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Update setup.md
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remove $ in bash section for easy copying of commands
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ggrimes committed May 31, 2024
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20 changes: 10 additions & 10 deletions learners/setup.md
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Expand Up @@ -13,8 +13,8 @@ permalink: /setup/
Each learner should setup a training folder e.g. `nf-training`

```bash
$ mkdir nf-training
$ cd nf-training
mkdir nf-training
cd nf-training
```


Expand Down Expand Up @@ -50,7 +50,7 @@ To install conda see [here](https://carpentries-incubator.github.io/introduction
An environment file is provided here [environment.yml](https://raw.githubusercontent.com/carpentries-incubator/workflows-nextflow/main/episodes/data/environment.yml)

```bash
# wget
wget
wget https://raw.githubusercontent.com/carpentries-incubator/workflows-nextflow/main/episodes/data/environment.yml

# or curl
Expand All @@ -60,13 +60,13 @@ curl -L -o environment.yml https://raw.githubusercontent.com/carpentries-incubat
To create the training environment run:

```bash
$ conda env create -n nf-training -f environment.yml
conda env create -n nf-training -f environment.yml
```

Then activate the environment by running

```bash
$ conda activate nf-training
conda activate nf-training
```

## Training scripts
Expand Down Expand Up @@ -104,7 +104,7 @@ The nextflow scripts for each episode, can be found in the respective episode fo
Inside the `nf-training` folder download the workshop dataset from Figshare, [https://figshare.com/articles/dataset/RNA-seq\_training\_dataset/14822481](https://figshare.com/articles/dataset/RNA-seq_training_dataset/14822481)

```bash
$ wget --content-disposition https://ndownloader.figshare.com/files/28531743
wget --content-disposition https://ndownloader.figshare.com/files/28531743

# or curl
curl -L -o data.tar.gz https://ndownloader.figshare.com/files/28531743
Expand All @@ -113,8 +113,8 @@ curl -L -o data.tar.gz https://ndownloader.figshare.com/files/28531743
Unpack gzipped tar file:

```bash
$ tar -xvf data.tar.gz
$ rm data.tar.gz
tar -xvf data.tar.gz
rm data.tar.gz
```

## Visual Studio Code editor setup
Expand Down Expand Up @@ -151,15 +151,15 @@ curl get.nextflow.io | bash
## Add Nextflow binary to your user's PATH:

```bash
$ mv nextflow ~/bin/
mv nextflow ~/bin/
# OR system-wide installation:
# sudo mv nextflow /usr/local/bin
```

Check the correct installation running the following command:

```bash
$ nextflow info
nextflow info
```

## nf-core/tools installation without conda
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