CRISPRCasFinder.pl: command not found

[Nikitakurilov]

Hi! Today I've been struggling to install CRISPRCasFinder on my computer for UBUNTU. I've been following the manual step by step, I've uncommented that one string in source.list file, I've ran installer_UBUNTU.sh, set the enviroment variables and everything worked just fine, but when i try to run an install test, it's just refusing to work by replaying "CRISPRCasFinder.pl: command not found". I am very new to ubuntu, i've installed it this day and there's a lot I'm missing, so I would despretly want to understand, why this error is accuring. I've tried to install this program for many times now, so this might be the problem as I don't know, how exactly does installation process is going on. I'll try my best to unswer your questions, but I might not be as skilled as it needs to be

[dcouvin]

Hi @Nikitakurilov, The program may not work well with current version of Linux Ubuntu... If you want, you can use the singularity container (download the image at the download page: https://crisprcas.i2bc.paris-saclay.fr/Home/Download). You can install singularity using this link: https://sylabs.io/guides/3.3/user-guide/installation.html . you should try a command like this: 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. Hope this will help

[Nikitakurilov]

Hi @dcouvin! Thank you so much for your support! I'll try to do it your way and will keep you posted.

[Nikitakurilov]

Okay, now I'm stuck on this one. I need your help, @dcouvin. I've successfully installed all the software needed, but when i try to install singularity, it clearly can't find a link, so what should i do?

$ export VM=sylabs/singularity-3.2-ubuntu-bionic64 && \ vagrant init $VM && \ vagrant up && \ vagrant ssh Bringing machine 'default' up with 'virtualbox' provider... ==> default: Box 'sylabs/singularity-3.2-ubuntu-bionic64' could not be found. Attempting to find and install... default: Box Provider: virtualbox default: Box Version: >= 0 The box 'sylabs/singularity-3.2-ubuntu-bionic64' could not be found or could not be accessed in the remote catalog. If this is a private box on HashiCorp's Vagrant Cloud, please verify you're logged in via vagrant login. Also, please double-check the name. The expanded URL and error message are shown below:

URL: ["https://vagrantcloud.com/sylabs/singularity-3.2-ubuntu-bionic64"] Error: The requested URL returned error: 404

[dcouvin]

Hi @Nikitakurilov , Thank you for your message. Sorry I have not seen this error before. Maybe you could try to install a previous version of Singularity. Hope this will help.

[imonteroo]

Hello. Is CRISPRCasFinder still having troubles with Ubuntu 20.04. I tried to install it but I do not see:

-bin folder with binary files (MacSyFinder, mkvtree2, vmatch2, vsubseqselect2) -src folder with source files (Vmatch) -macsyfinder-1.0.5 folder (MacSyFinder) -sel392v2.so file (needed for Vmatch) $MACSY_HOME

Is there any way to install it in a conda environment or any other way?