What is the recommendation for including Fragpipe in standartized workflows (snakemake/nextflow)?

[CrystalColeCrystal]

Hello!

I'm interested in you recommendation on how Fragpipe/MSfragger should be included in standartised workflows run with snakemake or nextflow? Should it be included as fragpipe or as msfragger? I'm intereseted in my workflow being HPC-friendly, so UI is really not needed. Is Fragpipe -headless mode equivalent to command-line MSfragger or no? Also, since MSfragger license does not permit distributing its Docker/Singularity images as discussed here #1888 what is the easiest way to ensure reproducibility of said workflow?

Thank you so much for your help!

[fcyu]

We have a FragPipe Docker image here https://hub.docker.com/r/fcyucn/fragpipe

You can run FragPipe in command line using the "headless" mode.

FragPipe and MSFragger are two different things.

Regarding MSFragger, you can not distribute any docker/singularity/snakemake/nextflow or other types of images due to the license.

Since MSFragger is just a single jar file, I don't see any issue regarding the reproducibility.

Best,

Fengchao

[punching-samuel]

We have a FragPipe Docker image here https://hub.docker.com/r/fcyucn/fragpipe

You can run FragPipe in command line using the "headless" mode.

FragPipe and MSFragger are two different things.

Regarding MSFragger, you can not distribute any docker/singularity/snakemake/nextflow or other types of images due to the license.

Since MSFragger is just a single jar file, I don't see any issue regarding the reproducibility.

Best,

Fengchao

Hello～
I tried to pull the docker image using singulairty, but I failed
'''
singularity pull fragpipe.sif docker://fcyucn/fragpipe
'''
I have tried many times. Is it possible to provide a singularity image? Because the several public clusters I am using now can only provide singularity. This problem has troubled me for a long time. Thank you very much for your help!

Best wishes,
Sammi

[fcyu]

I am not sure if your command is correct. Can you try singularity pull docker://fcyucn/fragpipe?

Actually, I have tested using both commands and they both work.

Thanks,

Fengchao

[punching-samuel]

I am not sure if your command is correct. Can you try singularity pull docker://fcyucn/fragpipe?

Actually, I have tested using both commands and they both work.

Thanks,

Fengchao

Thank you for your reply.

I checked, and it turns out the issue was related to a network error on my side. I pulled the image using a different PC and transferred the file to my remote Slurm system:

 singularity build fragpipe.sif docker-archive://fragpipe.tar
singularity shell fragpipe.sif
Singularity> /fragpipe_bin/fragPipe-22.0/fragpipe/bin/fragpipe -h

It worked fine. I will go through the tutorial and try out some workflows.

I also have a question: Since my Windows machine might not be able to handle the software’s visualization, if I use Linux for the analysis, will I get the same results?

Best wishes,
Sammi

[fcyu]

Since my Windows machine might not be able to handle the software’s visualization, if I use Linux for the analysis, will I get the same results?

Yes, the results will be the same.

Best,

Fengchao

[punching-samuel]

Since my Windows machine might not be able to handle the software’s visualization, if I use Linux for the analysis, will I get the same results?

Yes, the results will be the same.

Best,

Fengchao

I have another question that if I use fragpipe and PTM-shepherd to analyze peptidome (which means I have to choose the parameter 'non-specific enzyme'), will the space for database searching be very large if I also want to find noval PTM? Have you tried the experiment for finding PTM on peptidome?

Thank you!

sammi