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griffithlab / pVACtools

http://www.pvactools.org
BSD 3-Clause Clear License
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Set up singularity distribution #525

Open malachig opened 4 years ago

malachig commented 4 years ago

It seems like it might be possible to have creation of singularity images from the same Dockerfile we use to build our docker images.

I wonder if we could even have automated builds at Singularity Hub?

riederd commented 4 years ago

Here is a working singularity def file, including some other useful tools like bam-readcount and vt, needed for annotating vcfs. Attention, this is for the staging branch from github. Some would need to change the line "git checkout staging" to the branch one needs.

To build the singularity image, you'd need to first git clone the docker-pvactools into the same directory where you put the singularity def file: git clone git@github.com:griffithlab/docker-pvactools.git

HTH pVACtools.def.zip

malachig commented 4 years ago

Nice. Thanks!

CJBgon commented 4 years ago

I ran into some the same as issue #411 with a docker-pulled Singularity file (pvactools v1.5.7) on a HPC. I managed to circumvent the error by running it on a single core, which raises my suspicion that there is a possible faulty interaction between the temporary storage allocated to each core on the hpc and the singularity $TMP folder.

malachig commented 2 years ago

Is this actually needed now that it seems that Singularity can just run docker images: https://docs.sylabs.io/guides/2.6/user-guide/singularity_and_docker.html

We could test this ability using the pvactools docker. If it works, can close this issue.

cjfields commented 5 months ago

Just to confirm, I have been able to run pvactools successfully using singularity and the latest release (4.1.1). The only odd step is running VEP with the additional plugin. I download first to cache, then run directly.

singularity pull docker://griffithlab/pvactools:4.1.1

I just create a really simple bash wrapper to run the tools to run it as if it's command line:

...
PVACTOOLS_IMG=$SINGULARITY_CACHEDIR/pvactools_4.1.1.sif

singularity run $PVACTOOLS_IMG $@