Updated installation instructions

README.md

@@ -6,10 +6,47 @@ StxTyper is used to determine stx type from nucleotide sequence. Stx (Shiga-toxi
 
 # Installation
 
-## Prerequisites
+## Installing from binary
+
+### Prerequisites 
+
+#### NCBI BLAST+
+
+See below under "Compiling" for instructions to install.
+
+### Download and install Binary
+
+Download the latest binary tarball from https://github.com/ncbi/stxtyper/releases. Untar it and run the tests e.g.:
+
+    tar xvfz stxtyper_v*.tar.gz
+    cd stxtyper_v*/
+    ./test_stxtyper.sh
+
+Note that we are currently only publishing binary tarballs for x86 linux.
+
+## Installing with Bioconda
+
+You'll need Mamba ([Installation instructions](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html)) or Conda ([Installation instructions](https://docs.anaconda.com/miniconda/miniconda-install/)) first.
 
+    conda create -n stxtyper ncbi-stxtyper \
+      --channel conda-forge \
+      --channel bioconda \
+      --channel defaults \
+      --strict-channel-priority
 
-### NCBI BLAST
+or
+
+    micromamba create -n stxtyper ncbi-stxtyper \
+      --channel conda-forge \
+      --channel bioconda \
+      --channel defaults \
+      --strict-channel-priority
+
+## Compiling
+
+### Prerequisites
+
+#### NCBI BLAST+
 
 StxTyper needs NCBI BLAST binaries in your path (specifically tblastn). If you don't
 already have BLAST installed see https://www.ncbi.nlm.nih.gov/books/NBK569861/
@@ -27,15 +64,15 @@ Then run:
 
 If you install BLAST via conda in this way you will need to run `conda activate blast` before you can run StxTyper.
 
-### C compiler and make
+#### C compiler and make
 
 These are necessary if compiling from source. If using the binary distribution,
 or Bioconda you won't need to worry about these. They generally come standard
 for unix systems, if not the user will need to intall make and GCC. MacOS users
 will need to go to the [App store and install
 Xcode](https://apps.apple.com/in/app/xcode/id497799835?mt=12). 
 
-## Compiling
+### Compiling
 
 StxTyper should compile cleanly for Mac and Linux x86 and ARM, though our official policy is we only support x86 Linux.
 
@@ -44,15 +81,6 @@ StxTyper should compile cleanly for Mac and Linux x86 and ARM, though our offici
     make
     make test
 
-## Installing from binary
-
-Download the latest binary tarball from https://github.com/ncbi/stxtyper/releases. Untar it and run the tests e.g.:
-
-    tar xvfz stxtyper_v*.tar.gz
-    cd stxtyper_v*/
-    ./test_stxtyper.sh
-
-Note that we are currently only publishing binary tarballs for x86 linux.
 
 # Usage