Short-term access to a galaxy server for teaching
Hi, We would like to use Galaxy to introduce genomic analysis in our introductory graduate genetics course. Would anyone be willing to let us "borrow" a server for two hours (9-11 am Boston time, Sept 25)? The students will be uploading ~1M 30-bp reads, running QC and trimming barcodes, using BOWTIE to align them to the yeast genome and then MACS to call peaks. There will be about 40 users total. Each task runs quickly on the public server, but we are concerned about the queue times when dealing with a 90-min class. Thank you for any help or advice, best Max
Hi Max, An alternative approach, in case that becomes necessary, would be to set up your own temporary instance of Galaxy in the Amazon Web Services (AWS) Cloud as described at http://wiki.galaxyproject.org/CloudMan. Another Cloud-based option: if interested in installing Galaxy on an auto-scaling HPC cluster in the AWS Cloud from the "command line", I can provide the instructions to do so. The instructions were designed to allow those with access to a browser on a Linux, Mac or Windows [1] system and minimal computing experience perform the installation. Time to get Galaxy up and running using this method is estimated at one to two hours. Good luck! Notes: 1. Will require installation of Putty or similar program for secure access to the AWS virtual machine, 2. Both options mentioned above could be overkill, although eminently feasible, if all you need is Galaxy running on a single server, 3. Additional options are listed at http://wiki.galaxyproject.org/Big%20Picture/Choices -- Srinivas Maddhi Senior Systems Administrator Iowa Institute for Human Genetics ITS Research Services, The University of Iowa -----Original Message----- From: Max Heiman <heiman@genetics.med.harvard.edu> Date: Thursday, July 11, 2013 9:16 AM To: "galaxy-dev@bx.psu.edu" <galaxy-dev@bx.psu.edu> Subject: [galaxy-dev] Short-term access to a galaxy server for teaching
Hi,
We would like to use Galaxy to introduce genomic analysis in our introductory graduate genetics course. Would anyone be willing to let us "borrow" a server for two hours (9-11 am Boston time, Sept 25)?
The students will be uploading ~1M 30-bp reads, running QC and trimming barcodes, using BOWTIE to align them to the yeast genome and then MACS to call peaks. There will be about 40 users total. Each task runs quickly on the public server, but we are concerned about the queue times when dealing with a 90-min class.
Thank you for any help or advice,
best Max ___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Here's a cloud image that the Galaxy team often uses for workshops: http://wiki.galaxyproject.org/CloudWorkshop Good luck, J. On Jul 11, 2013, at 1:28 PM, Maddhi, Srinivas wrote:
Hi Max,
An alternative approach, in case that becomes necessary, would be to set up your own temporary instance of Galaxy in the Amazon Web Services (AWS) Cloud as described at http://wiki.galaxyproject.org/CloudMan.
Another Cloud-based option: if interested in installing Galaxy on an auto-scaling HPC cluster in the AWS Cloud from the "command line", I can provide the instructions to do so. The instructions were designed to allow those with access to a browser on a Linux, Mac or Windows [1] system and minimal computing experience perform the installation. Time to get Galaxy up and running using this method is estimated at one to two hours.
Good luck!
Notes: 1. Will require installation of Putty or similar program for secure access to the AWS virtual machine, 2. Both options mentioned above could be overkill, although eminently feasible, if all you need is Galaxy running on a single server, 3. Additional options are listed at http://wiki.galaxyproject.org/Big%20Picture/Choices
-- Srinivas Maddhi Senior Systems Administrator Iowa Institute for Human Genetics ITS Research Services, The University of Iowa
-----Original Message----- From: Max Heiman <heiman@genetics.med.harvard.edu> Date: Thursday, July 11, 2013 9:16 AM To: "galaxy-dev@bx.psu.edu" <galaxy-dev@bx.psu.edu> Subject: [galaxy-dev] Short-term access to a galaxy server for teaching
Hi,
We would like to use Galaxy to introduce genomic analysis in our introductory graduate genetics course. Would anyone be willing to let us "borrow" a server for two hours (9-11 am Boston time, Sept 25)?
The students will be uploading ~1M 30-bp reads, running QC and trimming barcodes, using BOWTIE to align them to the yeast genome and then MACS to call peaks. There will be about 40 users total. Each task runs quickly on the public server, but we are concerned about the queue times when dealing with a 90-min class.
Thank you for any help or advice,
best Max ___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (3)
-
Jeremy Goecks -
Maddhi, Srinivas -
Max Heiman