On Thu, Jun 30, 2011 at 7:55 AM, Leonor Palmeira <mlpalmeira@xxxxxxxxx
<mailto: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>
<mailto: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>>
<mailto: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
