Error when running

[smangul1]

Hi Jason,

Thanks for doing a great job making a USABLE version of the software.

I followed your instruction. Unfortunately, i am still getting an error

"perl: symbol lookup error: /PHShome/sv188/perl5/lib/perl5/x86_64-linux-thread-multi/auto/List/MoreUtils/XS/XS.so: undefined symbol: Perl_Istack_sp_ptr"

"perl: symbol lookup error: /PHShome/sv188/perl5/lib/perl5/x86_64-linux-thread-multi/auto/List/Util/Util.so: undefined symbol: Perl_Istack_sp_ptr
"

I am not familiar with perl. So i was unable to figure out the error. I was just wondering if you know what can cause the problem.

Thanks,
Serghei

[jason-weirather]

Hi @smangul1 are you using the Conda environment to run it? I was getting at least the HLA calling to work through there. I don't think I have the courage to go diving into Perl to sort out to much bugs. If you have suggestions I can maybe try to help. I've been working on WES pipelines for another project and Sachet, the author of Polysolver, has provided an updated version which also works with hg38.

https://hub.docker.com/r/sachet/polysolver/tags/

I've tested this out v4 and the Docker is working well for me. Unfortunately it only exists in Docker format, and they have no immediate plans to dig it out of there (which is why I made this hla-polysolver conda environment). As for the Docker, my choices are run local or run on google cloud and both work. I recommend you use that Docker if at all possible because Sachet made it and its going to be what the community is using most currently.

Another option is Optitype. Optitype plans to support mutation calling in the near future, and has good performance according to all parties I've spoken to. I believe they also do class II calling (or at least will do it in the future)

https://github.com/FRED-2/OptiType

[smangul1]

Thanks!
I think the problem was with perl path

Looks like it was fixed by running
export PERL5LIB="/PHShome/sv188/anaconda2/envs/polysolver/lib/perl5/5.22.0/"

maybe you can add this to conda build

S

[smangul1]

Wow! It works! I was able to run on our WXS data! Thanks a lot for releasing this conda package!
Do you think you can update it with

export PERL5LIB="/PHShome/sv188/anaconda2/envs/polysolver/lib/perl5/5.22.0/"

?

S

[jason-weirather]

@smangul1 awesome you were able to work through it!

As a stop-gap I've updated the documentation in the README for Conda instructions with the command that should do exactly what you have there for anyones path:

After activating the environment you need to set the perl5 path (thanks smangul1).

(polysolver)$ export PERL5LIB="$CONDA_PREFIX/lib/perl5/5.22.0/"

This looks like kind of a pain to do in Conda, because I need to figure out how to get an some shell script in some activate.d thing that will get fired off when it launches that can set the environment variable. The easier way I think will be to hack the code of the program to set the perl library globally if you launch any of those shell scripts. I'll leave this issue open to remind myself to do this.

Thanks for the fix!

[smangul1]

Great! I think conda and docker containers should be a must for any published tool. So we don't need t do this work :)