Closed priyankajain31784 closed 3 years ago
tderrien
commented
4 years ago Hello,
Sorry for the delay.
It seems the programs cannot find the correct PATH. Did you export them as mentioned in the Install section ?
export FEELNCPATH=${PWD}
export PERL5LIB=$PERL5LIB:${FEELNCPATH}/lib/
export PATH=$PATH:${FEELNCPATH}/scripts/
export PATH=$PATH:${FEELNCPATH}/utils/Best,
Thomas
kbohon2011
commented
4 years ago I installed on my linux server according to the instructions exactly in the Install section and am having the same error. FEELnc package cannot find the path for the perl scripts on test it seems.
./FEELnc/scripts/FEELnc_filter.pl -i transcript_chr38.gtf -a annotation_chr38.gtf -b transcript_biotype=protein_coding > candidate_lncRNA.gtf Can't locate Parallel/ForkManager.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at ./FEELnc/scripts/FEELnc_filter.pl line 10. BEGIN failed--compilation aborted at ./FEELnc/scripts/FEELnc_filter.pl line 10.
tderrien
commented
4 years ago Hello @kbohon2011,
Did you cd into the FEELnc directory before exporting the PATH?
e.g.
cd FEELnc
export FEELNCPATH=${PWD}
export PERL5LIB=$PERL5LIB:${FEELNCPATH}/lib/
export PATH=$PATH:${FEELNCPATH}/scripts/
export PATH=$PATH:${FEELNCPATH}/utils/Otherwise, you could also try the conda installation.
Let me know how is it going.
Best,
Thomas
kbohon2011
commented
4 years ago Thomas,
Unfortunately, I'm still unable to use this program.
Latest roadblock: FEELnc_filter.pl -i transcript_chr38.gtf -a annotation_chr38.gtf -b transcript_biotype=protein_coding > candidate_lncRNA.gtf Can't locate Parallel/ForkManager.pm in @INC (@INC contains: /usr/local/lib/perl5/ /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /media/set2iscsi/Kori_Corn_Diss/FEELnc/scripts/FEELnc_filter.pl line 10. BEGIN failed--compilation aborted at /media/set2iscsi/Kori_Corn_Diss/FEELnc/scripts/FEELnc_filter.pl line 10.
On Fri, Oct 2, 2020 at 2:16 AM Thomas Derrien notifications@github.com wrote:
Hello @kbohon2011 https://github.com/kbohon2011,
Did you cd into the FEELnc directory before exporting the PATH? e.g.
cd FEELnc export FEELNCPATH=${PWD} export PERL5LIB=$PERL5LIB:${FEELNCPATH}/lib/ export PATH=$PATH:${FEELNCPATH}/scripts/ export PATH=$PATH:${FEELNCPATH}/utils/
Otherwise, you could also try the conda installation https://github.com/tderrien/FEELnc#install-via-conda.
Let me know how is it going.
Best,
Thomas
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/tderrien/FEELnc/issues/41#issuecomment-702569105, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGLFQKVBZQ2PJKTIR4VVYNDSIV43RANCNFSM4OEIUBYA .
tderrien
commented
4 years ago Tx for the reply @kbohon2011. Could you paste the output of this command:
echo $FEELNCPATH; echo $PATHAn did you try the conda install feelnc?
tkm@tkm:~/Software/FEELnc/scripts$ ./FEELnc_filter.pl Can't locate Parser.pm in @INC (you may need to install the Parser module) (@INC contains: %LIB $/home/tkm/Software/FEELnc/lib/ $/home/tkm/Software/FEELnc/lib/ /home/tkm/Downloads/FEELnc-master/lib/Parser.pm /home/tkm/.cpan/build/Pod-Usage-1.69-0/t/inc/Pod/Parser.pm /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at ./FEELnc_filter.pl line 14. BEGIN failed--compilation aborted at ./FEELnc_filter.pl line 14.
tkm@tkm:~/Software/FEELnc/scripts$ ./FEELnc_codpot.pl Can't locate Parser.pm in @INC (you may need to install the Parser module) (@INC contains: /home/tkm/Software/FEELnc/scripts/_Inline/lib %LIB $/home/tkm/Software/FEELnc/lib/ $/home/tkm/Software/FEELnc/lib/ /home/tkm/Downloads/FEELnc-master/lib/Parser.pm /home/tkm/.cpan/build/Pod-Usage-1.69-0/t/inc/Pod/Parser.pm /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at ./FEELnc_codpot.pl line 20. BEGIN failed--compilation aborted at ./FEELnc_codpot.pl line 20.
tkm@tkm:~/Software/FEELnc/scripts$ ./FEELnc_classifier.pl Can't locate Bio/SeqFeature/database_part.pm in @INC (you may need to install the Bio::SeqFeature::database_part module) (@INC contains: %LIB $/home/tkm/Software/FEELnc/lib/ $/home/tkm/Software/FEELnc/lib/ /home/tkm/Downloads/FEELnc-master/lib/Parser.pm /home/tkm/.cpan/build/Pod-Usage-1.69-0/t/inc/Pod/Parser.pm /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at ./FEELnc_classifier.pl line 12. BEGIN failed--compilation aborted at ./FEELnc_classifier.pl line 12.