Skip to content
Snippets Groups Projects
Commit 02a1aa86 authored by Ruqian Lyu's avatar Ruqian Lyu
Browse files

update README

parent 68f45d8a
No related branches found
No related tags found
No related merge requests found
Pipeline #6854 passed
......@@ -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
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment