crisprcasfinder's Introduction

CRISPRCasFinder

CRISPRCasFinder is an updated, improved, and integrated version of CRISPRFinder and CasFinder.

References

The related publication is available at: https://doi.org/10.1093/nar/gky425

Further information are available at: https://crisprcas.i2bc.paris-saclay.fr.

Documentation

A more complete User Manual is available at the following link: https://crisprcas.i2bc.paris-saclay.fr/Home/DownloadFile?filename=CRISPRCasFinder_Viewer_manual.pdf.

Container

If you want to try CRISPRCasFinder without installing dependencies, The standalone version is also available as singularity container:

To run the container

singularity run shub://bneron/CRISPRCasFinder:4.2.18 -def General -cas -i my_sequence.fasta -keep

or download the image locally, and optionally rename it, then run it

singularity pull --name CRISPRCasFinder shub://bneron/CRISPRCasFinder:4.2.18 
./CRISPRCasFinder -def General -cas -i my_sequence.fasta -keep

For more information about singularity containers: https://www.sylabs.io/docs/

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crisprcasfinder's Issues

error running singularity container

If i pull and run the singularity container:

$ singularity pull shub://bneron/CRISPRCasFinder:4.2.18
$ ./bneron-CRISPRCasFinder-master-4.2.18.simg -def General -cas -i sequence.fasta -keep

i'm seeing the following error:

Traceback (most recent call last):
  File "/usr/local/bin/macsyfinder", line 322, in <module>
    worker_nb = args.worker_nb
  File "/usr/local/lib/python2.7/dist-packages/macsypy/config.py", line 188, in __init__
    self.options = self._validate(cmde_line_opt, values)
  File "/usr/local/lib/python2.7/dist-packages/macsypy/config.py", line 607, in _validate
    raise err
ValueError: /usr/local/share/macsyfinder/DEF: No such definition directory

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