How to use CRISPRCasFinder through singularity container

[WoCer2019]

Thanks for your nice tool! I have only used Conda, and I have never used Singularity Container.

First, I installed Singularity via mamba.

mamba create -n singularity -y singularity

Then, I downloaded the CrisprCasFinder.simg image from the CRISPR-Cas++ Download page.

When I ran the following code, an error happened.

mamba activate singularity

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 RES21092020_2 -in sequence.fasta

ERROR  : Image path doesn't exists
ABORT  : Retval = 255

Please tell me how to use CRISPRCasFinder through the singularity container. Thank you!

[dcouvin]

Dear @WoCer2019 ,

Thank you for your message. Unfortunately, for unknown reasons, the tool doesn't work with the conda version of singularity. Please use conda environment installer to install the version 4.3.2. conda env create -f ccf.environment.yml -n crisprcasfinder conda activate crisprcasfinder mamba init mamba activate mamba install -c bioconda macsyfinder=2.0 macsydata install -u CASFinder==3.1.0

Hope this helps! Best regards, @dcouvin

[WoCer2019]

Dear @dcouvin

Thanks for your reply! The installation of this tool has been done. The output files include rawCRISPRs.fna, result.json, folder GFF, and folder TSV. Is it correct? Thanks again!

Best regards, @WoCer2019

[dcouvin]

Dear @WoCer2019, Thank you for your message. Yes it is correct! Best regards, @dcouvin

[WoCer2019]

Thanks!