Galaxy Config Questions
Hi, Our lab is in the process of installing a local version of Galaxy on a computer with the following specs: - Mac Pro mid-2012 - OS X 10.8.3 - 2 2.4 GHz Intel Xeon Processors - 6 cores per processor, 12 cores total - 64 GB RAM This installation is meant to be used by a single user. We followed the instructions at http://wiki.galaxyproject.org/Admin/Get%20Galaxy and now have a working version of Galaxy available at localhost:8080, but we have a few questions before using it: 1. We want to use the NGS:Mapping tool 'Map with Bowtie for Illumina' which requires 'bowtie (0.12.7) with bowtie indexes'. Do we simply download the bowtie software, place it into /Users/administrator/galaxy-dist/tools, restart Galaxy, and the tool is available under NGS:Mapping ? 2. Continuing from question #1, does a type of 'package manager' exist for automating the installation of tools and dependencies? Can mercurial accomplish this or is this the purpose of the Tool Shed? 3. What is the purpose of the Galaxy-specific environment file and how is it used? 4. We have two hard drives: drive1 and drive2. Galaxy is installed on drive1 and our data files are on drive2. Will Galaxy know how to find the location of our data files on drive2? Also, will Galaxy know how to write the result of a job to drive2? 5. Does Galaxy come configured with an admin account and, if so, how is it accessed? 6. Does Galaxy use as many hardware resources as possible to execute each job (for example, all 12 cores)? If not, can it be configured to do so? Thank you for your help!
1. We want to use the NGS:Mapping tool 'Map with Bowtie for Illumina' which requires 'bowtie (0.12.7) with bowtie indexes'. Do we simply download the bowtie software, place it into /Users/administrator/galaxy-dist/tools, restart Galaxy, and the tool is available under NGS:Mapping ?
Correct, download the bowtie software, install and verify that it works. Once it does, you can place the binaries (or a symbolic link) to it in the tools dependecy directory (not tools). You need to specify the tools dependency directory in your universe_wsgi.ini file. You can also, see my response to #3. More information: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
2. Continuing from question #1, does a type of 'package manager' exist for automating the installation of tools and dependencies? Can mercurial accomplish this or is this the purpose of the Tool Shed?
Yes and no. Tool Shed is like a package manager, but not. More information here: http://wiki.galaxyproject.org/Tool%20Shed You will still need to install the tools, like bowtie, on your own and not via Galaxy.
3. What is the purpose of the Galaxy-specific environment file and how is it used?
Going off your question one, you could install bowtie anywhere. I think on OSX its /Applications/Bowtie2.app/ or some other locations /opt/bowti2/ etc. Then simply have a reference to using env.sh to setup the correct environmental paths. In your tools dependency folder you would have the following setup: tools_dependecy/bowtie2/1.03/env.sh tools_dependecy/bowtie2/default --> 1.03/ Note: default is a symbolic link to 1.03
4. We have two hard drives: drive1 and drive2. Galaxy is installed on drive1 and our data files are on drive2. Will Galaxy know how to find the location of our data files on drive2? Also, will Galaxy know how to write the result of a job to drive2?
Yes, see universe_wsgi.ini for this. Just update the paths. On OSX it could be /Volumes/someNameOfDrive/folder/on/drive
5. Does Galaxy come configured with an admin account and, if so, how is it accessed?
Yes, see universe_wsgi.ini (admin_users). You need to add an email address of the admin account.
6. Does Galaxy use as many hardware resources as possible to execute each job (for example, all 12 cores)? If not, can it be configured to do so?
You will need to configure your job runners and job workers for this. http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster Enjoy! -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebrenne@uci.edu On Wed, Jun 5, 2013 at 11:22 AM, Nicholas Kline <nxk60@case.edu> wrote:
Hi,
Our lab is in the process of installing a local version of Galaxy on a computer with the following specs:
- Mac Pro mid-2012 - OS X 10.8.3 - 2 2.4 GHz Intel Xeon Processors - 6 cores per processor, 12 cores total - 64 GB RAM
This installation is meant to be used by a single user. We followed the instructions at http://wiki.galaxyproject.org/Admin/Get%20Galaxy and now have a working version of Galaxy available at localhost:8080, but we have a few questions before using it:
1. We want to use the NGS:Mapping tool 'Map with Bowtie for Illumina' which requires 'bowtie (0.12.7) with bowtie indexes'. Do we simply download the bowtie software, place it into /Users/administrator/galaxy-dist/tools, restart Galaxy, and the tool is available under NGS:Mapping ?
2. Continuing from question #1, does a type of 'package manager' exist for automating the installation of tools and dependencies? Can mercurial accomplish this or is this the purpose of the Tool Shed?
3. What is the purpose of the Galaxy-specific environment file and how is it used?
4. We have two hard drives: drive1 and drive2. Galaxy is installed on drive1 and our data files are on drive2. Will Galaxy know how to find the location of our data files on drive2? Also, will Galaxy know how to write the result of a job to drive2?
5. Does Galaxy come configured with an admin account and, if so, how is it accessed?
6. Does Galaxy use as many hardware resources as possible to execute each job (for example, all 12 cores)? If not, can it be configured to do so?
Thank you for your help! ___________________________________________________________ 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/
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Adam Brenner -
Nicholas Kline