[galaxy-user] blastn: NameError: name 'cmd' is not defined
Hello all,
First of all I would like to thank you guys for developing and mainting this
so useful tool as Galaxy!
I have our own installation fo Galaxy (galaxy-dist version) with
ncbi-blast-plus. Calling blastn results to the following error message:
An error occurred running this job:*Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/tools/ncbi_blast_plus/hide_stderr.py", line
29, in
sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
NameError: name 'cmd' is not defined*
*
*
Could you please explain, what this error can mean?
The link to the shared history is* *
http://dmbcserv.dyndns.org:8080/u/hogart/h/test-of-blast* *
*
*
Thank you in advance!
___
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Re: [galaxy-user] blastn: NameError: name 'cmd' is not defined
Hi Sergei,
This is a bug in the script, I will ask Peter, the author, to look into it.
Thanks!
K
On Thu, Jun 30, 2011 at 12:44 PM, Sergei Ryazansky wrote:
> Hello all,
>
> First of all I would like to thank you guys for developing and mainting
> this so useful tool as Galaxy!
>
> I have our own installation fo Galaxy (galaxy-dist version) with
> ncbi-blast-plus. Calling blastn results to the following error message:
>
> An error occurred running this job:*Traceback (most recent call last):
> File "/home/galaxy/galaxy-dist/tools/ncbi_blast_plus/hide_stderr.py", line
> 29, in
> sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
> NameError: name 'cmd' is not defined*
> *
> *
> Could you please explain, what this error can mean?
> The link to the shared history is* *
> http://dmbcserv.dyndns.org:8080/u/hogart/h/test-of-blast* *
> *
> *
> Thank you in advance!
>
> ___
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org. Please keep all replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/
>
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
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use the Galaxy Development list:
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Re: [galaxy-user] blastn: NameError: name 'cmd' is not defined
Thanks for answer, but I have just updated the galaxy source code and
blastn works fine! Sorry for any inconvenience :)
30.06.2011 22:53, Kanwei Li пишет:
Hi Sergei,
This is a bug in the script, I will ask Peter, the author, to look
into it. Thanks!
K
On Thu, Jun 30, 2011 at 12:44 PM, Sergei Ryazansky
mailto:s.ryazan...@gmail.com>> wrote:
Hello all,
First of all I would like to thank you guys for developing and
mainting this so useful tool as Galaxy!
I have our own installation fo Galaxy (galaxy-dist version) with
ncbi-blast-plus. Calling blastn results to the following error
message:
An error occurred running this job:/Traceback (most recent call last):
File
"/home/galaxy/galaxy-dist/tools/ncbi_blast_plus/hide_stderr.py",
line 29, in
sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
NameError: name 'cmd' is not defined/
/
/
Could you please explain, what this error can mean?
The link to the shared history
is//http://dmbcserv.dyndns.org:8080/u/hogart/h/test-of-blast//
/
/
Thank you in advance!
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
Re: [galaxy-user] blastn: NameError: name 'cmd' is not defined
On Fri, Jul 1, 2011 at 4:35 PM, Sergei Ryazansky wrote: > Thanks for answer, but I have just updated the galaxy source code and blastn > works fine! Sorry for any inconvenience :) It was an error in the wrapper script's error handler, already fixed. Peter ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
