sci-f/sci-f.github.io

The Scientific Filesystem Specification and Documentation

sci-f.github.io's Issues

[proposal] allow for install with subset of apps

We can currently install the entire contents of a recipe.scif (the "publish one container" use case)

scif install recipe.scif

or break our recipe into more modular applications (the cluster "make your own container" example);

scif install samtools.scif
scif install bowtie.scif
scif install tophat.scif

There is a third use case where we have the first single file, but we only want to install a subset of applications. We should be able to do:

scif install recipe.scif samtools bowtie

to install all except tophat, for example.

Spec version / date query

Hi @vsoch!

Over on sylabs/singularity, @preminger is starting to take a look at our roadmap item to support SCIF in the new OCI mode: sylabs/singularity#1470

While pointing him toward some resources, I've noticed the spec version / date and it's a little confusing to me:

With this, it's rendering as:

How are we meant to refer to this version, when we document what we implement in Singularity's OCI-Mode? Usually if the minor version is 1.1 then I'd expect the full version string to be 1.1.1 - but here we have 1.0.0 Minor Version 1.1?

As an aside, the date is 2021-01-01 but it looks like the last change was actually 2023-02-24 for the appstart addition (#13)?

Github main page in the main repo

I'm not sure if this is an issue actually, but https://github.com/sci-f/sci-f.github.io/blob/master/0-index.md shows up in the main repo instead of the /pages subfolder.

Not a huge problem, but it seems to break the 'edit pencil button' link in the top right of the https://sci-f.github.io/ page.

After first release, think about a style guide

There are a lot of suggested best practices in the specification and discussed in the manuscript, and this would be good to put together into a cohesive style guide for a SCIF. See https://www.inwt-statistics.com/read-blog/inwts-guidelines-for-r-code.html for inspiration, pep8 for python, etc

Question:

Question on: https://www.github.com/sci-f/sci-f.github.io//tree/master/0-index.md#how-does-scif-related-to-containers

add docs for nextflow-scif

or minimally, a link to them! --> https://github.com/sci-f/nextflow-scif

cc @saramonzon thank you for this contribution, can't wait to test it out!

integrating 2+ virtual environments in a singularity container via sci-f

Hi,

I'm trying to figure out if this is possible. Recently asked this question. Is there perhaps a workaround related to %appenv or %apprun to facilitate? 😬

Qs: is there a good tutorial for using this in singularity?

I am learning how to use this to create apps for singularity.
However, every single tutorial I found, I ran into problems.
I would be grateful if someone can point me to the right direction.

For example, following tutorial here: https://sci-f.github.io/tutorial-preview-install#install-scif-in-singularity-using-recipe, I downloaded the Singularity definition file here: https://sci-f.github.io/tutorials/Singularity and ran the build command.
However, when I tried to run the app, it's complaining scif not found (among other thing).
I was under the impression I don't have to install scif since it's already integrated in singularity.

The following are the commands I tried to run along with the "not found" message.
Please let me know how I'm supposed to run this. Thanks!

mkdir -p /data/test_apps
cd /data/test_apps

wget https://sci-f.github.io/tutorials/Singularity

dzdo singularity build --tmpdir=/home/tmp hello-world.simg Singularity

singularity run --app hello-world-script hello-world.simg

/.singularity.d/actions/run: 3: /.singularity.d/env/94-appsbase.sh: SCIF_APPDATA_hello-world-echo=/scif/data/hello-world-echo: not found
/.singularity.d/actions/run: 4: /.singularity.d/env/94-appsbase.sh: SCIF_APPMETA_hello-world-echo=/scif/apps/hello-world-echo/scif: not found
/.singularity.d/actions/run: 5: /.singularity.d/env/94-appsbase.sh: SCIF_APPROOT_hello-world-echo=/scif/apps/hello-world-echo: not found
/.singularity.d/actions/run: 6: /.singularity.d/env/94-appsbase.sh: SCIF_APPBIN_hello-world-echo=/scif/apps/hello-world-echo/bin: not found
/.singularity.d/actions/run: 7: /.singularity.d/env/94-appsbase.sh: SCIF_APPLIB_hello-world-echo=/scif/apps/hello-world-echo/lib: not found

/.singularity.d/actions/run: 9: export: SCIF_APPDATA_hello-world-echo: bad variable name

fixed link