CHASM install

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Contents

Installation Instructions

  • Please ensure that your machine satisfies all necessary System Prerequisites.
  • If you are installing the full CHASM system, please follow the instructions in the following sections:
    • Installing CHASM
    • Setting up SNVBox Database
  • If you are installing VEST, please follow the instruction in the following sections:
    • Installing VEST
    • Setting up SNVBox Database
  • If you are installing just the SNVBox component, please follow the instructions in the following sections:
    • Installing SNVBox Only
    • Setting up SNVBox Database

Installing CHASM

  1. Download the CHASM install pack and extract the files to a location of your choice:
    > tar xvzf CHASMDL.tar.gz
    
  2. Set up system parameters (If you are using bash, please add the following commands to .bashrc):
    > export CHASMDIR=(installation directory)/CHASM
    

    If not, please add the equivalent commands to the appropriate profile script for the shell that you are using.
    NOTE: If using the export command make sure there are no spaces! (For example, export CHASMDIR = /home/me/CHASM will fail because there are spaces on either side of the = symbol.

  3. Test CHASM
    CHASM uses the PARF fortran90 implementation of Random Forest for classifier construction. The compiled PARF executable is distributed with CHASM for user convenience. If the PARF executable included with CHASM does not run on your system, you will need to download the PARF source and compile it. To test whether PARF is working properly:
    cd $CHASMDIR
    ./parf 
    

    If PARF is running properly, you should see the PARF help message. If you see the following, you will need to recompile PARF. See the section Compiling PARF below.

    $ ./parf: cannot execute binary file
    

Installing VEST

  1. Download the VEST install pack and extract the files to a location of your choice:
    > tar xvzf VESTDL.tar.gz
    
  2. Set up system parameters (If you are using bash, please add the following commands to .bashrc):
    > export VESTDIR=(installation directory)/VEST
    

    If not, please add the equivalent commands to the appropriate profile script for the shell that you are using.
    NOTE: If using the export command make sure there are no spaces! (For example, export VESTDIR = /home/me/VEST will fail because there are spaces on either side of the = symbol.

  3. Test VEST
    VEST uses the PARF fortran90 implementation of Random Forest for classifier construction. The compiled PARF executable is distributed with VEST for user convenience. If the PARF executable included with VEST does not run on your system, you will need to download the PARF source and compile it. To test whether PARF is working properly:
    cd $VESTDIR
    ./parf 
    

    If PARF is running properly, you should see the PARF help message. If you see the following, you will need to recompile PARF. See the section Compiling PARF below.

    $ ./parf: cannot execute binary file
    

Installing SNVBox Only

Only install code to retrieve features from the SNVBox.

  1. Please download a copy of snvGet (SNVBox interface code) and extract the files to a location of your choice.
  2. Set up system parameters (If you are using bash, please add the following commands to .bashrc):
    > export SNVBOXDIR= (installation directory)/SNVBox
    

    If not, please add the equivalent commands to the appropriate profile script for the shell that you are using.

Setting up SNVBox Database

  1. Download a copy of the latest SNVBox MySQL database. Warning: this is a large file and will require ~ 45 Gigabytes of space for the file and the loaded mysql database will also require ~40 Gb. After the database is loaded (may take several hours), you can delete the load file to reclaim the space.
  2. Create a database named "CHASM" and a user to access this database:
  3. > create database CHASM
    > grant ALL Privileges on CHASM.* to chasm_user@localhost identified by 'password';
    > grant RELOAD on *.* to chasm_user@localhost;
    

    Note: The database name can be anything, so long as it matches the database name specified in the snv_box.conf file in the CHASM install directory.

  4. On the commandline, please load the download dump file of SNVBox schema/data
  5. > gunzip < [Dump-filename].sql.gz | mysql -u chasm_user -p CHASM
    Password: password
    
  6. Please enter the correct MySQL information in the configuration file snv_box.conf (located in (Installation directory)/CHASM if you did the full CHASM installation or (Installation directory)/SNVBOX if you only installed SNV-Box): (Note: If default options are used and you are running SNV-Box on localhost, this file does not need to be edited):
  7. ; SNVBox configuration file
    ; Contains the Database specifications
    
    ; Database specifications
    chasmDB=[SNVBox MySQL Database name]
    db.user=[MySQL username]
    db.password=[MySQL password]
    db.host=[MySQL Server location]
    db.port=[MySQL Server port number]
    

Installing a CHASM software update over existing version

When updating CHASM, either install the updated version in a new directory, or backup the BuiltClassifiers directory, snv_box.conf and chasm_classifiers.conf files and restore the after unzipping the new CHASMDL.tar.gz file.

Installing a SNVBox software update over existing version

When installing an update to the snvGet (SNVBox interface code) either install the updated version in a new directory, or backup the snv_box.conf configuration file and restore after installing the new code.

Compiling PARF

Only necessary if parf binary does not run on your system.

Download and compile PARF

tar xvzf PARF.tar.gz
cd PARF
make

The default compiler specified in the PARF makefile is the Intel fortran compiler. This is a commericial compiler. If you do not already have it installed on your system, we suggest that you use the free gnu gcc fortran compiler gfortran. WARNING: some versions of gfortran (such as 4.6.1) have a bug and will not compile parf. We have succesfully compiled parf with gfortran 4.1.2 and gfortran 4.4.1.

To change the default fortran compiler, change the following lines in the makefile:

FC = /opt/intel/fce/9.1.039/bin/ifort
FFLAGS = -g -CB -traceback --static

For example, to use gfortran as the compiler:

FC = gfortran
FFLAGS = -O3 -fno-range-check

Copy the compiled PARF to the CHASM directory:

cp parf $CHASMDIR/

Python MySQLdb Module

$ gunzip MySQL-python-1.2.3.tar.gz
$ tar -xvf MySQL-python-1.2.3.tar
$ cd MySQL-python-1.2.3
$ python setup.py build
$ python setup.py install
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