fixes install; adds disclaimer

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