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simroux / VirSorter

Source code of the VirSorter tool, also available as an App on CyVerse/iVirus (https://de.iplantcollaborative.org/de/)
GNU General Public License v2.0
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conda recipe yeilds perl-file-which=5.22, with perl=5.26 #25

Closed kgh03 closed 6 years ago

kgh03 commented 6 years ago

following the conda recipe, i get perl version 5.26 but File:Which gets put into 5.22 and are not found in the @INC path.

i was able to fix this with cpan.

(virsorter) kelly@mason ~ $ wrapper_phage_contigs_sorter_iPlant.pl -f assembly.fasta --db 1 --wdir output_directory --ncpu 4 --data-dir /scratch/virsorter-data/ Can't locate File/Which.pm in @INC (you may need to install the File::Which module) (@INC contains: /usr/local/miniconda3/envs/virsorter/lib/site_perl/5.26.0/x86_64-linux-thread-multi /usr/local/miniconda3/envs/virsorter/lib/site_perl/5.26.0 /usr/local/miniconda3/envs/virsorter/lib/5.26.0/x86_64-linux-thread-multi /usr/local/miniconda3/envs/virsorter/lib/5.26.0 .) at /usr/local/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 47. BEGIN failed--compilation aborted at /usr/local/miniconda3/envs/virsorter/bin/wrapper_phage_contigs_sorter_iPlant.pl line 47.

(virsorter) kelly@mason ~ $ which perl /usr/local/miniconda3/envs/virsorter/bin/perl

(virsorter) kelly@mason ~ $ perl -v This is perl 5, version 26, subversion 0 (v5.26.0) built for x86_64-linux-thread-multi

(virsorter) root@mason ~ $ cpan install FIle:Which

simroux commented 6 years ago

Hi, If I understood correctly, you were able to successfully run VirSorter after installing File::Which separately from CPAN ? If so, thanks for reporting both the issue and the fix ! I will close this but make a link from the readme in case others have a similar problem.

chadsmith123 commented 6 years ago

I followed the installation instructions with conda 4.5.0 and also had this issue. In addition to File/Which.pm, I also had this error with Bio:Seq.pm and Parallel/Forkmanager.pm and thus ran:

cpan File:Which cpan Bio:Seq.pm cpan Parallel/ForkManager.pm

After installation of these modules VirSorter crashed after execution. Do you know if this crash is due to the installation of these packages or a problem with the system I am running it on (AWS EC2 8 CPUs, 32GB ram)?

Many thanks! virsorter_conda.log