diff --git a/README.md b/README.md index c23171f9e9d176e1589750b71ea9eb5f8e8a3c17..34c8f78b6f888556f3004e84141919f4b05fec56 100644 --- a/README.md +++ b/README.md @@ -25,6 +25,10 @@ Run the application: $ conda activate <path/tacos_env> # if not already activated $ tacos --help ``` +or +``` +$ <path/tacos_env>/bin/python -m tacos --help # no need to activate the environment +``` To run the tests: ``` diff --git a/tacos/__main__.py b/tacos/__main__.py new file mode 100644 index 0000000000000000000000000000000000000000..53b8076f916895a94e71413cb940119a3bb772f5 --- /dev/null +++ b/tacos/__main__.py @@ -0,0 +1,4 @@ +from tacos import cli + +if __name__ == "__main__": + cli.tacos() \ No newline at end of file diff --git a/tacos/cli.py b/tacos/cli.py index 96d076ebe3e7dd7868625a73b0b59f2d86a5550e..9f1ea35e659625a596d3bd85ac7b604d6cac2af6 100644 --- a/tacos/cli.py +++ b/tacos/cli.py @@ -8,6 +8,7 @@ from tacos.distance import hamming_pool @click.group() def tacos(): pass + @tacos.command() @click.option('--ignore_gap', 'ignore_gap', is_flag=True, help='enable coding gaps(i.e indels) as missing values') @click.option('-d','--separator', 'sep', default='\t', help='field separator [default: TAB]') @@ -123,5 +124,6 @@ def distance_matrix(ignore_gap, adjust, n_jobs, type, input_, output): f.write('\n') click.echo('Finished! Computed {} pairwise distances for {} genomes.'.format(len(genome_pairs), nr_genomes)) -if __name__ == '__main__': - tacos() \ No newline at end of file + +#if __name__ == '__main__': +# tacos() \ No newline at end of file