Mercurial > repos > pjbriggs > weeder2
diff README.rst @ 2:3c5f10f7dd40 draft
Updated to tool version 2.0.1 (use data table to locate freqfiles).
author | pjbriggs |
---|---|
date | Fri, 27 Nov 2015 11:06:28 -0500 |
parents | 571cb77ab9e7 |
children | f19e18ab01b1 |
line wrap: on
line diff
--- a/README.rst Tue Dec 09 11:27:19 2014 -0500 +++ b/README.rst Fri Nov 27 11:06:28 2015 -0500 @@ -30,7 +30,12 @@ <tool file="weeder2/weeder2_wrapper.xml" /> -You will also need to install ``weeder2`` from: +You also need to make a copy of the ``weeder2.loc`` file (a sample version is +provided here) which lists the species for which frequency files are available. +This file should be placed in the ``tool-data`` directory of your Galaxy +installation. + +Additionally you will need to install ``weeder2`` from: - http://159.149.160.51/modtools/downloads/weeder2.html @@ -41,20 +46,41 @@ Also the directory holding the Weeder2 executables should be on your ``PATH``. +Functional tests +================ + If you want to run the functional tests, copy the sample test files under sample test files under Galaxy's ``test-data/`` directory. Then: - ./run_tests.sh -id trimmomatic + ./run_tests.sh -id weeder2 You will need to have set the environment variables above. +Reference Data +============== + +Weeder2 requires reference data in the form of frequency files for each +species of interest. A set of reference files is provided as part of the +Weeder2 installation. + +Additional frequency files can be generated for novel species using the +``w2frequency_maker`` utility available via: + +- http://159.149.160.51/weederaddons/weeder2freq.html + +This page also explains what input data should be used. + +The location of the additional frequency files can then be specified by +adding them to the ``weeder2.loc`` file (see above). + History ======= ========== ====================================================================== Version Changes ---------- ---------------------------------------------------------------------- -2.0.0.0 - Initial version +2.0.1 - Explicitly specify frequency files in ``weeder2.loc``. +2.0.0 - Initial version ========== ======================================================================