From 02a1aa86e7a3e7a9294f59ccee101b695a84e7a3 Mon Sep 17 00:00:00 2001
From: rlyu <rlyu@svi.edu.au>
Date: Tue, 8 Jun 2021 10:49:39 +1000
Subject: [PATCH] update README

---
 README.md | 47 +++++++++++++++++++++++++----------------------
 1 file changed, 25 insertions(+), 22 deletions(-)

diff --git a/README.md b/README.md
index 2d029e2..bc25e60 100644
--- a/README.md
+++ b/README.md
@@ -77,25 +77,23 @@ one row and it has the text "bulk".
 
 ## Setup/installation
 
-### Install with nimble
-`sscocaller` uses `hts-nim`(https://github.com/brentp/hts-nim) that requires the `hts-lib` library. If you are building the `sscocaller` from
-source, you would need to install `hts-lib`
 
-```
-git clone --recursive https://github.com/samtools/htslib.git
-cd htslib && git checkout 1.10 && autoheader && autoconf && ./configure --enable-libcurl
+### Static builds 
 
-cd ..
-make -j 4 -C htslib
-export LD_LIBRARY_PATH=$HOME/htslib
-ls -lh $HOME/htslib/*.so
+The static bianry can be simply downloaded which works for GNU/Linux type OS: `./src/sscocaller`
+
+The static build was generated by using docker image docker://svirlyu/sscocaller_nsb adapted from https://github.com/brentp/hts-nim/blob/master/Dockerfile
+
+```
+/usr/local/bin/nsb -s ./src/sscocaller.nim -n sscocaller.nimble -o /mnt/src -- --d:release --threads:on
 ```
 
-Then, `sscocaller` can be installed using `nimble`
+A static binary build of `sscocaller` is available as downloadable artifacts at gitlab repo: "https://gitlab.svi.edu.au/biocellgen-public/sscocaller" or via
+the `Releases` tab
 
-`nimble install https://gitlab.svi.edu.au/biocellgen-public/sscocaller.git`
+### Install from bioconda
 
-The built binary in $HOME/.nimble/bin/sscocaller
+`sscocaller` is available as a conda package and can be [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/sscocaller/README.html)
 
 ### Using docker
 
@@ -110,21 +108,26 @@ docker run -it svirlyu/sscocaller
 /usr/bin/sscocaller -h
 
 ```
+### Install with nimble
+`sscocaller` uses `hts-nim`(https://github.com/brentp/hts-nim) that requires the `hts-lib` library. If you are building the `sscocaller` from
+source, you would need to install `hts-lib`
 
+```
+git clone --recursive https://github.com/samtools/htslib.git
+cd htslib && git checkout 1.10 && autoheader && autoconf && ./configure --enable-libcurl
 
-### Static builds 
-
-The static bianry can be simply downloaded which works for GNU/Linux type OS: `./src/sscocaller`
+cd ..
+make -j 4 -C htslib
+export LD_LIBRARY_PATH=$HOME/htslib
+ls -lh $HOME/htslib/*.so
+```
 
-The static build was generated by using docker image docker://svirlyu/sscocaller_nsb adapted from https://github.com/brentp/hts-nim/blob/master/Dockerfile
+Then, `sscocaller` can be installed using `nimble`
 
-```
-/usr/local/bin/nsb -s ./src/sscocaller.nim -n sscocaller.nimble -o /mnt/src -- --d:release --threads:on
-```
+`nimble install https://gitlab.svi.edu.au/biocellgen-public/sscocaller.git`
 
+The built package is located at $HOME/.nimble/bin/sscocaller
 
-A static binary build of `sscocaller` is available as downloadable artifacts at gitlab repo: "https://gitlab.svi.edu.au/biocellgen-public/sscocaller" or via
-the `Releases` tab
 
 
 ## Downstream analysis in R
-- 
GitLab