installing tabix on mac os x

first install homebrew (brew.sh)

copied following command into terminal

ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"

scg3.stanford.edu scg3 scg cluster

Rocks 6.0 (Mamba)

Profile built 16:27 16-Aug-2012

Kickstarted 16:32 16-Aug-2012

Welcome to scg3 login node!

2012-01-09 h_vmem request is per slot, not per job

https://web.stanford.edu/group/scgpm/cgi-bin/informatics/wiki/index.php/Scg3_user_guide

This system is for authorized users only.

2014-03-20 imposed new ulimit values on this machine 

           check ulimit -a: about 3.7G max memory per process

2014-05-08 scg3-ln02 is up, use that if this one feels slow

2014-06-02 5PM clean ln01 reboot, sorry for inconvenience

It appears that you have not set up your ssh key.

This process will make the files:

     /home/jmtoung/.ssh/id_rsa.pub

     /home/jmtoung/.ssh/id_rsa

     /home/jmtoung/.ssh/authorized_keys

Generating public/private rsa key pair.

Created directory '/home/jmtoung/.ssh'.

Enter passphrase (empty for no passphrase): 

Enter same passphrase again: 

Your identification has been saved in /home/jmtoung/.ssh/id_rsa.

Your public key has been saved in /home/jmtoung/.ssh/id_rsa.pub.

The key fingerprint is:

16:72:7b:4a:c5:f3:eb:c7:85:8a:cc:87:48:f4:db:d8 jmtoung@scg3-ln01.local

The key's randomart image is:

+--[ RSA 2048]----+

|                 |

|         .       |

|      . o +      |

|       o.+ o     |

|       .S.. .  . |

|       o.o.  .. .|

|       ..+ B.o . |

|        . B.E o  |

|           ...   |

+-----------------+

converting illumina kgp IDs to rs http://rpubs.com/Felix/9686

http://rpubs.com/Felix/9686

installing RMySQL on R

1. in R studio, run 'install.packages("RMySQL")'

also installing the dependency ‘DBI’

trying URL 'http://cran.rstudio.com/bin/macosx/contrib/3.0/DBI_0.2-7.tgz'
Content type 'application/x-gzip' length 270877 bytes (264 Kb)
opened URL
==================================================
downloaded 264 Kb

trying URL 'http://cran.rstudio.com/bin/macosx/contrib/3.0/RMySQL_0.9-3.tgz'
Content type 'application/x-gzip' length 2189176 bytes (2.1 Mb)
opened URL
==================================================
downloaded 2.1 Mb


The downloaded binary packages are in
/var/folders/gg/lmctk_xj7yd624447p6ghmnr0000gq/T//Rtmp8IiGaQ/downloaded_packages

installing mysql

1. downloaded mysql package from website

• google 'mysql community download'
• downloaded Mac OS X 10.7 (x86, 64-bit), DMG Archive
• (mysql-5.6.15-osx10.7-x86_64.dmg)
• installed 'mysql-5.6.15-osx10.7-x86_64.pkg' and 'MySQLStartupItem.pkg' and MySQL.prefPane

2. added /usr/local/mysql/bin to path:

• sudo nano /etc/paths

3. change the root password

• mysql -u root
• mysql> SET PASSWORD FOR 'root'@'localhost' = PASSWORD('******');
• Query OK, 0 rows affected (0.00 sec)

 4. added user jmtoung

• mysql> mysql> CREATE USER 'jmtoung'@'localhost' IDENTIFIED BY '*******';
• Query OK, 0 rows affected (0.00 sec)
• mysql> GRANT ALL PRIVILEGES ON * . * TO 'jmtoung'@'localhost';
• Query OK, 0 rows affected (0.00 sec)

5. install MySQL for python

• downloaded MySQL-python-1.2.4b4
• tar xzvf " "
• python setup.py build &> setup-build.log

6. fixed library issue

• [jmtoung@dn2m1i7oq:/usr/lib]: sudo ln -s /usr/local/mysql/lib/libmysqlclient.18.dylib /usr/lib/libmysqlclient.18.dylib

ssh without password

Step 1

 sys-jmtoung-mbr:Data jmtoung$ ssh-keygen -t rsa

Generating public/private rsa key pair.

Enter file in which to save the key (/Users/jmtoung/.ssh/id_rsa): 

Enter passphrase (empty for no passphrase): 

Enter same passphrase again: 

Your identification has been saved in /Users/jmtoung/.ssh/id_rsa.

Your public key has been saved in /Users/jmtoung/.ssh/id_rsa.pub.

The key fingerprint is:

c4:14:ed:6f:fd:d2:93:2d:e7:f7:f5:64:8c:58:d0:6a jmtoung@sys-jmtoung-mbr.local

The key's randomart image is:

+--[ RSA 2048]----+

|        oo       |

|       o  .  .   |

|        o.  . .  |

|       .  .  o   |

|        S  .E..  |

|           .oo.o |

|           .. .oB|

|              o=O|

|               =B|

+-----------------+

Step 2

sys-jmtoung-mbr:Data jmtoung$ cat ~/.ssh/id_rsa.pub | ssh jmtoung@buttelab-phi1.stanford.edu "cat - >> ~/.ssh/authorized_keys"

Step 3

[jmtoung@buttelab-phi1 .ssh]$ chmod 0600 authorized_keys