Loading README.md +84 −6 Original line number Diff line number Diff line Loading @@ -137,11 +137,50 @@ it could take significant resources to add support for these. ## Installation <span id="Install"><span> This script requires cellranger to be installed and exported to the PATH (version 3.0.0 or higher recommended). The script itself is exectuable and does not require installation to run but you can put it in your PATH or bin of your cellranger install if you wish to do so. We provide scripts to do this for your convenience. See the details below on how set up cellranger and launch_universc.sh. #### Download UniverSC To download UniverSC open a terminal prompt and enter the following commands. ``` cd $HOME/Downloads git clone https://github.com/TomKellyGenetics/universc.git cd universc ``` ### Quick Start If you already have cellranger installed, then you can run the script without installing it. ``` bash launch_universc.sh ``` You can call it in another directory by giving the path to the script. ``` cd $/HOME/my_project bash $HOME/Downloads/universc/launch_universc.sh ``` See the details below on how to install cellranger and launch_universc.sh add them to the PATH so that `launch_universc.sh` can be run from any directory. ### Runnning in a git repository If you are running code in a git repository you can add universc as a submodule. ``` cd $/HOME/my_git_repo git submodule add https://github.com/TomKellyGenetics/universc.git bash universc/launch_universc.sh ``` ### System Requirements In principle, the script can run on any Unix systems with cellranger installed. You can check whether Loading Loading @@ -203,16 +242,55 @@ A full example of installation is available in the [GitHub repository](https://g and on [DockerHub](https://hub.docker.com/r/tomkellygenetics/cellranger_clean/dockerfile). - Python 2.7.13 - rust 1.28.0 - clang 6.0 - go 1.11 - node 8.11.4 - Cython 0.28.0 - STAR 2.5.1b - bcl2fastq 2.19.1.403 - tsne 0.15 The following additional shell utilities are required. Mac OS and most Linux distributions come with these pre-installed. - make 3.81 - git 2.20.1 - sed (GNU sed) 4.4 - tar 2.8.3 - rename 0.20 (perl-rename) - perl 5.26.1 - rsync 2.6.9 Note that rename is installed by default on Mac, Ubuntu and Debian but a different version must be used on other Linux distrubutions. CentOS and Fedora: ``` sudo yum install prename ``` ``` sudo dnf install prename ``` Ret Hat Linux: ``` sudo rpm install prename ``` Arch Linux: ``` yay perl-rename ``` ##### Recommended software - node v8.11.4 - git-lfs 2.10.0 #### Harware requirements #### Hardware requirements - 8-core Intel or AMD processor (16 cores recommended) - 64GB RAM (128GB recommended) Loading Loading
README.md +84 −6 Original line number Diff line number Diff line Loading @@ -137,11 +137,50 @@ it could take significant resources to add support for these. ## Installation <span id="Install"><span> This script requires cellranger to be installed and exported to the PATH (version 3.0.0 or higher recommended). The script itself is exectuable and does not require installation to run but you can put it in your PATH or bin of your cellranger install if you wish to do so. We provide scripts to do this for your convenience. See the details below on how set up cellranger and launch_universc.sh. #### Download UniverSC To download UniverSC open a terminal prompt and enter the following commands. ``` cd $HOME/Downloads git clone https://github.com/TomKellyGenetics/universc.git cd universc ``` ### Quick Start If you already have cellranger installed, then you can run the script without installing it. ``` bash launch_universc.sh ``` You can call it in another directory by giving the path to the script. ``` cd $/HOME/my_project bash $HOME/Downloads/universc/launch_universc.sh ``` See the details below on how to install cellranger and launch_universc.sh add them to the PATH so that `launch_universc.sh` can be run from any directory. ### Runnning in a git repository If you are running code in a git repository you can add universc as a submodule. ``` cd $/HOME/my_git_repo git submodule add https://github.com/TomKellyGenetics/universc.git bash universc/launch_universc.sh ``` ### System Requirements In principle, the script can run on any Unix systems with cellranger installed. You can check whether Loading Loading @@ -203,16 +242,55 @@ A full example of installation is available in the [GitHub repository](https://g and on [DockerHub](https://hub.docker.com/r/tomkellygenetics/cellranger_clean/dockerfile). - Python 2.7.13 - rust 1.28.0 - clang 6.0 - go 1.11 - node 8.11.4 - Cython 0.28.0 - STAR 2.5.1b - bcl2fastq 2.19.1.403 - tsne 0.15 The following additional shell utilities are required. Mac OS and most Linux distributions come with these pre-installed. - make 3.81 - git 2.20.1 - sed (GNU sed) 4.4 - tar 2.8.3 - rename 0.20 (perl-rename) - perl 5.26.1 - rsync 2.6.9 Note that rename is installed by default on Mac, Ubuntu and Debian but a different version must be used on other Linux distrubutions. CentOS and Fedora: ``` sudo yum install prename ``` ``` sudo dnf install prename ``` Ret Hat Linux: ``` sudo rpm install prename ``` Arch Linux: ``` yay perl-rename ``` ##### Recommended software - node v8.11.4 - git-lfs 2.10.0 #### Harware requirements #### Hardware requirements - 8-core Intel or AMD processor (16 cores recommended) - 64GB RAM (128GB recommended) Loading
