CHASM install

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Contents

Installing for the first time

  • 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 just the SNVBox component, please follow the instructions in the following sections:
    • Installing SNVBox Only
    • Setting up SNVBox Database

Installing CHASM

  1. Please 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
    > export LD_LIBRARY_PATH=$CHASMDIR:$LD_LIBRARY_PATH
    

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

  3. Download and compile PARF
    tar xvzf PARF.tar.gz
    cd PARF
    make
    

    The default compiler specified in the PARF makefile is

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

    For gfortran:

    FC=gfortran
    FFLAGS= -O3 -fno-range-check
    
  4. Copy the PARF executable to the CHASM directory

Installing SNVBox Only

  1. Please download a copy of SNVBox 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 CHASMDIR= (installation directory)/CHASM
    > export LD_LIBRARY_PATH=$CHASMDIR:$LD_LIBRARY_PATH
    

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

Setting up SNVBox Database

  1. Please 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, you can delete the load file to reclaim the space.
  2. As root on MySQL, please 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 'dfltPass!';
    > grant RELOAD on *.* to chasm_user@localhost;
    
  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: dfltPass!
    
  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

Please use the following steps when installing this update over an existing copy:

(Let $CHASMDIR be the absolute path of the existing CHASM Installation directory)

1) Download CHASMDL.tar.gz and copy it to the parent directory of $CHASMDIR

> cp CHASMDL.tar.gz $CHASMDIR/..

2) Back up the following files and folders in your CHASM installation directory $CHASMDIR to an outside folder:

> cd $CHASMDIR
> mv $CHASMDIR/BuiltClassifiers .. 
> mv $CHASMDIR/snv_box.conf ..
> mv $CHASMDIR/chasm_classifiers.conf ..

3) Clean the CHASM Installation Directory $CHASMDIR and extract the contents of the downloaded file

> cd $CHASMDIR/..
> rm -rf $CHASMDIR
> tar xvzf CHASMDL.tar.gz

4) Restore the files/folders backed up in Step (2)

> mv BuiltClassifiers $CHASMDIR
> mv snv_box.conf $CHASMDIR
> mv chasm_classifiers.conf $CHASMDIR

Installing a SNVBox software update over existing version

Please use the following steps when installing this update over an existing copy:

(Let $CHASMDIR be the absolute path of the existing SNVBox Installation directory)

1) Download SNVBOXDL.tar.gz and copy it to the parent directory of $CHASMDIR

> cp SNVBOXDL.tar.gz $CHASMDIR/..

2) Back up the following files and folders in your CHASM installation directory $CHASMDIR to an outside folder:

> cd $CHASMDIR
> mv $CHASMDIR/snv_box.conf ..

3) Clean the CHASM Installation Directory $CHASMDIR and extract the contents of the downloaded file

> cd $CHASMDIR/..
> rm -rf $CHASMDIR
> tar xvzf SNVBOXDL.tar.gz
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