.sh script to run in the shell(qsub)

Theory behind mothur
1

Dear colleagues,

I’m new to bioinformatics and mothur. I’m learning from the official website. I’m using mothur on the server (shell) and the dist.seqs command is taking too long and my internet is not good (it’s disconnecting all the time). I would like some help to build a .sh script to run with the qsub command. I saw some scripts on the internet, but I did not understand. Any suggestion? I apologize for the silly question and thank you all for your attention.

Best Regards,

2

check with your server people because there are a number of flavors of qsub. You’ll need to write a batch file with all your commands (mine is https://github.com/krmaas/bioinformatics/blob/master/mothur.batch but if you have 1.39 take out the summary.tax at the end because I need to fix it to work with 1.39). You’ll put all the server info in your qsub then the command you want to run is

mothur mothur.batch