_url">https://github.com/yhoogstrate/segmentation-fold/archive/43edf7fd32dc87029e3babe00533b518f8048bd4.tar.gz</action>
+                    
+                <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>
+                </action>
+                
+                <action type="set_environment_for_install">
+                    <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>
+                
+                <action type="shell_command">
+                    cmake -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR .  &amp;&amp;
+                    make                                                                    &amp;&amp;
+                    make check                                                              &amp;&amp;
+                    make install
+                </action>
+                
+                <action type="set_environment">
+                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="set_to" name="SEGMENTATION_FOLD_DEFAULT_XML">$INSTALL_DIR/share/segmentation-fold/segments.xml</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            Installation of segmentation-fold requires:
+             - libboost                     (via toolshed)
+             - CMake                        (via toolshed)
+             - c++11 compliant compiler: g++ or clang
+        </readme>
+    </package>
+    
+    <package name="segmentation-fold-utils" version="2.0.1">
+        <install version="1.0">
+            <actions>
+                <action sha256sum="3a882b687f0977d1f25ef225992499fdc0d5ace687f104a9b557415aa1e7ab13" type="download_by_url">https://github.com/yhoogstrate/segmentation-fold/archive/43edf7fd32dc87029e3babe00533b518f8048bd4.tar.gz</action>
+                
+                <!-- Also install the python utils -->
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="cb689698d484" name="package_setuptools_19_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="setuptools" version="19.0" />
+                    </repository>
+
+                     <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="python" version="2.7.10" />
+                    </repository>
+
+                    <repository changeset_revision="f24fc0b630fc" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="numpy" version="1.9" />
+                    </repository>
+
+                    <repository changeset_revision="f8fecf1f6eba" name="package_pysam_0_8_2" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="pysam" version="0.8.2.1" />
+                    </repository>
+                    
+                    <repository changeset_revision="fbb72996807d" name="package_htseq_0_6" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="htseq" version="0.6.1" />
+                    </repository>
+                </action>
+                
+                <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                <action type="make_directory">$INSTALL_DIR/lib64/python</action>
+                <action type="shell_command">
+                    export PYTHONPATH="$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python"  &amp;&amp;
+                    cd scripts/energy-estimation-utility                                               &amp;&amp;
+                    echo "---------------------------------------------------------------------------" &amp;&amp;
+                    head -n 161 segmentation_fold_utils/XMLFile.py | tail -n 11                        &amp;&amp;
+                    echo "---------------------------------------------------------------------------" &amp;&amp;
+                    python setup.py install --home "$INSTALL_DIR" --install-scripts "$INSTALL_DIR/bin"
+                </action>
+                
+                <action type="set_environment">
+                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            Installation of segmentation-fold-utils requires:
+             - Python                       (via toolshed)
+             - numpy                        (via toolshed)
+             - pysam                        (via toolshed)
+        </readme>
+    </package>
+</tool_dependency>