Conda environment perl issue

Question

[Paulo]

Greetings.

I'm trying to use the program "https://github.com/rhysf/Synima" using a conda environment. I've created a new environment and used conda to download the needed depenencies and applications.

Perl
Bio-Perl
Python
R
Legacy-BLAST or BLAST+

running the second step which uses perl to start a script

' perl /home/h.paulocampiteli1/Synima/util/Blast_grid_all_vs_all.pl -r Repo_spec.txt '

the following error message appears

Can't locate File/Which.pm in @inc (you may need to install the File::Which module) (@inc contains: /home/h.paulocampiteli1/Synima/util/../modules/ /home/h.paulocampiteli1/.conda/envs/synima/lib/perl5/5.32/site_perl /home/h.paulocampiteli1/.conda/envs/synima/lib/perl5/site_perl /home/h.paulocampiteli1/.conda/envs/synima/lib/perl5/5.32/vendor_perl /home/h.paulocampiteli1/.conda/envs/synima/lib/perl5/vendor_perl /home/h.paulocampiteli1/.conda/envs/synima/lib/perl5/5.32/core_perl /home/h.paulocampiteli1/.conda/envs/synima/lib/perl5/core_perl .) at /home/h.paulocampiteli1/Synima/util/../modules/read_Blast.pm line 11.
BEGIN failed--compilation aborted at /home/h.paulocampiteli1/Synima/util/../modules/read_Blast.pm line 11.
Compilation failed in require at /home/h.paulocampiteli1/Synima/util/Blast_grid_all_vs_all.pl line 7.
BEGIN failed--compilation aborted at /home/h.paulocampiteli1/Synima/util/Blast_grid_all_vs_all.pl line 7.

If I change lib on the script the for perl locations, next line fails and the same issue happensbut read_BLAST can't be located.

Any ideas how to make File::Which available on the conda env? Another problem is its a private server I can't used sudo since I don't have admin privilages. I'm new on python/linux programming if any information missing I can add here

thanks in advance.

Answer 1

[Dave Carlson]

You can install that perl module with:

conda install -c bioconda perl-file-which

Note that you may run into more missing perl modules. If so, it's possible that you can add them with conda in a similar fashion.

[Paulo]

thanks for the answer!

I had already done that exactly addition trough conda. I check the packages in my environment

using $ conda list

a big list with downloded modules is printed and this perl-file-which is among them

name version Build Channel

perl-file-which 1.20 0 bioconda

this build "0" made me wonder if the command I used was somewhat old, so I kept searching for conda perl-file-which and fixed the problem with the following command

conda install -c conda-forge perl-file-which

thanks for the answer again