Merge pull request #20 from PROBIC/add-conda-instructions

Add installation instructions for conda installation

README.md

@@ -6,52 +6,33 @@ More about mGEMS in the article [Bacterial genomic epidemiology with mixed
 samples](https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000691)
 in Microbial Genomics.
 
-If you use mGEMS, please cite us as "Mäklin T, Kallonen T, Alanko J et
-al. Bacterial genomic epidemiology with mixed samples. Microb Genom
-2021, 7:11 (https://doi.org/10.1099/mgen.0.000691)"
-
-You should also cite the method that you used to estimate the input
-probability matrix to mGEMS, which is likely to be
-[mSWEEP](https://github.com/PROBIC/mSWEEP).
-
-To cite a specific version of mGEMS, visit the [releases
-page](https://github.com/PROBIC/mGEMS/releases) and find the doi for
-the version of the program that you used. Then, cite the version
-(v1.1.0 in the example) as "Tommi Mäklin. (2021). PROBIC/mGEMS:
-mGEMS-v1.1.0 (20 October 2021)
-(v1.1.0). Zenodo. (https://doi.org/10.5281/zenodo.5583245)". Citing
-the source code properly helps ensure that your analyses are
-reproducible. Please also cite [the
-article](https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000691)
-if you use mGEMS.
-
 ## Installation
-### Dependencies
-To run the binning + assembly pipeline, you will need a program that
-does pseudoalignment and another program that estimates an assignment
-probability matrix for the reads to the alignment targets.
+In addition to mGEMS, to run the binning pipeline, you will likely
+need a program that pseudoalignment and another program that estimates
+an assignment probability matrix for the reads to the alignment
+targets. Please see the Dependencies subsection for more details.
 
-We recommend to use [Themisto](https://github.com/algbio/themisto)
-(v2.0.0 or newer) for pseudoalignment and
-[mSWEEP](https://github.com/probic/mSWEEP) (v1.3.2 or newer) for
-estimating the probability matrix. For assembling the bins output by
-mGEMS, we recommend [shovill](https://github.com/tseemann/shovill) for
-typical use-cases but metagenomic assemblers like
-[MEGAHIT](https://github.com/voutcn/megahit) may perform better when
-the differences between the bins are especially small (see
-Supplementary Figure 2 of the mGEMS preprint).
+### Conda
+Install mGEMS from bioconda with
+```
+conda install -y -c bioconda -c conda-forge -c defaults mgems
+```
+
+check that the installation succeeded by running
+```
+mGEMS
+```
 
 ### mGEMS binaries
-mGEMS can be obtained in the form of a precompiled binary
+Precompiled binaries are available for
 * [Linux 64-bit binary](https://github.com/PROBIC/mGEMS/releases/download/v1.2.0/mGEMS_linux-v1.2.0.tar.gz)
 * [macOS 64-bit binary](https://github.com/PROBIC/mGEMS/releases/download/v1.2.0/mGEMS_macOS-v1.2.0.tar.gz)
 
-or by following the instructions below for compiling mGEMS from source.
-
 ### Compiling from source
 #### Requirements
 - C++17 compliant compiler.
 - cmake
+- git
 
 #### Compilation
 Clone the repository
@@ -67,6 +48,22 @@ make
 ```
 This will compile the mGEMS executable in the build/bin/ directory.
 
+### Dependencies
+We recommend to use [Themisto](https://github.com/algbio/themisto)
+(v2.0.0 or newer) for pseudoalignment and
+[mSWEEP](https://github.com/probic/mSWEEP) (v1.3.2 or newer) for
+estimating the probability matrix.
+
+For assembling the bins output by mGEMS, we recommend
+[shovill](https://github.com/tseemann/shovill) for typical use-cases
+but metagenomic assemblers like
+[MEGAHIT](https://github.com/voutcn/megahit) may perform better when
+the differences between the bins are especially small (see
+Supplementary Figure 2 of the mGEMS preprint). Shovill comes with an
+option to use different assemblers as the backend (default is SPAdes).
+
+mSWEEP and shovill can be easily installed from bioconda.
+
 ## Usage
 ### mGEMS
 The mGEMS executable provides three commands: mGEMS, mGEMS bin, and
@@ -168,6 +165,26 @@ mGEMS accepts the following input flags
 	--unique-only            (Optional) Write only the reads that are assigned to a single group.
 ```
 
+## Citation
+If you use mGEMS, please cite us as "Mäklin T, Kallonen T, Alanko J et
+al. Bacterial genomic epidemiology with mixed samples. Microb Genom
+2021, 7:11 (https://doi.org/10.1099/mgen.0.000691)"
+
+You should also cite the method that you used to estimate the input
+probability matrix to mGEMS, which is likely to be
+[mSWEEP](https://github.com/PROBIC/mSWEEP).
+
+To cite a specific version of mGEMS, visit the [releases
+page](https://github.com/PROBIC/mGEMS/releases) and find the doi for
+the version of the program that you used. Then, cite the version
+(v1.1.0 in the example) as "Tommi Mäklin. (2021). PROBIC/mGEMS:
+mGEMS-v1.1.0 (20 October 2021)
+(v1.1.0). Zenodo. (https://doi.org/10.5281/zenodo.5583245)". Citing
+the source code properly helps ensure that your analyses are
+reproducible. Please also cite [the
+article](https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000691)
+if you use mGEMS.
+
 ## License
 The source code from this project is subject to the terms of the MIT
 license. A copy of the MIT license is supplied with the project, or