Mercurial > repos > abaizan > kodoja
diff README.rst @ 1:4554fcd4ef6d draft
v0.0.6
author | peterjc |
---|---|
date | Wed, 05 Sep 2018 10:44:57 -0400 |
parents | 18fe33eb7775 |
children | ee917702dbd8 |
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--- a/README.rst Wed Mar 14 12:46:57 2018 -0400 +++ b/README.rst Wed Sep 05 10:44:57 2018 -0400 @@ -45,6 +45,27 @@ in the ``tool-data/`` folder. Sample files are included which explain the tab-based format to use. +For example, using https://doi.org/10.5281/zenodo.1406071 which is the +database provided with Kodoja:: + + $ cd /mnt/shared/data/ + $ mkdir kodojaDB_v1.0 + $ cd kodojaDB_v1.0 + $ wget https://zenodo.org/record/1406071/files/kodojaDB_v1.0.tar.gz + $ tar -zxvf kodojaDB_v1.0.tar.gz + +Then update your Galaxy configuration in ``tool-data/kraken_databases.loc`` +to add a line like this:: + + kodojaDB_v1.0_kraken(tab)KodojaDB v1.0 (kraken), Sept 2018(tab)/mnt/shared/data/kodojaDB_v1.0/krakenDB + +And likewise update ``tool-data/kaiju_databases.loc`` with a line like:: + + kodojaDB_v1.0_kaiju(tab)KodojaDB v1.0 (kaiju), Sept 2018(tab)/mnt/shared/data/kodojaDB_v1.0/kaijuDB + +At the time of writing, reloading the ``*.loc`` files required restarting +the Galaxy server. + History ======= @@ -53,6 +74,9 @@ Version Changes ------- ---------------------------------------------------------------------- v0.0.0 - Initial release covering ``kodoja_search.py`` v0.0.3. +v0.0.4 - Minor update to call ``kodoja_search.py`` v0.0.4. +v0.0.6 - Minor update to call ``kodoja_search.py`` v0.0.6. + - Document installing the Kodoja databases from Zenodo. ======= ======================================================================