[mira_talk] Re: MIRA in bash
- From: Felipe Lira <felipelira3@xxxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Fri, 9 Jan 2015 15:04:17 +0000 (UTC)
Thank you Bob.
Felipe Lira
Spanish National Center of Biotechnology - CNB/ CSIC
Microbial Biotechnology DepartmentFellow of http://obrasocial.lacaixa.es/
Antes de imprimir este mensaje piense bien si es realmente necesario
hacerlo.Before you print this e-mail, think well if it is really necessary.
El Viernes 9 de enero de 2015 15:51, Robert Bruccoleri
<bruc@xxxxxxxxxxxxxxxxxxxxx> escribió:
Dear Felipe,
It's doubtful that Mira can mess up your shell script.
Your first line isn't correct -- you need "#!/bin/sh" (the / is missing).
Also, add -x to get a log of commands and substitutions.
Please ask someone familiar with shell programming if you need more help
--- this doesn't look like a Mira problem.
Good luck! --Bob
On 01/09/2015 09:31 AM, Felipe Lira wrote:
Hello all,
I was trying to run MIRA in a bash script but it stops at the first genome
and don't follow the downstream steps. Any help or suggestions?
The short script that I tried: .... #!bin/sh
samples = " 1 2 3 4 5 "
for s in ${samples} do
time mira manifest_${s} >> log_output
done .......
Felipe Lira
Spanish National Center of Biotechnology - CNB/ CSIC
Microbial Biotechnology Department Fellow of http://obrasocial.lacaixa.es/
Antes de imprimir este mensaje piense bien si es realmente necesario hacerlo.
Before you print this e-mail, think well if it is really necessary.
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