This is a test version of Biostars. For the public version, visit https://www.biostars.org.
perl can't see path problem

Hi I'm trying to run pfam_scan.pl. I'm using conda but there's perl from ubuntu system. It conflicts with another? Or script can't see modules?

$ pfam_scan.pl 
Can't locate Moose.pm in @INC (you may need to install the Moose module) (@INC contains: /home/marcin/anaconda3/share/pfam_scan-1.6-4 /home/marcin/anaconda3/lib/perl5/5.32/site_perl /home/marcin/anaconda3/lib/perl5/site_perl /home/marcin/anaconda3/lib/perl5/5.32/vendor_perl /home/marcin/anaconda3/lib/perl5/vendor_perl /home/marcin/anaconda3/lib/perl5/5.32/core_perl /home/marcin/anaconda3/lib/perl5/core_perl .) at /home/marcin/anaconda3/share/pfam_scan-1.6-4/Bio/Pfam/HMM/HMMResultsIO.pm line 50.
protein pfamscan
• 2,196 views • link
updated by Ram Ram • written by Xylanaser Xylanaser

1 answer

Perl can't see the moose module:

conda install -c bioconda perl-moose
• 0 views • link
written by Carambakaracho Carambakaracho 
$ conda install -c bioconda perl-moose
Collecting package metadata (current_repodata.json): done
Solving environment: done

# All requested packages already installed.

:(

• 0 views • link
written by Xylanaser Xylanaser

try creating a brand new conda environment ?

And or copying Moose.pm to one of the directories listed in your @INC eg

/home/marcin/anaconda3/share/pfam_scan-1.6-4

find it with

find . -name "Moose.pm"
• 0 views • link
written by colindaven colindaven

Log in to answer this question.

More posts like this
  • error to run rnammer
    written by microorganism_001 • microorganism_001
    I have installed rnammer software to extract 16s rRNA gene and dependencies (hammer) but I am getting errors when run it. I have followed many …
  • Can't install Transdecoder -
    written by Pedro • Pedro
    I was trying to install TransDecoder to do Transcriptome annotation, but when I run make test, this shows up. I've tried to install the module …
  • Failing to compile kent utilities due to openSSL dependencies
    written by 4galaxy77 4galaxy77
    I would like to use the LOFTEE plugin for VEP on a cluster with no root permissions, but it fails with this error: ``` WARNING: …
  • Conda environment perl issue
    written by Paulo • 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 …
  • Fasta_reader isn't working.
    written by Riku • Riku
    Dear all, When I try to use the script, fasta_seq_length.pl in Trinity, it outputed the following error message. fasta_seq_length.pl fasta > fasta.seq_lens Can't locate fasta_reader.pm …
  • miRDeep2.pl error in make_html2.pl
    written by tikshyadav19 • tikshyadav19
    I have installed cpan install PDF::API2 And still got error Can't locate PDF/API2.pm in @INC (@INC contains: /home/nbri/Tikshana/Ath/small_RNA/mirDeep/mirdeep2/lib/perl5 /home/nbri/vaishali/TOMATO_SRNA/new_analysis/mirdeep2-master/lib/perl5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64 /perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 …
  • The problems when i install the miRDeep2
    written by 51203903042 • 51203903042
    I am trying to install mirdeep2. I tested make_html.pl and error appeared as following: Can't locate PDF/API2.pm in @inc (@inc contains: /home/students/anaconda3/lib/site_perl/5.26.2/PDF/API2.pm /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl …
  • Error in running PfamScan: Can't locate Bio/Pfam/Scan/PfamScan.pm in @INC
    written by basusudipto92 • basusudipto92
    Hi everyone, I am not being able to run PfamScan in my pc. Everytime it pops up with this error. $perl pfam_scan.pl Can't locate Bio/Pfam/Scan/PfamScan.pm …
  • Installation of Perl Modules
    written by Bioinfonext Bioinfonext
    How to install all perl modules in single command required to run circos on CentOS linux platform? **Installed perl version :** [root@psgl software]# perl -v …
  • run pfam scan
    written by dineshtripathy9658 • dineshtripathy9658
    I am trying to run pfam scan....but every time I get the same message: ``` Can't locate IPC/Run.pm in @INC (@INC contains: /userdata/dinesh/PfamScan/ /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 …