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Installation

The program CRISPRCASFinder.pl has been tested on three 64-bit Linux Ubuntu versions (14.04, 15.10, and 16.04), and on a Mac OS X 10.11 El Capitan.

For the moment CRISPRCasFinder.pl is only available for Mac OS and Linux Operating Systems.
The following packet managers are used for the installation :
  • apt-get (Linux, "sudo" command is also needed)
  • brew (Mac OS)

After download of the archive CRISPRCasFinder.zip, uncompress it and go into the CRISPRCasFinder repository:

unzip CRISPRCasFinder.zip
cd CRISPRCasFinder

Hierarchy of files contained in CRISPRCasFinder repository:

  • CRISPRCasFinder.pl (main program)
  • CRISPRCasViewer (folder with a stand alone viewer of CRISPRCasFinder.pl results). This folder mainly contains:
    1. CRISPRCasViewer.html (main HTML page of the standalone viewer that can be open in a web browser)
    2. css (folder containing CSS files)
    3. scripts (folder containing JavaScript files)
    4. example_result.json (JSON file that could be used as an example)
    5. README.txt (guideline concerning the use of CRISPRCasViewer)
    6. User_Manual.pdf (user manual with some examples of output)
  • CasFinder-2.0 (folder containing updated HMM profiles and definitions of Cas genes that are used with MacSyFinder)
  • installer_MAC.sh (MACOSX bash script used for installing the program in order to run CRISPRCasFinder.pl from the CRISPRCasFinder folder)
  • installer_UBUNTU.sh (UBUNTU bash script used for installing the program in order to run CRISPRCasFinder.pl from the CRISPRCasFinder folder)
  • installer_README.txt (guideline concerning the installation)
  • install_test (folder of data allowing to test the installation). This folder contains:
    1. sequence.fasta (example of FASTA file)
    2. Crisprs_REPORT.tsv (CRISPR predictions on sequence.fasta)
    3. Cas_REPORT.tsv (Cas prediction on sequence.fasta)
  • supplementary_files, folder containing the following files:
    1. CRISPR_crisprdb.csv (CSV file containing summary information on CRISPR arrays extracted from CRISPRdb during its last update)
    2. repeatDirection.tsv (file containing orientation of CRISPRdb consensus repeats using CRISPRDirection)
    3. Repeat_List.csv (CSV file containing consensus DRs from CRISPRdb, their ID and their number of occurrence in the database)
    4. crispr.css (CSS file allowing to visualize results like in current CRISPRdb)

Launch the installation

If your operating system is Mac OS, Xcode programming environment (version 5.0 or upper) library must be installed.

Users must have rights on the folder containing the files. Unix users must have sudo rigths.

The installer_README.txt describes steps and their command lines to performe install and to check it.

Changes should be:
  • at the end of the install steps:
    - a bin folder with some binary files (clustalw2, macsyfinder, mkvtree2, vmatch2, vsubseqselect2)
    - a src folder with some source files (vmatch, macsyfinder)
    - the sel392v2.so file (needed for vmatch)
    - a redefinition of $PATH
  • at the end of the checking step:
    - a Result_* folder which contains the results of a launch of CRISPRCASFinder.pl on the sequence data located in the install_data folder

Software Dependencies

BioPerl modules

Perl programming language must be installed on your computer to run this program.
Following BioPerl or Perl's modules must be installed: Class::Struct, Bio::DB::Fasta, Bio::Tools::Run::Alignment::Clustalw, Bio::Tools::Run::Alignment::Muscle, Date::Calc, File::Copy, Bio::Seq, Bio::SeqIO, and JSON::Parse. See the following link for further information (https://www.cpan.org/modules/).

Check installation

Once the installation is complete, users can compare their results with TSV files contained in the above mentioned install_test folder. Please note that some minor differences could be observed in function of the version of EMBOSS that has been installed (e.g. version 5.0.0 or version 6.6.0).