Mercurial > repos > abaizan > kodoja
diff README.rst @ 3:d4111d1de76f draft default tip
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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--- a/README.rst Mon Sep 10 09:16:13 2018 -0400 +++ b/README.rst Fri Sep 14 09:55:56 2018 -0400 @@ -54,17 +54,29 @@ $ 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:: +Each installed version of Kodoja (or Kraken or Kaiju) will have its own +``*.loc`` files, which Galaxy will merge into a single list. e.g.:: + + $ find /path/to/galaxy/tool-data -name kaiju_databases.loc + $ find /path/to/galaxy/tool-data -name kraken_databases.loc + +Edit a ``kraken_databases.loc`` file to add a line like this, where +``(tab)`` represents inserting a tab character (NOT spaces):: 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:: +And likewise update ``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. +the Galaxy server, or doing this explicitly via the "Data tables registry" +available under Server Administration if logged into Galaxy as an administator. + +It is our personal preference to work with ``tool-data/kraken_databases.loc`` +and ``tool-data/kaiju_databases.loc``, but if these are being ignored, you +*may* need to enable this by adding the XML data table entries from our file +``tool_data_table_conf.xml.sample`` to ``config/tool_data_table_conf.xml``. History @@ -80,6 +92,9 @@ v0.0.7 - Minor update to call ``kodoja_search.py`` v0.0.6. - Update help text, including zeros in columns 6 and 7. - Support ``$GALAXY_SLOTS``, defaulting to using four threads. +v0.0.8 - Minor update to call ``kodoja_search.py`` v0.0.8. + - Option to capture the ``kodoja_VRL.tsv`` read table. + - Accept ``kraken_databases.loc`` entry style for old Kraken wrapper. ======= ======================================================================