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.

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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