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
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@@ -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
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@@ -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.
