[galaxy-dev] Error message

2013-08-01 Thread Mark Edward Fabreag
Good day!

While I was uploading the file (through FileZilla), I encountered this
message box:
[image: Inline image 1]
Will this affect uploading process?

Thank you.
image.png___
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Re: [galaxy-dev] Error message

2013-08-01 Thread Dannon Baker
It shouldn't, unless the root cause of that error also affected the FTP
transfer.  Does FileZilla say there are any transmission errors?


On Thu, Aug 1, 2013 at 1:16 AM, Mark Edward Fabreag merfabr...@gmail.comwrote:

 Good day!

 While I was uploading the file (through FileZilla), I encountered this
 message box:
 [image: Inline image 1]
 Will this affect uploading process?

 Thank you.

 ___
 Please keep all replies on the list by using reply all
 in your mail client.  To manage your subscriptions to this
 and other Galaxy lists, please use the interface at:
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image.png___
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[galaxy-dev] Error message with terminated jobs

2012-05-01 Thread Christophe Caron

Hi,

We run Galaxy and Sun Grid Engine cluster environment (DRMAA API).

When i start a job (e.g. : blast), the job runs on the cluster, and 
produces results output files. But in the history web interface, the job 
status is in error with this message :


malloc: using debugging hooks
/bin/sh: module: line 1: syntax error: unexpected end of file
/bin/sh: error importing function definition for `module'
malloc: using debugging hooks

Any clue ?

Thanks in advance

--

Christophe Caron

Station Biologique / Service Informatique et Bio-informatique
Place Georges Teissier  29680 Roscoff

Analysis and Bioinformatics for Marine Science
   http://abims.sb-roscoff.fr/

christophe.ca...@sb-roscoff.fr

tél: +33 (0)2 98 29 25 43 / +33 (0)6 07 83 54 77






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[galaxy-dev] ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires a GATK Key file

2012-04-27 Thread Carlos Borroto
It seems like GATK authors at Broad really really want you to phone
home every time you use their software. I'm getting this error while
running the lastest version:
ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option
requires a GATK Key file. Please see
http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home for more
information and instructions on how to obtain a key.

From the Phone_home wiki page:
How to Obtain a GATK Key
To obtain a GATK key, email gsah...@broadinstitute.org with the
subject line GATK Key Request. In your email, please provide us with
the reason(s) you need to run the GATK with the phone-home feature
disabled. Please be as explicit as possible about why you cannot
participate in the phone home feature. Note that the key you will be
issued is linked to the email address you used to contact us.

In general I don't have an issue with phone home features from
software providers I trust, and I do completely trust The Broad
Institute. Although, this does sound a little draconian how is being
imposed.

Nevertheless, I would like to ask for an easier way to deactivate the
use of -et NO_ET on Galaxy GATK's wrappers. Right now I'm manually
commenting the relevant line, but I think this means my mercurial
repository won't get any update from upstream, or that I will have to
deal with merging.

Regards,
Carlos
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