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https://github.com/kdm9/stacks

My changes to Stacks, the reduced representation sequencing assembler and variant caller
https://github.com/kdm9/stacks

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My changes to Stacks, the reduced representation sequencing assembler and variant caller

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README 

        
The Stacks Pipeline

-------------------



0. Prerequisites



Stacks should build on any standard UNIX-like environment (Apple OS X, Linux, 

etc.) Stacks is an independent pipeline and can be run without any additional

external software. 



     Note: Apple OS X does not use the GNU Compiler Collection, which is 

     standard on Linux-based systems. Instead, Apple distributes CLANG, 

     which is a nice compiler but does not yet support the OpenMP library

     which Stacks relies on for parallel processing. Stacks can still be built

     and run on an Apple system, however, you will have to disable building

     with OpenMP (supply the --disable-openmp flag to configure) and use

     non-parallelized code. If you want to install a parallelized version of

     Stacks, you can install GCC by hand, or using a package system such as 

     Homebrew (http://brew.sh/) or MacPorts (http://www.macports.org/).



Several Perl scripts are distributed with Stacks to run the pipeline components and

upload pipeline output to the MySQL database serer. For these to work, you must have

the Perl DBI module installed with the MySQL driver. Most Linux distributions will

include the Perl DBI module, but if not Perl modules are easily installed with the

cpan tool.



1. Install optional components:



The performance of Stacks can be improved by installing two, optional external libraries.

First, to enable reading of BAM files, install Samtools: 



    http://samtools.sourceforge.net/.



    Note: Stacks is not yet compatible with newer Samtools versions that use HTSlib. For

    now, you must use Samtools version 0.1.19, which was the last non-HTSlib version:

       http://sourceforge.net/projects/samtools/files/samtools/0.1.19/



Second, to lower memory usage install Google's SparseHash class.



    http://code.google.com/p/sparsehash/



If you are running a version of Linux, the above software can be installed via the 

package manager. If you are using Ubuntu, you can install the following packages:



% sudo apt-get install libdbd-mysql-perl

% sudo apt-get install libsparsehash-dev

% sudo apt-get install samtools

% sudo apt-get install libbam-dev



A similar set of commands can be executed on a RedHat derived Linux system using yum,

or another package manager on other Linux distributions.



2. Build the software. Stacks uses the standard autotools install:



% tar xfvz stacks_x.xx.tar.gz

% cd stacks_x.xx

% ./configure



You can change the root of the install location (/usr/local/ on most

operating systems) by specifying the --prefix command line option to

the configure script.



% ./configure --prefix=/home/smith/local



You can enable Sparsehash and BAM by adding the following options:



% ./configure --enable-sparsehash --enable-bam



You probably need to specify the BAM library location:



% ./configure --enable-bam \

              --with-bam-include-path=/usr/local/include/bam \

              --with-bam-lib-path=/usr/local/lib



Or, if you installed with Ubuntu packages:



% ./configure --enable-bam \

              --with-bam-include-path=/usr/include/samtools \

              --with-bam-lib-path=/usr/lib



% make



You can speed up the build if you have more than one processor:



% make -j 8



3. Install the software.



% sudo make install



A default Stacks install will install files in the following way:



/usr/local/bin - stacks executables and perl scripts



/usr/local/share/stacks - PHP files for the web interface 

                          and SQL files for creating the 

                          MySQL database



The pipeline is now ready to run. The remaining install instructions are to get the

web interface up and running. The web interface is very useful for visualization and

more or less required for building genetic maps. However, Stacks does not depend on

the web interface to run.



The Stacks Web Interface

------------------------



To visualize data, Stacks uses a web-based interface (written in PHP) that interacts 

with a MySQL database server. MySQL provides various functions to store, sort, and 

export data from a database. For this to work, you must have a PHP-enabled Apache web 

server installed as well as the MDB2 Pear module to provide MySQL interaction.



