PennCNV used to be a module on p33 - now it is gone.

[idaElken]

Hi,

I have used penncnv/1.0.4 on p33 and now need to use it again both on p33 and p697. However, when trying to load it, apparently it disappeared. I imagine it was removed in an upgrade (?) since I'm the only one who used it in the past :-P

Best wishes,
Ida

[ofrei]

@idaElken Is this the right package: https://github.com/WGLab/PennCNV ?

Do you need a specific version, i.e. 1.0.5? (as mentioned here in the instructions http://penncnv.openbioinformatics.org/en/latest/user-guide/install/ )?

[ofrei]

I found pennCNV on this list:
https://www.uio.no/tjenester/it/forskning/aktuelt/abel-newsletter-1-2018.html
It would be interesting to see if other software from this list is also no longer available.

[idaElken]

@idaElken Is this the right package: https://github.com/WGLab/PennCNV ?

Do you need a specific version, i.e. 1.0.5? (as mentioned here in the instructions http://penncnv.openbioinformatics.org/en/latest/user-guide/install/ )?

Absolutely correct.

As far as I can tell, this update does not change the actual algorithms (from 1.0.4 that I used before) but is simply to simplify installation/improve error messages (https://github.com/WGLab/PennCNV/releases), so 1.0.5 seems to be absolutely fine.

Alex' three suggestions for options:
(1) Sandeep and/or me help you directly, i.e. by making a singularity container that runs penncnv
(2) We reach out to Sabry at TSD and he helps as part of AUS (Advanced Users Support)
(3) We make a request for installing additional software on Colossus. This is reasonable as they've had it previously , but now it's gone. Yet I think it's not many users who need PennCNV, so if we can easily solve it ourself then I wouldn't bother TSD with this question.

This may be helpful (?) if we end up installing ourselves (yourselves ;-) ):
20160805: PennCNV has been dockerized by Roman Hillje at the University of Zurich, Switzerland. The docker image and related documentation are available at https://hub.docker.com/r/romanhaa/penncnv/. (?)

Let me know if you want me to reach out to Sabry or how we should do it?

[ofrei]

@idaElken Thank you for pointing out to the Docker image by Roman Hillje. I've converted it to singularity container by running
singularity build penncnv.sif docker://romanhaa/penncnv (locally on my ubuntu laptop) and imported this container to p697 project into /cluster/projects/p697/ofrei/comorment/ . Could you try it out? If you are not quite familiar with with Singularity, here are "getting started" instructions : https://github.com/comorment/demo .

I couldn't run examples provided by PennCNV because singularity container is read-only. This is actually different from a docker container, which is writable. There are options to make a writable singularity container (persistent overlays and writable images , see links here ) - but both require sudo, it seem we can't use them. Either way here is an error I get:

I hope the above problem is specific to the PennCNV exmaple (runex.pl), and the actual PennCNV software might still work if PennCNV software tries to write outside of the container.

[ofrei]

Hey, it's a success (thanks to apptainer/singularity#1790 ). Here is what I did:

cd /cluster/projects/p697/ofrei/comorment
singularity build --sandbox new.simg penncnv.sif
singulairty shell --no-home --writable new.simg
# now running commands within singularity container:
cd /opt/PennCNV-1.0.5/example/
perl runex.pl 1

[idaElken]

Hey, it's a success (thanks to hpcng/singularity#1790 ). Here is what I did:

cd /cluster/projects/p697/ofrei/comorment
singularity build --sandbox new.simg penncnv.sif
singulairty shell --no-home --writable new.simg
# now running commands within singularity container:
cd /opt/PennCNV-1.0.5/example/
perl runex.pl 1

That's fantastic news - thank you so much! I won't be able to test it further until (at earliest) Friday I'm afraid. But thank you looking forward to it!

/Ida

[ofrei]

From https://hub.docker.com/r/romanhaa/penncnv/ :

Note: To keep the image size small, it doesn't contain any R (which means visualize_cnv.pl won't be able to export jpegs).

@idaElken is this a problem?

[idaElken]

Thanks for letting me know!
No, this is not an issue since I usually use an Rpackage called iPsychCNV to visualize the CNVs with - it is much more convenient. I need to import this package to p697 (imported to p33 ages ago - if I run into issues I'm likely to ask you and Sandeep (be warned!)

[idaElken]

Hi,
Does each person need to install the container themselves?

-cause currently I don't find this folder:
/opt/PennCNV-1.0.5/example/
neither: /opt/PennCNV-1.0.5/, only /opt/

But if I try to run:
singularity build --sandbox new.simg penncnv.sif
it says "build target already exists" (?)

/Ida

[ofrei]

@idaElken could you try to skip singularity build --sandbox new.simg penncnv.sif command, and run continue with these?

singulairty shell --no-home --writable new.simg
# now running commands within singularity container:
cd /opt/PennCNV-1.0.5/example/
perl runex.pl 1

The build target already exists error is because singularity build --sandbox new.simg penncnv.sif command tries to generate new.simg file which already exist. You may either change the name (i.e. use singularity build --sandbox penncnv_ida.simg penncnv.sif, or simply re-use my container called new.simg.

[idaElken]

This is what I tried:

[ofrei]

(to keep his up to date - the problem is solved by "module purge" and using singularity from /bin folder)

[ofrei]

@idaElken It seem we solved this with singularity - closing the ticket now.