Problem with stdin/stdout

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Problem with stdin/stdout

Mariette
Hi everyone,

I'm facing a quite weird problem. We're processing files coming from NGS
so in order to save some disk place (temporary generated files could be
huge), we decided to create ergatis a componant that grep multiple
commande lines, just so we do outside of ergatis.

for exemple, in the iteration xml file we would like to use bwa like this :
   $;BWA_EXEC$; aln $;DATABASE$; $;I_FILE_PATH$; | $;BWA_EXEC$; samse
$;DATABASE$; - $;I_FILE_PATH$; | $;SAMTOOLS_EXEC$; view
$;SAMTOOLS_VIEW_OPTIONS$; - | cut -f 1 -

This works just fine for small samples but doesn't for huge files ...
even if the command line copied in a shell works perfectly !
My first guess would be that as ergatis manage stdin and stdout using
the <param><key>stdout<..> there is something going wrong when making
such a command line.
Could that be the problem ? If yes how to handle it ?

thanks for your reply,
Jerome

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Re: Problem with stdin/stdout

Joshua Orvis

Could you post the XML for one of the resulting <command> elements generated when you do a command such as this?

JO


On Thu, Mar 17, 2011 at 8:21 AM, Mariette <[hidden email]> wrote:
Hi everyone,

I'm facing a quite weird problem. We're processing files coming from NGS
so in order to save some disk place (temporary generated files could be
huge), we decided to create ergatis a componant that grep multiple
commande lines, just so we do outside of ergatis.

for exemple, in the iteration xml file we would like to use bwa like this :
  $;BWA_EXEC$; aln $;DATABASE$; $;I_FILE_PATH$; | $;BWA_EXEC$; samse
$;DATABASE$; - $;I_FILE_PATH$; | $;SAMTOOLS_EXEC$; view
$;SAMTOOLS_VIEW_OPTIONS$; - | cut -f 1 -

This works just fine for small samples but doesn't for huge files ...
even if the command line copied in a shell works perfectly !
My first guess would be that as ergatis manage stdin and stdout using
the <param><key>stdout<..> there is something going wrong when making
such a command line.
Could that be the problem ? If yes how to handle it ?

thanks for your reply,
Jerome

------------------------------------------------------------------------------
Colocation vs. Managed Hosting
A question and answer guide to determining the best fit
for your organization - today and in the future.
http://p.sf.net/sfu/internap-sfd2d
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users


------------------------------------------------------------------------------
Colocation vs. Managed Hosting
A question and answer guide to determining the best fit
for your organization - today and in the future.
http://p.sf.net/sfu/internap-sfd2d
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users