########################################################################################## # # # Software : SCRATCH-1D (SCRATCH Suite of One-Dimensional Predictors) # # Release : 1.3 (Dec 2020) # # # # Author(s) : Christophe Magnan (cmagnan@ics.uci.edu) # # Copyright : Institute for Genomics and Bioinformatics # # University of California, Irvine # # # ########################################################################################## SCRATCH-1D Version 1.3 - Installation Guide =========================================== Operating systems compatibility and requirements ================================================ SCRATCH-1D package should be compatible with any Unix-based operating system but may require a few additional installation steps in some cases, see below. If a problem occurs during the installation or if SCRATCH-1D is not running properly, please read the information reported below about the possible problems that may occur with SCRATCH-1D or contact us (pfbaldi@ics.uci.edu). 1) Blast software The 32 bit linux version of blast is provided by default in the 'pkg' sub-folder of the package but can, probably should, and in some cases has to be replaced by the 64 bit or Mac OS version of the blast software for improved performances and compatibility on such systems. Compiled versions of blast are available here: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/ replace the version provided in the package by the downloaded one without changing the installation folder name (even the release number). 2) 1D-BRNN software 1D-BRNN source code is compiled during the installation process using gcc compiler. This part of the installation assumes you have a relatively recent version of gcc installed on your system (it should be the case on most linux distributions). If this is not the case, you can either install gcc compiler on your system or modify the provided makefile (pkg/1D-BRNN_3.3/src/makefile) to replace gcc by the compiler of your choice. 3) Perl installation Most scripts in SCRATCH-1D are written in perl. These scripts assume perl is installed in the default location for linux operating systems: /usr/bin/perl If perl is not installed in this folder of your system, please create a symlink to your perl installation in /usr/bin. Package installation on Linux systems ===================================== To install SCRATCH-1D, unarchive the downloaded tarball : tar -xvzf SCRATCH-1D_1.3.tar.gz Change directory to the resulting folder : cd SCRATCH-1D_1.3 Run the provided installation script : perl install.pl Due to various dependencies, installation will be static, i.e. once installed the software will need to remain wherever it was installed. The root folder of the software (SCRATCH-1D_1.3) can be renamed before installation and the package can be installed anywhere but its location after installation must not be changed without re-installing the software using the provided installation script. Scripts can however be called from anywhere on your system as long as the permissions are correctly set. Note also that the 'tmp' folders in the package must not be removed or renamed as they are used by the various predictors and tools to store intermediate files during a run. Temporary files are removed after each run and several instances of SCRATCH-1D can run simultaneously. Testing SCRATCH-1D installation =============================== To test the software installation, change directory to the 'doc' sub-folder : cd /doc Run SCRATCH-1D on the provided test dataset: ../bin/run_SCRATCH-1D_predictors.sh test.fasta test.out 4 (if your computer has less than 4 cores, replace 4 by 1 in the command line above) The 4 output files: - test.out.ss - test.out.ss8 - test.out.acc - test.out.acc20 should respectively be identical to the provided files : - test.hom.ss - test.hom.ss8 - test.hom.acc - test.hom.acc20 The most common issue encountered by users of the previous SCRATCH-1D releases comes from the incompatibility between the blast binaries delivered with SCRATCH-1D and the operating system used to run the software. The blast binaries provided by default in this package are not compatible with any type of operating system so in many cases these binaries need to be replaced by the ones specifically compiled for the given operating system, see instructions on top of this file. Program Usage ============= The documentation of the software is available in the "doc" sub-folder. Enjoy!