diff --git a/README.md b/README.md index 23a7cf4..814a1b0 100644 --- a/README.md +++ b/README.md @@ -22,42 +22,42 @@ See step-by-step instructions: Clone the project: ```bash -$ git clone https://github.com/pierrepo/autoclassweb.git -$ cd autoclassweb +git clone https://github.com/pierrepo/autoclassweb.git +cd autoclassweb ``` Create and activate a conda environment: ```bash -$ conda env create -f environment.yml -$ conda activate autoclassweb +conda env create -f environment.yml +conda activate autoclassweb ``` Install [AutoClass C](https://ti.arc.nasa.gov/tech/rse/synthesis-projects-applications/autoclass/autoclass-c/): ```bash -$ wget https://ti.arc.nasa.gov/m/project/autoclass/autoclass-c-3-3-6.tar.gz -$ tar zxvf autoclass-c-3-3-6.tar.gz -$ rm -f autoclass-c-3-3-6.tar.gz -$ export PATH=$PATH:$(pwd)/autoclass-c +wget https://ti.arc.nasa.gov/m/project/autoclass/autoclass-c-3-3-6.tar.gz +tar zxvf autoclass-c-3-3-6.tar.gz +rm -f autoclass-c-3-3-6.tar.gz +export PATH=$PATH:$(pwd)/autoclass-c ``` If you use a 64-bit operating system, install the standard 32-bit C libraries: ```bash -$ sudo apt install -y libc6-i386 +sudo apt install -y libc6-i386 ``` Copy config template and update config file `config/autoclassweb.cfg` accordingly: ```bash -$ cp config/autoclassweb-template.cfg config/autoclassweb.cfg +cp config/autoclassweb-template.cfg config/autoclassweb.cfg ``` Run AutoClassWeb alone: ```bash -$ make run +make run ``` or with gunicorn: ```bash -$ make run-gunicorn +make run-gunicorn ``` AutoClassWeb is then available at @@ -68,19 +68,19 @@ Install Docker with the following [instructions](https://docs.docker.com/install Build image: ```bash -$ make docker-build +make docker-build ``` Run container: ```bash -$ make docker-run +make docker-run ``` AutoClassWeb is then available at Clean unused images: ```bash -$ make docker-clean +make docker-clean ``` A Docker image of [AutoClassWeb](https://hub.docker.com/r/biocontainers/autoclassweb) is also available in the [Biocontainers](https://biocontainers.pro/) docker repository.