From 8f63ec9782311921d7ae9daccc3a8d8559863777 Mon Sep 17 00:00:00 2001 From: Trevor Keller Date: Tue, 23 Mar 2021 12:06:14 -0400 Subject: [PATCH 1/3] revise Miniconda instructions --- _episodes/13-cluster.md | 23 +++++++++++++++-------- index.md | 2 +- setup.md | 7 ++++--- 3 files changed, 20 insertions(+), 12 deletions(-) diff --git a/_episodes/13-cluster.md b/_episodes/13-cluster.md index 965b21a..571bea6 100644 --- a/_episodes/13-cluster.md +++ b/_episodes/13-cluster.md @@ -167,16 +167,23 @@ $ 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 +straightaway. Finally, install Snakemake: + +``` +$ conda install -y -c biodonda graphviz matplotlib numpy snakemake ``` {: .language-bash} @@ -208,7 +215,7 @@ 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 From 714d1588a6350f166a07ad79b0a7ccb3f291f7cd Mon Sep 17 00:00:00 2001 From: Trevor Keller Date: Tue, 23 Mar 2021 12:12:50 -0400 Subject: [PATCH 2/3] all I do is typo --- _episodes/13-cluster.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/_episodes/13-cluster.md b/_episodes/13-cluster.md index 571bea6..52cf8f7 100644 --- a/_episodes/13-cluster.md +++ b/_episodes/13-cluster.md @@ -180,10 +180,11 @@ 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 -straightaway. Finally, install Snakemake: +straightaway. Finally, install Snakemake from the [bioconda channel]( +https://anaconda.org/bioconda): ``` -$ conda install -y -c biodonda graphviz matplotlib numpy snakemake +$ conda install -y -c bioconda graphviz matplotlib numpy snakemake ``` {: .language-bash} From 2e1e7c17e84ff7be41dd02f05118ce939cd623c4 Mon Sep 17 00:00:00 2001 From: Trevor Keller Date: Tue, 23 Mar 2021 12:15:25 -0400 Subject: [PATCH 3/3] split word to satisfy codespell --- _episodes/13-cluster.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_episodes/13-cluster.md b/_episodes/13-cluster.md index 52cf8f7..3e4a4af 100644 --- a/_episodes/13-cluster.md +++ b/_episodes/13-cluster.md @@ -180,7 +180,7 @@ 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 -straightaway. Finally, install Snakemake from the [bioconda channel]( +straight away. Finally, install Snakemake from the [bioconda channel]( https://anaconda.org/bioconda): ```