Mercurial > repos > bebatut > humann2_reduce_table

annotate README.rst @ 2:f6b9ae94a0e7 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'38ee3fbdc89e93fa2266e9a4e755a086bf564cc6\n'-dirty
author bebatut
date Wed, 01 Mar 2017 11:34:33 -0500
parents abe72aa5a8b9
children 92fba38bac3e
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abe72aa5a8b9 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f126d56aa160b10437d9dabf5c9e32fd4569fee6\n'-dirty
bebatut
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1 Galaxy wrappers for HUMAnN2
abe72aa5a8b9 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f126d56aa160b10437d9dabf5c9e32fd4569fee6\n'-dirty
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2 ===========================
abe72aa5a8b9 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f126d56aa160b10437d9dabf5c9e32fd4569fee6\n'-dirty
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abe72aa5a8b9 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f126d56aa160b10437d9dabf5c9e32fd4569fee6\n'-dirty
bebatut
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4 Galaxy should be able to automatically install the dependencies, i.e. the
abe72aa5a8b9 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f126d56aa160b10437d9dabf5c9e32fd4569fee6\n'-dirty
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5 HUMAnN2 binaries and its dependencies.
abe72aa5a8b9 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f126d56aa160b10437d9dabf5c9e32fd4569fee6\n'-dirty
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abe72aa5a8b9 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f126d56aa160b10437d9dabf5c9e32fd4569fee6\n'-dirty
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7 After installation, you must tell Galaxy about the defaut database with
abe72aa5a8b9 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f126d56aa160b10437d9dabf5c9e32fd4569fee6\n'-dirty
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8 clade-specific marker genes used for taxonomic profiling (MetaPhlAn2), and where
abe72aa5a8b9 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f126d56aa160b10437d9dabf5c9e32fd4569fee6\n'-dirty
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9 to find it:
abe72aa5a8b9 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f126d56aa160b10437d9dabf5c9e32fd4569fee6\n'-dirty
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abe72aa5a8b9 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f126d56aa160b10437d9dabf5c9e32fd4569fee6\n'-dirty
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11 * Put the ``metaphlan2_db.loc`` file in the ``tool-data/`` folder, after uncommenting last line
abe72aa5a8b9 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f126d56aa160b10437d9dabf5c9e32fd4569fee6\n'-dirty
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12 * Download whole MetaPhlan2 source code: https://bitbucket.org/biobakery/metaphlan2/get/2.5.0.zip
abe72aa5a8b9 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f126d56aa160b10437d9dabf5c9e32fd4569fee6\n'-dirty
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13 * Unzip it
abe72aa5a8b9 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f126d56aa160b10437d9dabf5c9e32fd4569fee6\n'-dirty
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14 * Move ``db_v20`` folder into ``dependency_dir/metaphlan2/2.5.0/bebatut/package_metaphlan2_2_5_0/...`` folder