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annotate README.rst @ 18:2caada2d49bc draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'adf695285ea7366d6c5d48e416c4e00d83b9e733\n'-dirty
author bebatut
date Thu, 02 Mar 2017 09:25:07 -0500
parents b0cd2569ccfb
children 56e8ce2f3c96
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7838137cbc7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
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1 Galaxy wrappers for HUMAnN2
7838137cbc7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
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2 ===========================
7838137cbc7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
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7838137cbc7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
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4 Galaxy should be able to automatically install the dependencies, i.e. the
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b0cd2569ccfb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 79571d981d7d56657699be8aa24a40a36a8d0ab5-dirty
bebatut
parents: 12
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5 HUMAnN2 binaries and its dependencies.
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7838137cbc7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
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7838137cbc7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
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7 After installation, you must tell Galaxy about the defaut database with
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b0cd2569ccfb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 79571d981d7d56657699be8aa24a40a36a8d0ab5-dirty
bebatut
parents: 12
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8 clade-specific marker genes used for taxonomic profiling (MetaPhlAn2), and where
b0cd2569ccfb planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 79571d981d7d56657699be8aa24a40a36a8d0ab5-dirty
bebatut
parents: 12
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9 to find it:
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7838137cbc7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
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7838137cbc7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
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11 * Put the ``metaphlan2_db.loc`` file in the ``tool-data/`` folder, after uncommenting last line
7838137cbc7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
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12 * Download whole MetaPhlan2 source code: https://bitbucket.org/biobakery/metaphlan2/get/2.5.0.zip
7838137cbc7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
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13 * Unzip it
7838137cbc7f planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 450bf3326f301c344103272b0d761e8625ce0c44-dirty
bebatut
parents:
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14 * Move ``db_v20`` folder into ``dependency_dir/metaphlan2/2.5.0/bebatut/package_metaphlan2_2_5_0/...`` folder