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dcouvin / CRISPRCasFinder

A Perl script allowing to identify CRISPR arrays and associated Cas proteins from DNA sequences
https://crisprcas.i2bc.paris-saclay.fr
GNU General Public License v3.0
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vmatch2 #30

Closed drob2727 closed 3 years ago

drob2727 commented 3 years ago

I have been trying to use this program with singularity. I thought all the dependencies were going to be inside that package. I'm not sure how to install vmatch2 with singularity. Im including my command to show whats going on

(base) David-2:Downloads DavidMRobinson$ singularity exec -B $PWD CrisprCasFinder.simg perl /Users/DavidMRobinson/Downloads/CRISPRCasFinder/CRISPRCasFinder.pl -so /Users/DavidMRobinson/Downloads/CRISPRCasFinder/sel392v2.so -cf /Users/DavidMRobinson/Downloads/CRISPRCasFinder/CasFinder-2.0.3 -drpt /Users/DavidMRobinson/Downloads/CRISPRCasFinder/supplementary_files/repeatDirection.tsv -rpts /Users/DavidMRobinson/Downloads/CRISPRCasFinder/supplementary_files/Repeat_List.csv -cas -def G -out RES21092020_2 -in megahit_frx_bon_final_assembly.fasta ################################################################

--> Welcome to /Users/DavidMRobinson/Downloads/CRISPRCasFinder/CRISPRCasFinder.pl (version 4.2.19)

################################################################

vmatch2 is not installed, please install it and try again. [ 5.367732] reboot: Power down

dcouvin commented 3 years ago

Dear @drob2727 , Please note that you should try a command like this (taking into account the paths existing inside the singularity image): singularity exec -B $PWD CrisprCasFinder.simg perl /usr/local/CRISPRCasFinder/CRISPRCasFinder.pl -so /usr/local/CRISPRCasFinder/sel392v2.so -cf /usr/local/CRISPRCasFinder/CasFinder-2.0.3 -drpt /usr/local/CRISPRCasFinder/supplementary_files/repeatDirection.tsv -rpts /usr/local/CRISPRCasFinder/supplementary_files/Repeat_List.csv -cas -def G -out RESULTfolder -in sequence.fasta Hope this will help! Best regards and happy 2021! David

drob2727 commented 3 years ago

Thanks! Do I need to have all the sequences from the metagenomes classified before I run this program or can I just use the contig names to see what comes up?

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From: David Couvin notifications@github.com Sent: Wednesday, January 6, 2021 3:37:33 PM To: dcouvin/CRISPRCasFinder CRISPRCasFinder@noreply.github.com Cc: David Robinson drob2727@unm.edu; Mention mention@noreply.github.com Subject: Re: [dcouvin/CRISPRCasFinder] vmatch2 (#30)

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Dear @drob2727https://github.com/drob2727 , Please note that you should try a command like this (taking into account the paths existing inside the singularity image): singularity exec -B $PWD CrisprCasFinder.simg perl /usr/local/CRISPRCasFinder/CRISPRCasFinder.pl -so /usr/local/CRISPRCasFinder/sel392v2.so -cf /usr/local/CRISPRCasFinder/CasFinder-2.0.3 -drpt /usr/local/CRISPRCasFinder/supplementary_files/repeatDirection.tsv -rpts /usr/local/CRISPRCasFinder/supplementary_files/Repeat_List.csv -cas -def G -out RESULTfolder -in sequence.fasta Hope this will help! Best regards and happy 2021! David

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dcouvin commented 3 years ago

You will need to have your sequences in a multi-FASTA file to run the program