Merge branch 'development'

Author: Jon Palmer

.gitignore

@@ -2,11 +2,5 @@
 *.pyc
 */.DS_Store
 */*.pyc
-dockerbuild/tmhmm-2.0c.Linux.tar.gz
-dockerbuild/signalp-4.1c.Linux.tar.Z
-dockerbuild/phobius.tar.gz
-dockerbuild/gm_key_64.gz
-dockerbuild/funannotate-genemark.tar.gz
-dockerbuild/funannotate-braker.tar.gz
-dockerbuild/RepBaseRepeatMaskerEdition-20170127.tar.gz
-sample_data/*
+dockerbuild/
+sample_data/

MANIFEST.in

@@ -0,0 +1,10 @@
+include README.md
+include LICENSE.md
+include docs/*
+include funannotate/aux_scripts/*
+include funannotate/config/*
+include funannotate/utilities/*
+include funannotate/html_template/*
+include funannotate/html_template/css/*
+include funannotate/html_template/js/*
+include scripts/*

README.md

@@ -2,3 +2,21 @@
 [![DOI](https://zenodo.org/badge/48254740.svg)](https://zenodo.org/badge/latestdoi/48254740)
 
 funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Installation, usage, and more information can be found at [http://funannotate.readthedocs.io](http://funannotate.readthedocs.io)
+
+#### Quickstart:
+
+COMING SOON: the pipeline can be installed with conda (via bioconda):
+```
+#add appropriate channels
+conda config --add channels defaults
+conda config --add channels bioconda
+conda config --add channels conda-forge
+
+#then create environment
+conda create -n funannotate funannotate
+```
+
+To install just the python funannotate package, you can do this with pip:
+```
+pip install funannotate
+```