Merge pull request #38 from tkphd/miniconda

revise Miniconda instructions

Author: ocaisa

_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

index.md

@@ -35,7 +35,7 @@ At the end of this lesson, you will know how to:
 > <https://docs.conda.io/en/latest/miniconda.html>.
 > 
 > 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).

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