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v0.0.8, expose kodoja_VRL.tsv output
author peterjc
date Fri, 14 Sep 2018 09:55:56 -0400
parents ee917702dbd8
children
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2:ee917702dbd8 3:d4111d1de76f
52 $ mkdir kodojaDB_v1.0 52 $ mkdir kodojaDB_v1.0
53 $ cd kodojaDB_v1.0 53 $ cd kodojaDB_v1.0
54 $ wget https://zenodo.org/record/1406071/files/kodojaDB_v1.0.tar.gz 54 $ wget https://zenodo.org/record/1406071/files/kodojaDB_v1.0.tar.gz
55 $ tar -zxvf kodojaDB_v1.0.tar.gz 55 $ tar -zxvf kodojaDB_v1.0.tar.gz
56 56
57 Then update your Galaxy configuration in ``tool-data/kraken_databases.loc`` 57 Each installed version of Kodoja (or Kraken or Kaiju) will have its own
58 to add a line like this:: 58 ``*.loc`` files, which Galaxy will merge into a single list. e.g.::
59
60 $ find /path/to/galaxy/tool-data -name kaiju_databases.loc
61 $ find /path/to/galaxy/tool-data -name kraken_databases.loc
62
63 Edit a ``kraken_databases.loc`` file to add a line like this, where
64 ``(tab)`` represents inserting a tab character (NOT spaces)::
59 65
60 kodojaDB_v1.0_kraken(tab)KodojaDB v1.0 (kraken), Sept 2018(tab)/mnt/shared/data/kodojaDB_v1.0/krakenDB 66 kodojaDB_v1.0_kraken(tab)KodojaDB v1.0 (kraken), Sept 2018(tab)/mnt/shared/data/kodojaDB_v1.0/krakenDB
61 67
62 And likewise update ``tool-data/kaiju_databases.loc`` with a line like:: 68 And likewise update ``kaiju_databases.loc`` with a line like::
63 69
64 kodojaDB_v1.0_kaiju(tab)KodojaDB v1.0 (kaiju), Sept 2018(tab)/mnt/shared/data/kodojaDB_v1.0/kaijuDB 70 kodojaDB_v1.0_kaiju(tab)KodojaDB v1.0 (kaiju), Sept 2018(tab)/mnt/shared/data/kodojaDB_v1.0/kaijuDB
65 71
66 At the time of writing, reloading the ``*.loc`` files required restarting 72 At the time of writing, reloading the ``*.loc`` files required restarting
67 the Galaxy server. 73 the Galaxy server, or doing this explicitly via the "Data tables registry"
74 available under Server Administration if logged into Galaxy as an administator.
75
76 It is our personal preference to work with ``tool-data/kraken_databases.loc``
77 and ``tool-data/kaiju_databases.loc``, but if these are being ignored, you
78 *may* need to enable this by adding the XML data table entries from our file
79 ``tool_data_table_conf.xml.sample`` to ``config/tool_data_table_conf.xml``.
68 80
69 81
70 History 82 History
71 ======= 83 =======
72 84
78 v0.0.6 - Minor update to call ``kodoja_search.py`` v0.0.6. 90 v0.0.6 - Minor update to call ``kodoja_search.py`` v0.0.6.
79 - Document installing the Kodoja databases from Zenodo. 91 - Document installing the Kodoja databases from Zenodo.
80 v0.0.7 - Minor update to call ``kodoja_search.py`` v0.0.6. 92 v0.0.7 - Minor update to call ``kodoja_search.py`` v0.0.6.
81 - Update help text, including zeros in columns 6 and 7. 93 - Update help text, including zeros in columns 6 and 7.
82 - Support ``$GALAXY_SLOTS``, defaulting to using four threads. 94 - Support ``$GALAXY_SLOTS``, defaulting to using four threads.
95 v0.0.8 - Minor update to call ``kodoja_search.py`` v0.0.8.
96 - Option to capture the ``kodoja_VRL.tsv`` read table.
97 - Accept ``kraken_databases.loc`` entry style for old Kraken wrapper.
83 ======= ====================================================================== 98 ======= ======================================================================
84 99
85 100
86 Bug Reports 101 Bug Reports
87 =========== 102 ===========