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Remove leading $ for commande line
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pierrepo committed Aug 18, 2021
1 parent ebb80d2 commit 17fc1b2
Showing 1 changed file with 15 additions and 15 deletions.
30 changes: 15 additions & 15 deletions README.md
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Expand Up @@ -22,42 +22,42 @@ See step-by-step instructions: <https://github.com/pierrepo/autoclassweb-server>

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 <http://127.0.0.1:5000>
Expand All @@ -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 <http://127.0.0.1:5000>

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.
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