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.molter@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<hrh@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<hrh@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/
Hans-Rudolf Hotz wrote:
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
Thanks Hans, FWIW, I have a crummy little script I use to translate encoded/decoded dataset IDs and return datasets' disk paths, attached. Maybe others will find this useful. --nate
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.molter@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<hrh@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<hrh@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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participants (2)
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Hans-Rudolf Hotz -
Nate Coraor