Stacks on Ubuntu 14.04 LTS

install dependencies:

  apt-get install build-essential zlib1g-dev vim
  apt-get install libsparsehash-dev mysql-server php5 apache2 php-mdb2 php-mdb2-driver-mysql libdbd-mysql-perl samtools libbam-dev

for ease of compilation, symlink sparsehash to /usr/local/include:

  sudo ln -s /usr/include/google /usr/local/include/sparsehash

get stacks:

  wget http://creskolab.uoregon.edu/stacks/source/stacks-1.21.tar.gz

untar stacks:

  tar -xzvf stacks-1.21.tar.gz && cd stacks-1.21

configure stacks:

  ./configure \
          --enable-sparsehash \
          --enable-bam \
          --with-sparsehash-include-path=/usr/local/include \
          --with-bam-include-path=/usr/include/samtools \
          --with-bam-lib-path=/usr/lib

compile stacks:
```
  make
```
install stacks:
```
  sudo make install
```
add a mysql superuser for stacks_user (replace 'some_pass' with your password) by logging in (use password you created during apt-get above):
```
  mysql -u root -p
```

create a stacks user and give local privileges on all databases (replace 'some_pass' with your password):

  mysql> CREATE USER 'stacks_user'@'localhost' IDENTIFIED BY 'some_pass';
  mysql> GRANT ALL PRIVILEGES ON *.* TO 'stacks_user'@'localhost' WITH GRANT OPTION;

logout:
```
  mysql> \q
```

fill in the mysql configuration parameters:

  cd /usr/local/share/stacks/sql/
  sudo cp mysql.cnf.dist mysql.cnf
  sudo vim mysql.cnf

make the mysql.cnf file look like the following (replace 'some_pass' with your password):
```
  [client]
  user=stacks_user
  password=some_pass
  host=localhost
  port=3306
```

fill in the php configuration parameters:

  cd /usr/local/share/stacks/php
  sudo cp constants.php.dist constants.php
  sudo vim constants.php

make the constants.php file look like the following (replace 'some_pass' with your password):

  //
  // Credentials to access Stacks MySQL databases
  //
  $db_user     = "stacks_user";
  $db_pass     = "some_pass";
  $db_host     = "localhost";

change the permissions on the stacks export folder:

  cd /usr/local/share/stacks/php/
  sudo chown www-data /usr/local/share/stacks/php/export

add a fully-qualified domain name config file for apache2:
```
  sudo vim /etc/apache2/conf-avaialable/fqdn.conf
```
edit the file to contain the following:
```
  ServerName localhost
```
enable this fqdn file:
```
  sudo a2enconf fqdn
```

add a virtual host entry for stacks:

  sudo vim /etc/apache2/sites-available/stacks.conf

paste the following into that new file:

  <VirtualHost *:80>
          DocumentRoot /var/www/html

          # Available loglevels: trace8, ..., trace1, debug, info, notice, warn,
          # error, crit, alert, emerg.
          # It is also possible to configure the loglevel for particular
          # modules, e.g.
          #LogLevel info ssl:warn

          ErrorLog ${APACHE_LOG_DIR}/error.log
          CustomLog ${APACHE_LOG_DIR}/access.log combined

          <Directory "/usr/local/share/stacks/php">
          Require all granted
          </Directory>

          Alias /stacks "/usr/local/share/stacks/php"
  </VirtualHost>

disable the default virtual host file:
```
  sudo a2dissite 000-default
```
enable the new virtual host file:
```
  sudo a2ensite stacks
```
reload the apache configuration to pick up the new changes:
```
  service apache2 reload
```
visit:
```
  http://localhost/stacks
```

brantfaircloth/stacks-config.md

Stacks on Ubuntu 14.04 LTS

khaled8523 commented Aug 4, 2017