Mercurial > repos > test-svm > kmersvm_test
changeset 6:f5cb27465a59 draft
Uploaded
| author | test-svm |
|---|---|
| date | Mon, 06 Aug 2012 18:20:28 -0400 |
| parents | f99b5099ea55 |
| children | 9d903ccdaa59 |
| files | kmersvm/README.txt |
| diffstat | 1 files changed, 16 insertions(+), 7 deletions(-) [+] |
line wrap: on
line diff
--- a/kmersvm/README.txt Sun Aug 05 16:50:57 2012 -0400 +++ b/kmersvm/README.txt Mon Aug 06 18:20:28 2012 -0400 @@ -2,12 +2,12 @@ ************* KmerSVM requires the following software: - *Shogun Toolbox, v0.9.3 - v1.10 - *Swig - *Numpy - *Bitarray - *R - *ROCR R Package + *Shogun Toolbox, v0.9.3 - v1.10 (http://www.shogun-toolbox.org/) + *Swig (http://www.swig.org) + *Numpy (numpy.scipy.org) + *Bitarray (http://pypi.python.org/pypi/bitarray/) + *R (http://www.r-project.org) + *ROCR R Package (Available through CRAN) Further, KmerSVM has been tested on Python 2.6, 2.7. @@ -29,7 +29,7 @@ the built-in tool "Fetch Sequences", which looks for genomes in *.nib or *.2bit format. Download genomes related to your data and update the 'alignseq.loc' file to include the location of these genomes according -to directions in that file. +to directions in that file. FASTA files can also be provided by the user. Move the file sample_roc_chen.png to the 'tool-data' file. @@ -60,3 +60,12 @@ *train_predictions.out IDs for KmerSVM tests can be found by calling run_functional_tests.sh with the '-list' flag. + +Non-Galaxy-Based Usage: +*********************** +The KmerSVM suite can be ran without using the Galaxy framework. Each tool exists as +a standalone Python script (all located in /scripts) which can be called from the command +line. Specific documentation can be found within each tool's Python file. A general +workflow can be found in INSERT_PAPER_TITLE_HERE, which can be followed by calling +each of the relevant Python scripts, with the exception that users will have to provide +needed FASTA files themselves.