search

splicebox / PsiCLASS

Simultaneous multi-sample transcript assembler for RNA-seq data
16 stars 4 forks source link

An issue with perl multi-threading #16

Closed sagnikbanerjee15 closed 3 years ago

sagnikbanerjee15 commented 3 years ago

Hello,

I have integrated psiclass into a gene annotator pipeline called finder. You can check out the preprint https://www.biorxiv.org/content/10.1101/2021.02.04.429837v1.full

One of the users has reported an issue with Perl multi-threading. The precise error returned by psiclass is

This Perl not built to support threads
Compilation failed in require at /home/i7_station/bin/finder/dep/psiclass_terminal_exon_length_modified/psiclass line 9.
BEGIN failed--compilation aborted at /home/i7_station/bin/finder/dep/psiclass_terminal_exon_length_modified/psiclass line 9.

The line from the psiclass file is Use threads;

The user is running finder within a conda environment that has perl-thread installed. But still it returns this error. Could you please look into it?

Thanks.

mourisl commented 3 years ago

Thanks for the information. I just checked perl's documentation, it seems this "threads" was introduced in Perl 5.8. Could the user install the newer version of perl in Conda? My system uses perl 5.16.

sagnikbanerjee15 commented 3 years ago

I have requested the user to post the version of perl. I have provided an environment.yml file from which the conda environment was constructed (https://github.com/sagnikbanerjee15/Finder/blob/master/environment.yml). In this file perl version is set to 5.26.

sagnikbanerjee15 commented 3 years ago

Hi,

The user was able to fix it after a fresh reinstallation.

Thanks

mourisl commented 3 years ago

Thank you for letting us know!