Merge branch '3.0' of github.com:biobakery/MetaPhlAn into 3.0

README.md

@@ -1,5 +1,5 @@
 # MetaPhlAn: Metagenomic Phylogenetic Analysis
-![Build MetaPhlAn package](https://github.com/biobakery/MetaPhlAn/workflows/Build%20MetaPhlAn%20package/badge.svg?branch=3.0)
+![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat) ![PyPI - Downloads](https://img.shields.io/pypi/dm/metaphlan?label=MetaPhlAn%20on%20PyPi) ![MetaPhlAn on DockerHub](https://img.shields.io/docker/pulls/biobakery/metaphlan?label=MetaPhlAn%20on%20DockerHub) ![Build MetaPhlAn package](https://github.com/biobakery/MetaPhlAn/workflows/Build%20MetaPhlAn%20package/badge.svg?branch=3.0)
 ## What's new in version 3
 * New MetaPhlAn marker genes extracted with a newer version of ChocoPhlAn based on UniRef
 * Estimation of metagenome composed by unknown microbes with parameter `--unknown_estimation`
@@ -23,11 +23,7 @@ MetaPhlAn relies on ~1.1M unique clade-specific marker genes (the latest marker
 * orders of magnitude speedups compared to existing methods.
 * metagenomic strain-level population genomics
 
-If you use MetaPhlAn version 1, please cite:
-
-[**Metagenomic microbial community profiling using unique clade-specific marker genes.**](https://www.nature.com/articles/nmeth.2066) *Nicola Segata, Levi Waldron, Annalisa Ballarini, Vagheesh Narasimhan, Olivier Jousson, &  Curtis Huttenhower*. Nature Methods 9, 811-814 (2012)
-
-If you use MetaPhlAn2, please cite:
+If you use MetaPhlAn, please cite:
 
 [**MetaPhlAn2 for enhanced metagenomic taxonomic profiling.**](http://www.nature.com/nmeth/journal/v12/n10/pdf/nmeth.3589.pdf) *Duy Tin Truong, Eric A Franzosa, Timothy L Tickle, Matthias Scholz, George Weingart, Edoardo Pasolli, Adrian Tett, Curtis Huttenhower & Nicola Segata*. Nature Methods 12, 902-903 (2015)
 
@@ -38,19 +34,19 @@ If you use StrainPhlAn, please cite the MetaPhlAn2 paper and the following Strai
 -------------
 
 ## Installation
-The best way to install MetaPhlAn is through conda via the Bioconda channel. If you have not configured you Anaconda installation in order to fetch packages from Bioconda, please follow [these steps](https://bioconda.github.io/user/install.html#set-up-channels) in order to setup the channels.
+The best way to install MetaPhlAn is through conda via the Bioconda channel. If you have not configured you Anaconda installation in order to fetch packages from Bioconda, **please follow [these steps](https://bioconda.github.io/user/install.html#set-up-channels) in order to setup the channels.**
 
 You can install MetaPhlAn by running
 
 ```
-$ conda install -c bioconda metaphlan
+$ conda install -c bioconda python=3.7 metaphlan
 ```
 
 For installing it from the source code and for further installation instructions, please see the Wiki at the [Installation](https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-3.0#installation) paragraph.
 
 -------------
 
-## MetaPhlAn2 and StrainPhlAn tutorials and resources
+## MetaPhlAn and StrainPhlAn tutorials and resources
 
 In addition to the information on this page, you can refer to the following additional resources.
 
@@ -62,6 +58,6 @@ In addition to the information on this page, you can refer to the following addi
 
 * The [MetaPhlAn](https://forum.biobakery.org/c/Microbial-community-profiling/MetaPhlAn/) and [StrainPhlAn](https://forum.biobakery.org/c/Microbial-community-profiling/StrainPhlAn/) Discourse forum.
 
-* Related tools including [PanPhlAn](https://github.com/segatalab/panphlan) (and its [tutorial](https://github.com/segatalab/panphlan/wiki/Home)), [GraPhlAn](https://github.com/segatalab/graphlan) (and it [tutorial](https://github.com/biobakery/biobakery/wiki/graphlan)), [PhyloPhlAn2](https://github.com/biobakery/phylophlan) (and its [tutorial](https://github.com/biobakery/biobakery/wiki/phylophlan)), [HUMAnN2](https://github.com/biobakery/humann/) (and its [tutorial](https://github.com/biobakery/biobakery/wiki/humann2)).
+* Related tools including [PanPhlAn](https://github.com/segatalab/panphlan) (and its [tutorial](https://github.com/segatalab/panphlan/wiki/Home)), [GraPhlAn](https://github.com/segatalab/graphlan) (and it [tutorial](https://github.com/biobakery/biobakery/wiki/graphlan)), [PhyloPhlAn 3](https://github.com/biobakery/phylophlan) (and its [tutorial](https://github.com/biobakery/biobakery/wiki/phylophlan)), [HUMAnN](https://github.com/biobakery/humann/) (and its [tutorial](https://github.com/biobakery/biobakery/wiki/humann2)).
 
 * The related [bioBakery workflows](https://github.com/biobakery/biobakery/wiki/biobakery_workflows)