EST-PAC Installation Instructions for Mac OS X

Once you have downloaded the scripts (here), you can follow this instructions to make EST-PAC working on your machine.

Step 1:

Installation of Mysql, PHP and Apache :

As the originally shipped PHP does not come with the possibility of displaying GD image, one have to download and install MySQL and PHP packages:

MySQL
- Get the correct DMG (standard 5.0) here
And the Installation instructions are here
- Install the MySQLStartupItem.pkg if you want to start MySQL at Startup
and don't forget to install the Mysql preference panel (MySQL.prefPane) by double click on it.

After having installed MySQL, it is recommended (by the MySQL team), to run the mysql_secure_installation script,
you should use this version as the original script did not update the root password with the OLD_PASSWORD function.

To do so
- download the file, then move it to /usr/local/mysql/bin/ by typing in the same Terminal you used for installing MySQL
  sudo mv /Where you have downloaded/mysql_secure_installation_old /usr/local/mysql/bin/mysql_secure_installation_old
  - Your administrator password will be needed here
- Change the ownership and permissions rights
  sudo chown root bin/mysql_secure_installation_old
  sudo chgrp wheel bin/mysql_secure_installation_old
  sudo chmod 755 bin/mysql_secure_installation_old
- run it also from the same Terminal
  sudo bin/mysql_secure_installation_old
  And follow the instructions appearing on the screen
PHP
- Get the latest version of PHP here
- Then follow the instructions provided on the web page
Apache
- The apache distributed by Mac work fine, nothing need to be done at this point

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Step 2:

Modification of MySQL, PHP and Apache:

MySQL

To be on the safe side stop MySQL by using the Preferences Panel, then proceed as described above
- As the package used to install MySQL doesn't contain a configuration file (my.cnf or my.ini), one need to create one.
  The values contain in this configuration file depends a lot your system. To do so type in Terminal if:
  - Your system has little memory (<= 64M) where MySQL is only used from time to time.
    sudo cp /usr/local/mysql/support-files/my-small.cnf /usr/local/mysql/data/my.cnf
  - Your system has little memory (32M - 64M) where MySQL plays an important part.
    sudo cp /usr/local/mysql/support-files/my-medium.cnf /usr/local/mysql/data/my.cnf
  - Your system has 512M where the system runs mainly MySQL.
    sudo cp /usr/local/mysql/support-files/my-large.cnf /usr/local/mysql/data/my.cnf
  - Your system has 1G-2G where the system runs mainly MySQL.
    sudo cp /usr/local/mysql/support-files/my-huge.cnf /usr/local/mysql/data/my.cnf
- Once the appropriate file have been copied, one should modify the file in order to make the innodb table type working.
  To do so type in terminal (admin password will be needed):
  - sudo su
    pico /usr/local/mysql/data/my.cnf
  Then in the pico Terminal, scroll down until you found these lines:
```
# Uncomment the following if you are using InnoDB tables
#innodb_data_home_dir = /usr/local/mysql/data/
#innodb_data_file_path = ibdata1:2000M;ibdata2:10M:autoextend
#innodb_log_group_home_dir = /usr/local/mysql/data/
#innodb_log_arch_dir = /usr/local/mysql/data/
# You can set .._buffer_pool_size up to 50 - 80 %
# of RAM but beware of setting memory usage too high
#innodb_buffer_pool_size = 384M
#innodb_additional_mem_pool_size = 20M
# Set .._log_file_size to 25 % of buffer pool size
#innodb_log_file_size = 100M
#innodb_log_buffer_size = 8M
#innodb_flush_log_at_trx_commit = 1
#innodb_lock_wait_timeout = 50
```
  Then uncomment lines 2-5, 8-9, and 11-14 to get something like that:
```
# Uncomment the following if you are using InnoDB tables
innodb_data_home_dir = /usr/local/mysql/data/
innodb_data_file_path = ibdata1:2000M;ibdata2:10M:autoextend
innodb_log_group_home_dir = /usr/local/mysql/data/
innodb_log_arch_dir = /usr/local/mysql/data/
# You can set .._buffer_pool_size up to 50 - 80 %
# of RAM but beware of setting memory usage too high
innodb_buffer_pool_size = 384M
innodb_additional_mem_pool_size = 20M
# Set .._log_file_size to 25 % of buffer pool size
innodb_log_file_size = 100M
innodb_log_buffer_size = 8M
innodb_flush_log_at_trx_commit = 1
innodb_lock_wait_timeout = 50
```

Then to set the permissions correctly type:
sudo chown -R mysql /usr/local/mysql/data/
If someone find a value to be changed, please contact Yvan Strahm

PHP

In the file php.ini, normally located here: /usr/local/php/lib/php.ini, everything after a semi-colon " ; " will NOT be read by PHP.
To edit this file type in Terminal:

sudo pico /usr/local/php/lib/php.ini

Then change the following lines:

Change the line: short_open_tag = Off to
short_open_tag = On
Change the line: allow_call_time_pass_reference = Off to
allow_call_time_pass_reference = On

You will have to decide:

How long you will let PHP run to execute a script. To do so change the number of second at this line
max_execution_time = 30
to something bigger like 300 or even 3600
How much memory a script can consume at:
memory_limit = 64
Change 64M to something more close to 512M (depending of your machine's RAM)

In order to debug problems, it is wise to change these lines:

error_reporting = E_ALL to
error_reporting = E_ALL & ~E_NOTICE
display_errors = Off todisplay_errors = On
; error_log = filename could be something like that
error_log = /var/log/php_errorsThe name "php_errors" could be replaced by something of your choice.

