diff --git a/README.md b/README.md index 44eab76c..087b2ab4 100644 --- a/README.md +++ b/README.md @@ -5,14 +5,26 @@ All dependencies are installed via [conda](https://www.continuum.io/downloads) using the [bioconda](https://github.com/bioconda/bioconda-recipes) channel. The workflow and some dependencies require Python 3.5. +## Using `conda` + To install: ``` conda install -c bioconda \ - bbmap diamond fastqc megahit prodigal samtools snakemake spades verse + bbmap diamond fastqc megahit prodigal \ + samtools snakemake spades subread +``` + +Maxbin2 and MEGAHIT for macOS are not current in the bioconda channel. For those dependencies, we've made them available to install as: + +``` +conda install -c brwnj maxbin2 ``` -Or as an isolated environment using our `environment.yml` file: +## Creating an Environment + +Not necessary, but this can isolate ATLAS dependencies in a separate work +environment. Using `environment.yml`: ``` conda env create -f environment.yml @@ -21,13 +33,11 @@ conda env create -f environment.yml And load and unload that environment using `source activate atlas_env` and `source deactivate atlas_env`, respectively. -In the future we plan to push `atlas` to Bioconda and PyPI, but currently -to install you will need to download or clone `atlas`. +## Finishing the Install -Then within that environment and from within the 'atlas' folder: +Finally, from within the 'atlas' source folder: ``` -cd atlas python setup.py install ``` @@ -49,11 +59,12 @@ Commands: make-config prepopulate a configuration file with samples and defaults ``` +ATLAS will soon be pushed to the Anaconda Cloud for easier install. + # Getting Started -After installing, one needs to download the required databases and create a -sample configuration file. +After installing, one needs to download the required databases and create a sample configuration file. ## Databases @@ -67,8 +78,7 @@ atlas download -o /databases The downloads use approximately 40 GB of disk space. -Configuration File ------------------- +## Configuration File To create a simple configuration file (which you can later edit), run: @@ -87,11 +97,8 @@ $ tree /my-data └── Sample-2_R2.fastq.gz ``` -Paired-end, single-end (currently with some caveats), and interleaved paired-end -FASTQs are supported. - -**Single-end currently works, but parameters to assemblers still need to be -altered such that they are not input as interleaved paired-end.** +Paired-end, single-end (though some file names still suggest otherwise), and +interleaved paired-end FASTQs are supported. ## Assembly @@ -106,4 +113,24 @@ atlas assemble config.yaml By default, this will write results into our current working directory across the total number of CPU cores available. -For more complete documentation and advanced configuration options, see our [docs](https://non-broken-link). + +# Disclaimer + +This material was prepared as an account of work sponsored by an agency of the +United States Government. Neither the United States Government nor the United +States Department of Energy, nor Battelle, nor any of their employees, nor any +jurisdiction or organization that has cooperated in the development of these +materials, makes any warranty, express or implied, or assumes any legal +liability or responsibility for the accuracy, completeness, or usefulness or +any information, apparatus, product, software, or process disclosed, or +represents that its use would not infringe privately owned rights. + +Reference herein to any specific commercial product, process, or service by +trade name, trademark, manufacturer, or otherwise does not necessarily +constitute or imply its endorsement, recommendation, or favoring by the United +States Government or any agency thereof, or Battelle Memorial Institute. The +views and opinions of authors expressed herein do not necessarily state or +reflect those of the United States Government or any agency thereof. + +PACIFIC NORTHWEST NATIONAL LABORATORY operated by BATTELLE for the UNITED +STATES DEPARTMENT OF ENERGY under Contract DE-AC05-76RL01830