0. Prerequisites



If you want to export data in Microsoft Excel Spreadsheets, you will need the 

Spreadsheet::WriteExcel Perl module.



Most server installations will provide Apache, MySQL, Perl, and PHP by default. While 

installing these components is beyond these instructions, here are some links that might

be useful:



  1. MySQL Database: http://www.mysql.com/downloads/mysql/

  2. Spreadsheet Perl Module: http://search.cpan.org/~jmcnamara/Spreadsheet-WriteExcel-2.37/

  3. MDB2 Pear Module: http://pear.php.net/package/MDB2/

  4. MDB2 MySQL driver: http://pear.php.net/package/MDB2_Driver_mysql/



(PHP modules are  easily installed with the pear tool. Many operating systems already

 have these tools installed - such as OS X and some Linux distributions. Most Linux systems

 will provide all of these tools as packages that can be installed using yum, apt-get, or a

 similar piece of software.)



1. Edit the MySQL configuration file, installed in

/usr/local/share/stacks/sql/mysql.cnf.dist, to enable access to the

database from the Stacks scripts.



% cd /usr/local/share/stacks/sql/

% cp mysql.cnf.dist mysql.cnf



Edit the file to reflect the proper username, password, and host to

use to access MySQL.



The various scripts that access the database will search for a MySQL

configuration file in your home directory before using the

Stacks-distributed copy. If you already have a personal account set up

and configured (in ~/.my.cnf) you can continue to use these

credentials instead of setting up new, common ones.



If you just installed MySQL and have not added any users, you can do so with these

commands:



% mysql

mysql> GRANT ALL ON *.* TO 'stacks_user'@'localhost' IDENTIFIED BY 'stackspassword';



Edit /usr/local/share/stacks/sql/mysql.cnf to contain the username and password

you specified to MySQL.



(This information was taken from: http://dev.mysql.com/doc/refman/5.1/en/grant.html)



2. Enable the Stacks web interface in the Apache webserver.



Add the following lines to your Apache configuration to make the Stacks PHP

files visible to the web server and to provide a easily readable URL to access

them: 



        Order deny,allow

        Deny from all

        Allow from all

	Require all granted



Alias /stacks "/usr/local/share/stacks/php"



A sensible way to do this is to create the file stacks.conf with the above lines.



If you are using Apache 2.3 or earlier:

---------------------------------------

Place the stacks.conf file in either



/etc/apache2/conf.d/ or /etc/httpd/conf.d/



directory (depending on your Linux distro) and 

restart the apache server:



# vi /etc/apache2/conf.d/stacks.conf

# apachectl restart



(See the Apache configuration for more information on what these do:

http://httpd.apache.org/docs/2.0/mod/core.html#directory)



If you are using Apache 2.4 or later:

---------------------------------------

Place the stacks.conf file in



/etc/apache2/conf-available



directory and then create a symlink to it in the



/etc/apache2/conf-enabled



directory. Then restart Apache. Like so:



# vi /etc/apache2/conf-available/stacks.conf

# ln -s /etc/apache2/conf-available/stacks.conf /etc/apache2/conf-enabled/stacks.conf

# apachectl restart



3. Provide access to the MySQL database from the web interface



Edit the PHP configuration file (constants.php.dist) to allow it access to the 

MySQL database. Change the file to include the proper database

username ($db_user), password ($db_pass), and hostname ($db_host). Rename the 

distribution file so it is active.



% cp /usr/local/share/stacks/php/constants.php.dist /usr/local/share/stacks/php/constants.php

% vi /usr/local/share/stacks/php/constants.php



You may find it advantageous to create a specific MySQL user with limited

permissions - SELECT, UPDATE, and DELETE to allow users to interact

with the database through the web interface.



4. Enable web-based exporting from the MySQL database.



Edit the stacks_export_notify.pl script to specify the email and SMTP

server to use in notification messages.



Ensure that the permissions of the php/export directory allow the

webserver to write to it. Assuming your web server user is 'www':



% chown www /usr/local/share/stacks/php/export