Using new version of MacSyFinder on CRISPRCasFinder.pl about crisprcasfinder HOT 7 OPEN

So it turns out that I do not have MacSyFinder installed properly. I went back to install the newest version of MacSyFinder, but I believe some of the macsyfinder options in the CRISPRCasFinder.pl script (-d and -p) are outdated, and it is giving me an error

macsyfinder: error: unrecognized arguments: -d and -p

Instead of downloading and installing the older version of MacSyFinder (I had been encountering problems getting the old version 1.0.5 to set up following gem-pasteur/macsyfinder#11), can we change the bit of the CRISPRCasFinder.pl script where macsyfinder is called, precisely remove/updating the -d and -p options? Comparing the option menus for the two MacSyFinder versions (1.0.5 and 2.0rc6), I can't see to figure out what the -d and -p from 1.0.5 is replaced by in the new version

From the CRISPRCasFinder.pl script:

 if ( (-d $casfinder) and (-d $casdb) and (-d $profiles) ) {
          #if($default){
            $macsyfinder = "macsyfinder -w $cpuMacSyFinder -d $casdb -p $profiles --sequence-db $proteome all --out-dir $casDir ";
            #$macsyfinder = "macsyfinder -w $cpuMacSyFinder -d $casdb -p $profiles --sequence-db $proteome all --out-dir $casDir ";
            $macsyfinder .= $addToMacSy; # --multi-loci General-CAS
          #}
          #else{
            #$macsyfinder = "macsyfinder -w $cpuMacSyFinder -d $casdb -p $profiles --sequence-db $proteome all --out-dir $casDir "; #--multi-loci 'CAS*' --min-genes-required 'CAS*' 1";
          #}
    }
    #elsif($default){
        #$macsyfinder = "macsyfinder -w $cpuMacSyFinder --sequence-db $proteome all --out-dir $casDir"; #MacSyfinder without new definitions/profiles
    #}
    else{
        $macsyfinder = "macsyfinder -w $cpuMacSyFinder --sequence-db $proteome all --out-dir $casDir"; #MacSyfinder without new definitions/profiles

Thank you

Marcus

from crisprcasfinder.

Hi Marcus,
Thank you for your message. We will try to update with the new version of MacSyFinder as soon as possible...
Best,
David

from crisprcasfinder.

Thank you very much David. Greatly appreciated!

from crisprcasfinder.

Dear all. Was wondering if there is an update on the status of this thread? Thanks

Marcus

from crisprcasfinder.

Hi all, is there any update? I have been facing the same problem. Please let me know if anyone figured it out already.

from crisprcasfinder.

Dear All, thank you for your messages. Please be patient. A new version is coming soon.
Best,
David

from crisprcasfinder.

Dear All, please note that CRISPRCasFinder vers 4.3.2 is now available and it includes the new version of MacSyFinder. Please see the new installation through the conda environment (https://github.com/dcouvin/CRISPRCasFinder#condabiocondamamba).
Best,
David

from crisprcasfinder.