Skip to content

Commit

Permalink
feat: slides on env creation updated
Browse files Browse the repository at this point in the history
  • Loading branch information
@cmeesters
cmeesters committed Apr 10, 2024
1 parent bf5a550 commit b2dd4cb
Showing 1 changed file with 90 additions and 52 deletions.
142 changes: 90 additions & 52 deletions slides/common/software_environment.tex
View file
Original file line number Diff line number Diff line change
Expand Up @@ -291,7 +291,7 @@ \subsection{Using Conda}
\frametitle{Searching Software with Conda v. Mamba}
First you might want to look for software. This is done with
\begin{lstlisting}[language=Bash, style=Shell]
$ micromamba search <softwarename>
$ mamba search <softwarename>
\end{lstlisting}
\pause
\begin{task}
Expand Down Expand Up @@ -327,69 +327,107 @@ \subsection{Using Conda}
\end{hint}
\end{frame}

%snakemake 8.10.4 hdfd78af_0 bioconda
%snakemake-executor-plugin-slurm 0.4.2 pyhdfd78af_0 bioconda
%snakemake-executor-plugin-slurm-jobstep 0.1.11 pyhdfd78af_0 bioconda
%snakemake-interface-common 1.17.1 pyhdfd78af_0 bioconda
%snakemake-interface-executor-plugins 9.1.0 pyhdfd78af_0 bioconda
%snakemake-interface-report-plugins 1.0.0 pyhdfd78af_0 bioconda
%snakemake-interface-storage-plugins 3.1.1 pyhdfd78af_0 bioconda
%snakemake-minimal 8.10.4 pyhdfd78af_0 bioconda
%snakemake-storage-plugin-fs 0.1.5 pypi_0 pypi


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{frame}[fragile]
\frametitle{Conda / Mamba Environments}
With Conda/Mamba, we can activate and deactivate environments, which bundle our software. E.\,g. a software stack per workflow to ensure reproducible runs.
\pause
To generate a new we can run
\begin{lstlisting}[language=Bash, style=Shell]
$ micromamba create @-n@ <environment_name>
\end{lstlisting}
This will create a new environment with a given name in your home directory. Alternatively, i.\,e. when dealing with file number quotas, you can point the environment to a different filesystem, e.\,g.:
\begin{lstlisting}[language=Bash, style=Shell]
$ micromamba create \
> @-p@ /path/to/project/fs/<environment_name>
\end{lstlisting}
\frametitle{A first Environment for \Snakemake!}
\begin{task}
Type along!
\end{task}
\begin{onlyenv}<1|handout:0>
We can create a new environment:
\begin{lstlisting}[language=Bash, style=Shell]
$ mamba @create@ ...
\end{lstlisting}
using the \altverb{create} keyword.
\end{onlyenv}
\begin{onlyenv}<2|handout:0>
We can create a new environment:
\begin{lstlisting}[language=Bash, style=Shell]
$ mamba create \
> ...
\end{lstlisting}
you may write everything in \emph{one} line. The \altverb{\\} breaks a line and \altverb{>} continues it - it is only to fit everything on a slide.
\end{onlyenv}
\begin{onlyenv}<3|handout:0>
We can create a new environment:
\begin{lstlisting}[language=Bash, style=Shell]
$ mamba create \
> ...
\end{lstlisting}
you may write everything in \emph{one} line. The \altverb{\\} breaks a line and \altverb{>} continues it - it is only to fit everything on a slide.
\end{onlyenv}
\begin{onlyenv}<4|handout:0>
We can create a new environment:
\begin{lstlisting}[language=Bash, style=Shell]
$ mamba create \
> @-c@ conda-forge @-c@ bioconda ...
\end{lstlisting}
\altverb{-c} selects a "channel".
\end{onlyenv}
\begin{onlyenv}<5|handout:0>
We can create a new environment:
\begin{lstlisting}[language=Bash, style=Shell]
$ mamba create \
> -c conda-forge -c bioconda \
> @-n@ snakemake ...
\end{lstlisting}
\altverb{-n} denotes the name of the environment.
\end{onlyenv}
\begin{onlyenv}<6|handout:0>
We can create a new environment:
\begin{lstlisting}[language=Bash, style=Shell]
$ mamba create \
> -c conda-forge -c bioconda \
> -n snakemake
> snakemake snakemake-executor-plugin-slurm \
> snakemake-storage-plugin-fs
\end{lstlisting}
and finally the software list to be installed.
\end{onlyenv}
\vfill
\begin{docs}[What is an \emph{Environment}?]
With Conda/Mamba, we can activate and deactivate "environments". These bundle our software. I.\,e. a software stack per workflow to ensure reproducible runs with specific software versions.
\end{docs}
\end{frame}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{frame}[fragile]
\frametitle{\HandsOn{Creating your own Environment}}
Now, create your first environment. We will
\begin{itemize}
\item work in the \altverb{snakemake_tutorial} directory with
\item a \textit{named} environment
\item use the downloaded \altverb{environment.yaml} file to define the software stack
\item pre-compile all Python files with the \altverb{--pyc} flag
\end{itemize}
\begin{lstlisting}[language=Bash, style=Shell,breaklines=true]
$ micromamba create --pyc -f environment.yaml -n snakemake-tutorial
\end{lstlisting}
\frametitle{\HandsOn{Listing Environments}}
Over time you will have several environments. (So far, there is one + \altverb{base}) To list them all, simply run:
\begin{lstlisting}[language=Bash, style=Shell]
$ mamba env list
\end{lstlisting}
\end{frame}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{frame}[fragile]
\frametitle{Listing Environments}
Over time you will have several environments. (So far, there is one.) To list them all, simply run:
\begin{lstlisting}[language=Bash, style=Shell]
$ micromamba env list
\end{lstlisting}
\end{frame}
\frametitle{\HandsOn{Activating Environments}}
It is time to activate our fresh environment:
\begin{lstlisting}[language=Bash, style=Shell]
$ mamba activate snakemake
\end{lstlisting}
Your prompt should now feature the name of the environment: \altverb{snakemake}.
\end{frame}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{frame}[fragile]
\frametitle{Creating, Activating, Deactivating Environments}
We can create, activate and deactivate environments with
\begin{lstlisting}[language=Bash, style=Shell]
$ micromamba create [other args] -n <environment name>
$ micromamba activate <environment name>
$ micromamba deactivate
\end{lstlisting}
\begin{task}
Activate the environment you just created!
\end{task}
\frametitle{\HandsOn{Checking on Installed Software}}
\begin{lstlisting}[language=Bash, style=Shell]
$ (snakemake) mamba list
\end{lstlisting}
And you should see
\begin{lstlisting}[style=Plain]
snakemake
snakemake-executor-plugin-slurm
snakemake-executor-plugin-slurm-jobstep
snakemake-interface-common
snakemake-interface-executor-plugins
snakemake-interface-report-plugins
snakemake-interface-storage-plugins
snakemake-minimal
snakemake-storage-plugin-fs
\end{lstlisting}
\ldots along with version infos, channel source and hashsums of all the dependencies.
\end{frame}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Expand Down

0 comments on commit b2dd4cb

Please # to comment.