Running Time Of Cufflinks On Main Galaxy

Question: Running Time Of Cufflinks On Main Galaxy

5.8 years ago by

Dear Galaxy team, in the last two days I am trying to run Cufflinks on some sam files, but the work is kept in queue. Actually I performed cufflinks on the same files some times ago, but with different parameters and it worked after some hours. Is this a problem due to my new parameters or are the servers currently overused? Thank you for your help Davide Davide Degli Esposti, PhD Epigenetic (EGE) Group International Agency for Research on Cancer Tel. +33 4 72738036 Fax. +33 4 72738322 150, cours Albert Thomas 69372 Lyon Cedex 08 France This message and its attachments are strictly confidential. If you are not the intended recipient of this message, please immediately notify the sender and delete it. Since its integrity cannot be guaranteed, its content cannot involve the sender's responsibility. Any misuse, any disclosure or publication of its content, either whole or partial, is prohibited, exception made of formally approved use

rna-seq cufflinks • 1.0k views

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modified 5.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 5.8 years ago by Davide Degli Esposti • 80

5.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hi Davide, The public Main Galaxy server has been quite busy the last week or so. But it is actually a bit less busy at this time comparatively, so you may have noticed your jobs moving along. The most effective strategy when using the public resource is to queue your jobs then leave them in the grey "waiting to run" state until they complete. Stopping/restarting will effectively move them back to the end of the queue, increasing wait time. There are always some times when Main is busier than others. If your jobs are urgent, a local or cloud instance are the alternatives, with a cloud instance often being the preferred choice for scientific users. Even though a cloud instance does have fees for compute resource through Amazon, the Galaxy portion is of course free and pretty much ready to go, with just a little initial set-up: http://getgalaxy.org http://usegalaxy.org/cloud And while different types of tools run on different resources here, the parameters used for any particular tool would have no effect on how long a job is in queue. Queue times are only dependent on how many people (worldwide) are utilizing the public resources at any given time. Take care, Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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