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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit 68b62fd9a9d5586ccd539779873af17124b7dbb5
author earlhaminst
date Wed, 09 May 2018 05:52:40 -0400
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9838eed606ad planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit 68b62fd9a9d5586ccd539779873af17124b7dbb5
earlhaminst
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1 Installation
9838eed606ad planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit 68b62fd9a9d5586ccd539779873af17124b7dbb5
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2 ------------
9838eed606ad planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit 68b62fd9a9d5586ccd539779873af17124b7dbb5
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9838eed606ad planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit 68b62fd9a9d5586ccd539779873af17124b7dbb5
earlhaminst
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4 After installing the ``export_to_cluster`` tool, you need to setup an environment variable to specify the directory where users are expected to save their files. One way to do that is:
9838eed606ad planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit 68b62fd9a9d5586ccd539779873af17124b7dbb5
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9838eed606ad planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit 68b62fd9a9d5586ccd539779873af17124b7dbb5
earlhaminst
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6 1) create a directory called ``EXPORT_DIR_PREFIX`` in your tool dependencies directory (which by default is ``database/dependencies/``, but can be changed in your Galaxy config file)
9838eed606ad planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit 68b62fd9a9d5586ccd539779873af17124b7dbb5
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7 2) in this directory, create a file called ``env.sh`` with a content similar to the following template::
9838eed606ad planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit 68b62fd9a9d5586ccd539779873af17124b7dbb5
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9838eed606ad planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit 68b62fd9a9d5586ccd539779873af17124b7dbb5
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9 EXPORT_DIR_PREFIX=/PATH/WHERE/TO/SAVE/FILES; export EXPORT_DIR_PREFIX
9838eed606ad planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit 68b62fd9a9d5586ccd539779873af17124b7dbb5
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9838eed606ad planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit 68b62fd9a9d5586ccd539779873af17124b7dbb5
earlhaminst
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11 3) create a symlink called ``default`` inside the ``EXPORT_DIR_PREFIX`` directory pointing to the same directory, e.g.::
9838eed606ad planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit 68b62fd9a9d5586ccd539779873af17124b7dbb5
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9838eed606ad planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit 68b62fd9a9d5586ccd539779873af17124b7dbb5
earlhaminst
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13 $ cd TOOL_DEPENDENCIES_DIR/EXPORT_DIR_PREFIX/
9838eed606ad planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit 68b62fd9a9d5586ccd539779873af17124b7dbb5
earlhaminst
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14 $ ln -s . default
9838eed606ad planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit 68b62fd9a9d5586ccd539779873af17124b7dbb5
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9838eed606ad planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit 68b62fd9a9d5586ccd539779873af17124b7dbb5
earlhaminst
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16 Alternatively, you could define the ``EXPORT_DIR_PREFIX`` environment variable in your ``config/job_conf.xml`` file for the destination where the ``export_to_cluster`` tool is going to run (for an example, see ``_JAVA_OPTIONS`` in ``config/job_conf.xml.sample_advanced``), but this would define the environment variable also for all the other tools that use that destination (normally not a problem, but worth to mention).
9838eed606ad planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit 68b62fd9a9d5586ccd539779873af17124b7dbb5
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