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v0.0.6
author peterjc
date Wed, 05 Sep 2018 10:44:57 -0400
parents 18fe33eb7775
children ee917702dbd8
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0:18fe33eb7775 1:4554fcd4ef6d
43 You must tell Galaxy about any Kraken and Kaiju databases using configuration 43 You must tell Galaxy about any Kraken and Kaiju databases using configuration
44 files ``kraken_databases.loc`` and ``kaiju_databases.loc`` which are located 44 files ``kraken_databases.loc`` and ``kaiju_databases.loc`` which are located
45 in the ``tool-data/`` folder. Sample files are included which explain the 45 in the ``tool-data/`` folder. Sample files are included which explain the
46 tab-based format to use. 46 tab-based format to use.
47 47
48 For example, using https://doi.org/10.5281/zenodo.1406071 which is the
49 database provided with Kodoja::
50
51 $ cd /mnt/shared/data/
52 $ mkdir kodojaDB_v1.0
53 $ cd kodojaDB_v1.0
54 $ wget https://zenodo.org/record/1406071/files/kodojaDB_v1.0.tar.gz
55 $ tar -zxvf kodojaDB_v1.0.tar.gz
56
57 Then update your Galaxy configuration in ``tool-data/kraken_databases.loc``
58 to add a line like this::
59
60 kodojaDB_v1.0_kraken(tab)KodojaDB v1.0 (kraken), Sept 2018(tab)/mnt/shared/data/kodojaDB_v1.0/krakenDB
61
62 And likewise update ``tool-data/kaiju_databases.loc`` with a line like::
63
64 kodojaDB_v1.0_kaiju(tab)KodojaDB v1.0 (kaiju), Sept 2018(tab)/mnt/shared/data/kodojaDB_v1.0/kaijuDB
65
66 At the time of writing, reloading the ``*.loc`` files required restarting
67 the Galaxy server.
68
48 69
49 History 70 History
50 ======= 71 =======
51 72
52 ======= ====================================================================== 73 ======= ======================================================================
53 Version Changes 74 Version Changes
54 ------- ---------------------------------------------------------------------- 75 ------- ----------------------------------------------------------------------
55 v0.0.0 - Initial release covering ``kodoja_search.py`` v0.0.3. 76 v0.0.0 - Initial release covering ``kodoja_search.py`` v0.0.3.
77 v0.0.4 - Minor update to call ``kodoja_search.py`` v0.0.4.
78 v0.0.6 - Minor update to call ``kodoja_search.py`` v0.0.6.
79 - Document installing the Kodoja databases from Zenodo.
56 ======= ====================================================================== 80 ======= ======================================================================
57 81
58 82
59 Bug Reports 83 Bug Reports
60 =========== 84 ===========