diff --git a/TakeHome.md b/TakeHome.md index 2388bef75c2b9062f444d3be80025317c076873a..5f7220bf36f3b5ba8ff40dca197e42a06645dc19 100644 --- a/TakeHome.md +++ b/TakeHome.md @@ -7,8 +7,16 @@ password provided via e-mail. All image files referred to below can be found on Sciebo. -We provide three options in order of recommendation, -but take what works best for you. +We provide three options, in short-- + +Recommended for Mac, Windows and Linux: +* Docker - with the user matching inside and outside the container + +As during course, not technically recommended, but should work: +* Docker - with permissive permissions + +Recommended for Linux, and in particular HPC's where Singularity is installed: +* Singularity ### Where's Rstudio? The Rstudio Docker is not mentioned below, as @@ -56,19 +64,6 @@ not relevant on your machine. > Note: if you did not configure a docker group during install, you may need > to preface all commands above with `sudo`. -## Singularity -A container option targeted more at convenience and less at security. -(was not available on host machines during the course). - -1. Install Singularity as appropriate for your machine (including via VM for Windows or Mac): https://docs.sylabs.io/guides/3.0/user-guide/installation.html -2. Download pre-build image from course from sciebo `rnaseq-workshop.sif` -3. Run! - - `singularity run rnaseq-workshop.sif`, all files within your home directory should be automatically accessible - - do you need some other directory of files? you can add them with `--bind` like this `singularity run --bind <your_directory>:/mnt/ rnaseq-workshop.sif` will - make the files available under `/mnt/` in the image. For instance, if I was working on the HHU HPC I might want to run - `singularity run --bind /gpfs/project/alden101/projectA:/mnt/ rnaseq-workshop.sif` to mount my folder 'projectA' in my large storage folder on the HPC. -4. Resuming is the exact same as running. - ## Docker - with permissive permissions. This is what we used during the course, and no, it is still not good @@ -90,3 +85,21 @@ Docker to run a public facing web server, the risks could be worse. 6. All info on adjusting directories, retrying, resuming, and maybe needing `sudo` is the same as for the other Docker option above. +## Singularity +A container option targeted more at convenience and less at security. +(was not available on host machines during the course). + +>Unfortunately, it is also only actually easy under _linux_, which is why +>this is at the bottom of the list. However, it still may be exactly what you +>want to e.g. work on the HPC or similar. + +1. Install Singularity as appropriate for your machine (including via VM for Windows or Mac): https://docs.sylabs.io/guides/3.0/user-guide/installation.html, + note on the HHU HPC (and probably many others) it's already available as a module (all you need to do is `module load Singularity`). +2. Download pre-build image from course from sciebo `rnaseq-workshop.sif` +3. Run! + - `singularity run rnaseq-workshop.sif`, all files within your home directory should be automatically accessible + - do you need some other directory of files? you can add them with `--bind` like this `singularity run --bind <your_directory>:/mnt/ rnaseq-workshop.sif` will + make the files available under `/mnt/` in the image. For instance, if I was working on the HHU HPC I might want to run + `singularity run --bind /gpfs/project/alden101/projectA:/mnt/ rnaseq-workshop.sif` to mount my folder 'projectA' in my large storage folder on the HPC. +4. Resuming is the exact same as running. +