Closed idaElken closed 3 years ago
@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/ )?
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 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?
@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.
Hey, it's a success (thanks to https://github.com/hpcng/singularity/issues/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
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
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?
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!)
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
@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
.
This is what I tried:
(to keep his up to date - the problem is solved by "module purge" and using singularity from /bin folder)
@idaElken It seem we solved this with singularity - closing the ticket now.
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