Hi Colin

Please keep all replies on the list by using "reply all"


You are aware of the 'download' button (ie the disk icon), aren't-you?

Unless, you have a log-in requiorement for your galaxy server, you can
also use this url to copy the data to a different server with 'wget'.

Or you try to find out the dataset number (eg by setting up 'reports' or
just by looking at the filesystem) and you do an 'scp' to your other server

Regards, Hans




On 06/29/2011 11:58 PM, colin molter wrote:
Hi Hans,
just one more small galaxy question.
I finished the whole process of transforming the data using galaxy. Now i
would like to get these data into my server's filesystem. Something exactly
opposite to the adding of datafile to a datalibrary would be ideal.
(so getting a dataset from the history to the filesystem).

thx for your time,
regards,
colin

2011/6/29 colin molter<colin.mol...@gmail.com>

it finished! and results seems perfect.
it is just very very slow: nearly 10 hours for 25Gb.

it seems that in future version of illumina preprocessed data, there will
be no longer need of the groomer.
thx
colin.


2011/6/29 Hans-Rudolf Hotz<h...@fmi.ch>



On 06/28/2011 07:06 PM, colin molter wrote:

hi hans,
you are right.
it seems that even if i stopped galaxy
(i just stopped the run.sh command)

i still have a job running:
root     10441 97.0  0.0  77496  1772 pts/6    R    11:59 402:48 python
/opt/galaxy-central/tools/**fastq/fastq_groomer.py
/fs1/GenomicsData/ERP0005

it seems that the transformation of a fastq file is taking a lot of time
(it
uses 100%of cpu since 7hours).
does it sound normal?


I am not very familiar with 'fastq_groomer.py' and without knowing the
size of your fasta file, it is impossible to tell.

Have you tried a subset of your fasta file? May be your data is corrupt
resulting in an endless loop?


Hans



  i think i have better to kill that job and to try another way.

i stopped the job and it works
thx.


2011/6/28 Hans-Rudolf Hotz<h...@fmi.ch>

  Hi Colin


  I launched a big job on my local galaxy server (for which I am admin).
The

job was to put local dir in the datalist.
It took too long and i wanted to stop it .... but how?? i failed to
find a
solution.


go to the admin view ->   'Manage jobs' and there you can kill individual
jobs.


  To stop the job i thought that stopping the galaxy running instance
could

make it. (AM I RIGHT?)


possible, but sounds like an 'overkill' to me. I would first try the
'soft'
method described above....and use this only as a last resort.


  Unfortunately, i failed to restart galaxy. I have the following error:



  are you sure you have killed the galaxy process? Since this part of
the
error message tells me that Galaxy (or another service) is still using
the
port number.


  socket.error: (98, 'Address already in use')



How did you stop galaxy?



Regards, Hans







--
Colin Molter
University of Brussels - InSilico Team - http://insilico.ulb.ac.be/




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