If you plan to upload big file you should change these line

post_max_size = 8M to post_max_size = 80M
upload_max_filesize = 2M to upload_max_filesize = 80M

Here some minor changes

magic_quotes_gpc = Off to magic_quotes_gpc = ON
dbx.colnames_case = "lowercase" to dbx.colnames_case = "unchanged"
Remove the ; form session.save.path line
ession.gc_dvisor = 1000 to session.gc_dvisor = 100
session.bug_compat_42 = 0 session.bug_compat_42 = 1

Apache

If you used the disk image provided by entropy.ch you shouldn't make any changes in the apache configuration. Otherwise:

You have to change (uncommented) the lines concerning the PHP module in /private/etc/httpd/httpd.conf
- Open a Terminal window, go to Application -> Utilities -> Terminal.
- To become superuser type: sudo su and your password (you need to have administrator rights).
- Open httpd.conf in a neutral text editor: nano /etc/httpd/httpd.conf
- In the nano window, press Control W followed by php4 return. It will bring you to this line #LoadModule php4_module libexec/httpd/libphp4.so . Remove the pound sign if any.
- Re-press Control W and type php4 until your reach this line: #AddModule mod_php4.c. Here again remove the pound sign if any.
- Go to System Preference -> Sharing and under Service tick Personal Web Sharing to start apache
- Open your favourite browser and type: http://127.0.0.1/~yourname and if everything is fine you will see a web page.
But depending of the job's type Apache need to be tune up
- Change the TimeOUT value to 3600 from 300

If someone find a value to be changed, please contact Yvan Strahm

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Step 3:

Modification of EST-PAC scripts:

First, you have to rename the correct config file:

In your case rename the file config.inc.php in the folder est-pac/inc/ as follow:

config.inc.php.MAC to config.inc.php

Now you have to edit it

Line 7:
Replace "your name" by the user name hosting the est-pac. In my case it is $config['install_dir'] = '/Users/yvan/Sites/est-pac/';
Lines 12 and 13:
Replace DB1 and/or delete DB2 by the name of your database, the username and the password shouldn't be modified as they are used by the scripts to connect the database
Line 16:
One can blast locally if the value of $config['blast_local'] = 1 if set to 0 Blast Job are send to NCBI.
Line 22:
Change the "db_name" by the name of the database you formatdb your self (see formatdb note). For example if you formatted two dbs, ecoli.nt and sts like This:
formatdb -o T -p F -i ecoli.nt -n ecoli.nt
formatdb -o T -p F -i sts -n sts
Then this line will look like that: $config['blast_databases'] = array('sw/ncbi/db/ecoli.nt' , 'sw/ncbi/db/sts');

Secondly, You have to edit the line 24 in inc/db.inc.php

By deleting the starting # from line 24 in the file /inc/db.inc.php

# $server = $server .":localhost:/private/tmp/mysql.sock";
becomes
$server = $server .":localhost:/private/tmp/mysql.sock";
This line indicates where PHP can find the socket for MySQL. You can also fix this problem by using the Apple recipe here

data folder

First you have to give the folder data the correct user / group and permission combination. Type in Terminal:
- sudo su
chown -R "your name" /Users/"your login name"/Sites/est-pac/data
chgrp -R www /Users/"your login name"/Sites/est-pac/data
chmod 775 /Users/"your login name"/Sites/est-pac/data

Download Blast executables and database

Executable

Download from NCBI the BLASTALL programs. Look for the blast-x.x.xx-ppc32-macosx.tar.gz file.
Put them in the est-pac/sw/ncbi/ directory, then untar them (just double click them!)
Make sure that you put the content of the newly create directory (BlastX.x.x) into the est-pac/sw/ncbi/ directory and not in est-pac/sw/ncbi/BlastX.x.x/!

Databases

From NCBI download the database you are interested in, for example: ecoli.nt.gz
Move the downloaded file in est-pac/sw/ncbi/db/
In Terminal type
- cd /Users/"your login name"/Sites/est-pac/sw/ncbi/db
gunzip -c ecoli.nt.gz |../bin/formatdb -o T -p F -i stdin -t ecoli.nt -n ecoli.nt . This command is for a nucleotide db! If you want to formatdb proteinic sequences type formatdb -o T -p T -i ecoli.aa -n ecoli.aa
Note: Use the -o T option only if the ID line (after>) is UNIQUE, otherwise don't use it
The name after the -n option should be put in this line in the config.inc.php file.
For the one interested this page could be interesting ....

Download HMMER and PFAM database

Download HMMER in est-pac/sw/hmmer/.
Untar put them in the est-pac/sw/hmmer/ directory
Make sure that you put the content of the newly create directory (hmmer-x.x.x) into the est-pac/sw/hmmer/ directory
Download Pfam_ls into /Sites/est-pac/hmmer/db/ and untar it

Download ESTScan

Download this already compiled version of ESTScan
Unzip it in the est-pac/sw/ directory

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Before trying to open a web browser in order to connect the database, it could be helpful if you start the program "Console" located in Utilities.
Then open the log /var/log/httpd/error.log. One gets useful hints here when things go wrong

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In order to test the installation, type in your browser this URL:

http://127.0.0.1/~your Mac OS X username/est-pac/login.php

This window will appears where you will have to enter your MySQL admin login and password, then hit submit me!

then you will see this:

Enter root as Username and root as Password, choose the database you want to enter,

and hit Login, et voilà!

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Running the jobs controller

In Terminal type

cd /Users/Your Login Name/Sites/est-pac
then followed by this command: php job_runners_start.php folowed by the database's name you are working with, if it is DB1 it will be :
php job_runners_start.php DB1

If you get this error message

Can't connect to local MySQL server through socket '/tmp/mysql.sock' (61)

Be sure you uncomment line 24 in inc/db.inc.php (See step 3)

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