diff --git a/_episodes/13-cluster.md b/_episodes/13-cluster.md index 965b21a..3e4a4af 100644 --- a/_episodes/13-cluster.md +++ b/_episodes/13-cluster.md @@ -167,16 +167,24 @@ $ tar -xvzf pipeline.tar.gz ``` {: .language-bash} -If Snakemake and Python are not already installed on your cluster, -you can install them using the following commands: +If Snakemake and Python are not already installed on your cluster, you can +install them in an Anaconda Python environment using the following commands: ``` $ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -$ bash Miniconda3-latest-Linux-x86_64.sh -b -$ echo 'export PATH=~/miniconda3/bin:~/.local/bin:$PATH' >> ~/.bashrc -$ source ~/.bashrc -$ conda install -y matplotlib numpy graphviz -$ pip install --user snakemake +$ bash Miniconda3-latest-Linux-x86_64.sh +``` +{: .language-bash} + +This is an interactive installation through the command line. Review and accept +the license agreement, then work through the prompts. The defaults are probably +fine. Accept its offer to initialize your environment (`conda init`), then run +the suggested command to load the `conda` base environment so you can use it +straight away. Finally, install Snakemake from the [bioconda channel]( +https://anaconda.org/bioconda): + +``` +$ conda install -y -c bioconda graphviz matplotlib numpy snakemake ``` {: .language-bash} @@ -208,7 +216,7 @@ Here we've used SLURM's `sbatch` command and arguments for setting time limits and resources with snakemake wildcards defining the requested values. We've also specified where to save SLURM logs and what to call them. **Note** that -this folder must already exist. If the folders don't exist, snakemake will hang. +this folder must already exist. If the folders don't exist, Snakemake will hang. Values for any command line argument to snakemake can be defined in our profile, although a value is required (e.g. the `--use-conda` argument could be diff --git a/index.md b/index.md index 0f89c97..286eb12 100644 --- a/index.md +++ b/index.md @@ -35,7 +35,7 @@ At the end of this lesson, you will know how to: > . > > To install snakemake, please run the following in a command-line terminal: -> `conda install snakemake` +> `conda install -c bioconda snakemake` > > The files used in this lesson can be downloaded > [here](files/snakemake-lesson.zip). diff --git a/setup.md b/setup.md index d90ba52..ddd5700 100644 --- a/setup.md +++ b/setup.md @@ -17,12 +17,13 @@ includes several significant performance improvements over "vanilla" Python. ## Snakemake -Once you have a Miniconda environment configured, please install Snakemake with +Once you have a Miniconda environment configured, please install Snakemake from +the [bioconda channel](https://anaconda.org/bioconda) with ``` -conda install snakemake +$ conda install -c bioconda snakemake ``` -{: .source} +{: .language-bash} ## Shell and SSH