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aertslab / pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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Updated singularity container [results] #258

Closed gaelcge closed 3 years ago

gaelcge commented 3 years ago

Hi guys Would it be possible to have the latest version of pySCENIC (0.11) on singularityhub? Thanks

cflerin commented 3 years ago

HI @gaelcge ,

We haven't been using singularity hub for a while, instead everything is on Docker Hub. The most recent version is now available there. You can build it for singularity with: singularity build aertslab-pyscenic-0.11.0.sif docker://aertslab/pyscenic:0.11.0. Do you need it to be on singularity hub in particular?

gaelcge commented 3 years ago

Hi Chris The latest singularity image is downloaded from singularity hub when we run nextflow scenicprotocol so it would be great to have 0.11 on the hub. But I can also specify the build when running the command. Thanks Gael

On Thu, Feb 11, 2021 at 6:18 AM Chris C Flerin notifications@github.com wrote:

HI @gaelcge https://github.com/gaelcge ,

We haven't been using singularity hub for a while, instead everything is on Docker Hub. The most recent version is now available there. You can build it for singularity with: singularity build aertslab-pyscenic-0.11.0.sif docker://aertslab/pyscenic:0.11.0. Do you need it to be on singularity hub in particular?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/aertslab/pySCENIC/issues/258#issuecomment-777375750, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFQDA6KFRNPPFWXE3RYNGCTS6O4HVANCNFSM4XNHGMRA .

-- Gael Cagnone, Ph.D Computational biologist at the Montreal Single-Cell Academy CHU-Sainte Justine Research Center, University of Montréal s gael.cagnone@umontreal.cainglecellacademy@gmail.com https://www.joyallab.com/single-cell-academy https://www.joyallab.com/single-cell-academy New single-cell project? https://app.kognitions.com/projform/1567771615025x566347978085223900 [image: https://www.joyallab.com/single-cell-academy] https://www.joyallab.com/single-cell-academy

cflerin commented 3 years ago

Hi @gaelcge ,

Ok now I understand what you need -- but instead of using singularity hub, you can point the pipeline to the new container on Docker Hub (and Nextflow will handle the download and generation of the singularity image automatically). Using the SCENICprotocol nextflow pipeline, you could just do:

nextflow run aertslab/SCENICprotocol -profile singularity,test --pyscenic_container aertslab/pyscenic:0.11.0

BUT, you will run into a problem doing this with the new container (see #260). The pySCENIC 0.11.0 container has the newest Scanpy installed, while the default container for SCENICprotocol pipeline (0.9.18) has an older version, which I guess is what is causing this error. One possibility I would suggest using the newer Nextflow pipeline: VSN Pipelines, which has a number of workflows for single cell. The one most equivalent to the SCENICprotocol would be single_sample_scenic (you can find a tutorial for this one here. So, I'll close this and address the new error in #260.

Sergio-ote commented 1 year ago

I am sorry @cflerin, I do not know if I am missing something, but why is this option still available (2 years later!) if the pipeline will not run? I am trying to run pySCENIC in a cluster and, after overcoming some installation restrictions, I managed to submit a job. I was surprised to find out that this was causing it to finish, and now I have to set up the installation using the VSN Pipelines.

Why not just deprecating this option and indicating that it should be run using the VSN Pipelines in the documentation from the very beginning?

ghuls commented 1 year ago

@Sergio-ote pySCENIC Docker/Podman/Singularity/Apptainer containers building and usage instructions can be found at: https://pyscenic.readthedocs.io/en/latest/installation.html#docker-podman-and-singularity-apptainer-images