[mira_talk] Re: specifying working directory without actually cd'ing into it?
- From: Evan <evan@xxxxxxxxxxx>
- To: Leonor Palmeira <mlpalmeira@xxxxxxxxx>
- Date: Thu, 30 Jun 2011 08:05:54 -0700
Except things like modified path variables aren't always easily
accomplishable when using tools like cron/at/make to schedule assemblies.
Hence the request...
On Thu, Jun 30, 2011 at 7:55 AM, Leonor Palmeira <mlpalmeira@xxxxxxxxx>wrote:
> Well, this is exactly the same...
> You just keep your 'mira.bash' script somewhere in your $PATH, and then,
> you just call it with:
>
> mira.bash /some/path <your mira parameters>
>
> Problem solved.
> Wasn't this clear from my previous post?
>
> Leonor.
>
>
> On 30/06/11 16:45, Evan wrote:
>
>> Simply put.... because:
>> -------------------
>> mira --new-pram=/some/path is easier than:
>> -------------------
>> #!/bin/bash
>>
>> dir=$1
>> pars=($*)
>> pars=${pars[@]:1}
>>
>> olddir=`pwd`
>> mkdir $dir
>> cd $dir
>> mira $pars
>> cd $olddir
>> -------------------
>>
>> On Thu, Jun 30, 2011 at 7:26 AM, Leonor Palmeira <mlpalmeira@xxxxxxxxx
>> <mailto:mlpalmeira@xxxxxxxxx>> wrote:
>>
>> On 29/06/11 08:17, Evan wrote:
>>
>> It makes scripting calls to mira a bit cumbersome at times when
>> running
>> a batch of assemblies or wanting a project to run on an ssd drive.
>>
>>
>> Not sure I understand the need for this feature :-)
>> But what don't you embed 'mira' in a small 'mira.bash' script that
>> would look like this (and would hide the 'cd' part away from you).
>> This would allow you to simply launch mira by:
>>
>> ./mira.bash your_directory --fasta --project=project_name [... all
>> your MIRA options...] >& your_directory/log_assembly.__**txt
>>
>> -------------------
>> #!/bin/bash
>>
>> dir=$1
>> pars=($*)
>> pars=${pars[@]:1}
>>
>> olddir=`pwd`
>> mkdir $dir
>> cd $dir
>> mira $pars
>> cd $olddir
>> -------------------
>>
>> Cheers,
>> Leonor.
>>
>>
>> On Jun 28, 2011 5:15 PM, "Bastien Chevreux" <bach@xxxxxxxxxxxx
>> <mailto:bach@xxxxxxxxxxxx>
>> <mailto:bach@xxxxxxxxxxxx <mailto:bach@xxxxxxxxxxxx>>> wrote:
>> > On Jun 27, 2011, at 23:04 , Evan wrote:
>> >> Does anyone know if its possible to run mira from a different
>> directory then where I want the <projectname>_assembly folder to
>> be created?
>> >
>> > No, not at the moment. Is there a special reason why going
>> via "cd"
>> is not wanted?
>> >
>> > B.
>> >
>> >
>> > --
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>> >
>>
>>
>> --
>> Leonor Palmeira, PhD
>>
>> Phone: +32 4 366 42 69
>> Email: mlpalmeira AT ulg DOT ac DOT be
>>
>> http://sites.google.com/site/_**_leonorpalmeira<http://sites.google.com/site/__leonorpalmeira>
>>
>> <http://sites.google.com/site/**leonorpalmeira<http://sites.google.com/site/leonorpalmeira>
>> >
>>
>> Immunology-Vaccinology, Bat. B43b
>> Faculty of Veterinary Medicine
>> Boulevard de Colonster, 20
>> University of Liege, B-4000 Liege (Sart-Tilman)
>> Belgium
>>
>>
>>
> --
> Leonor Palmeira, PhD
>
> Phone: +32 4 366 42 69
> Email: mlpalmeira AT ulg DOT ac DOT be
> http://sites.google.com/site/**leonorpalmeira<http://sites.google.com/site/leonorpalmeira>
>
> Immunology-Vaccinology, Bat. B43b
> Faculty of Veterinary Medicine
> Boulevard de Colonster, 20
> University of Liege, B-4000 Liege (Sart-Tilman)
> Belgium
>
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