Mercurial > repos > iuc > package_python_bioformats_1_0_4

changeset 0:4327b98ec35e draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
author iuc
date Tue, 09 Jun 2015 12:21:30 -0400
parents
children
files tool_dependencies.xml
diffstat 1 files changed, 41 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Jun 09 12:21:30 2015 -0400
@@ -0,0 +1,41 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="javabridge" version="1.0.11">
+        <repository changeset_revision="8d338153c3dc" name="package_javabridge_1_0_11" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="python_bioformats" version="1.0.4">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">https://pypi.python.org/packages/source/p/python-bioformats/python-bioformats-1.0.4.tar.gz#md5=b5b316f9da734d82ebb0254f22c30b1f</action>
+                <action type="make_directory">$INSTALL_DIR/lib/python</action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="4778b172b895" name="package_atlas_3_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="atlas" version="3.10.2" />
+                    </repository>
+                    <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="numpy" version="1.9" />
+                    </repository>
+                    <repository changeset_revision="8d338153c3dc" name="package_javabridge_1_0_11" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="javabridge" version="1.0.11" />
+                    </repository>
+                </action>
+                <action type="shell_command">
+                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
+                    python setup.py install --install-lib $INSTALL_DIR/lib/python
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable action="set_to" name="PYTHON_BIOFORMATS_ROOT_DIR">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            
+                Python-bioformats is a Python wrapper for Bio-Formats, a standalone Java library for reading and
+                writing life sciences image file formats. Bio-Formats is capable of parsing both pixels and metadata
+                for a large number of formats, as well as writing to several formats.  Python-bioformats uses the
+                python-javabridge to start a Java virtual machine from Python and interact with it.
+            
+        </readme>
+    </package>
+</tool_dependency>