Mercurial > repos > iuc > package_python_bioformats_1_0_4

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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
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4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
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1 <?xml version="1.0"?>
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
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2 <tool_dependency>
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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3 <package name="javabridge" version="1.0.11">
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
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4 <repository changeset_revision="8d338153c3dc" name="package_javabridge_1_0_11" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
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5 </package>
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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6 <package name="python_bioformats" version="1.0.4">
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
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7 <install version="1.0">
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
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8 <actions>
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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9 <action type="download_by_url">https://pypi.python.org/packages/source/p/python-bioformats/python-bioformats-1.0.4.tar.gz#md5=b5b316f9da734d82ebb0254f22c30b1f</action>
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
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10 <action type="make_directory">$INSTALL_DIR/lib/python</action>
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
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11 <action type="set_environment_for_install">
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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12 <repository changeset_revision="4778b172b895" name="package_atlas_3_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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13 <package name="atlas" version="3.10.2" />
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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14 </repository>
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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15 <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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16 <package name="numpy" version="1.9" />
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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17 </repository>
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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18 <repository changeset_revision="8d338153c3dc" name="package_javabridge_1_0_11" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
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19 <package name="javabridge" version="1.0.11" />
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
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20 </repository>
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
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21 </action>
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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22 <action type="shell_command">
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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23 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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24 python setup.py install --install-lib $INSTALL_DIR/lib/python
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
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25 </action>
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
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26 <action type="set_environment">
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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27 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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28 <environment_variable action="set_to" name="PYTHON_BIOFORMATS_ROOT_DIR">$INSTALL_DIR</environment_variable>
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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29 </action>
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
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30 </actions>
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
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31 </install>
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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32 <readme>
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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33
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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34 Python-bioformats is a Python wrapper for Bio-Formats, a standalone Java library for reading and
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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35 writing life sciences image file formats. Bio-Formats is capable of parsing both pixels and metadata
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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36 for a large number of formats, as well as writing to several formats. Python-bioformats uses the
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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37 python-javabridge to start a Java virtual machine from Python and interact with it.
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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38
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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39 </readme>
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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40 </package>
4327b98ec35e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/packages/package_python_bioformats_1_0_4 commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
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41 </tool_dependency>