@ -1,6 +1,6 @@
@@ -1,6 +1,6 @@
# 2019-snakemake-cli
[![travis ](https://img.shields.io/travis/charlesreid1/2019-snakemake-cli.svg )](https://travis-ci.org/charlesreid1/2019-snakemake-cli)
[![travis ](https://img.shields.io/travis/charlesreid1/2019-snakemake-cli.svg )](https://travis-ci.org/charlesreid1/2019-snakemake-cli.svg )
[![license ](https://img.shields.io/github/license/charlesreid1/2019-snakemake-cli.svg )](https://github.com/charlesreid1/2019-snakemake-cli/blob/master/LICENSE)
An example of a Snakemake command line interface
@ -18,7 +18,7 @@ a command line tool called `bananas`.
@@ -18,7 +18,7 @@ a command line tool called `bananas`.
This runs through the installation and usage
of 2019-snakemake-cli.
## Installing bananas
## Installing banana
Start by setting up a virtual environment,
and install the required packages into the
@ -37,13 +37,13 @@ python setup.py build install
@@ -37,13 +37,13 @@ python setup.py build install
Now you can run
```
which bananas
which banana
```
and you should see `bananas` in your virtual
environment 's `bin/` directory.
and you should see `bananas` in your Python
distribution 's `bin/` directory.
## Running bananas
## Running banana
Move to the `test/` directory and run the tests
with the provided config and params files.
@ -66,7 +66,7 @@ Run the goodbye workflow with Beth params:
@@ -66,7 +66,7 @@ Run the goodbye workflow with Beth params:
```
rm -f goodbye.txt
bananas workflow-goodbye params-beth
./run workflow-goodbye params-beth
```
# Details
@ -80,10 +80,3 @@ An alternative arrangement would be for users
@@ -80,10 +80,3 @@ An alternative arrangement would be for users
to provide a Snakefile via rules in the working
directory, or via a Github URL or a remote URL.
# Tags
* `v1.0` - initial version, [ctb/2018-snakemake-cli ](https://github.com/ctb/2018-snakemake-cli )
* `v2.0` - Snakemake workflow bundled as installable Python package, Snakefile bundled with
Python package, command line interface provided to wrap Snakemake API call