Bioinformatics IT troubleshooting software installations
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Hi all,
Today I will be installing Mysql in the 32-bit system. But there is a problem : ERROR 2002 (HY000): Can’t connect to local MySQL server through socket ‘/var/lib/mysql/mysql.sock’ (2)
For RedHat Linux (Fedora Core/Cent OS)
do the following:
1)To start mysql server:/etc/init.d/mysqld start
2)To stop mysql server:
/etc/init.d/mysqld stop
3) To restart mysql server
/etc/init.d/mysqld restart
Then type mysql and we get a prompt like mysql>
To quit from mysql type : q -
For Bowtie,
First Download the Bowtie and after having done that, type ./bowtie in the command prompt.
Try using one of the commands from Bowtie Manual and it will give an error: “bash:bowtie:command not found”
To resolve this issue, change the path in the .bashrc(~) file in the home directory, since my bowtie was installed in “Sujata” directory,so we save the path like this:
1)PATH=$PATH:/root/Sujata/bowtie-0.12.7
2)export PATH -
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For TopHat installations, keep in mind that we need to install Bowtie and Samtools.
Follow the instructions as given the the url below:
http://tophat.cbcb.umd.edu/tutorial.html
But still there might be error. So , a crude way might be a solution, which is, keep all the files of Samtools and TopHat in the same folder and the Bowtie, which has been already installed , specify the path in .bashrc and run the command for tophat. -
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This is the support forum for sites hosted on WordPress.com. You are referring to a self-hosted WordPress.org install, which is supported here http://wordpress.org/support/
More about the difference between COM and ORG here: http://support.wordpress.com/com-vs-org/
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