Galaxy Config Questions

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Galaxy Config Questions

Nicholas Kline
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!
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Re: Galaxy Config Questions

Adam Brenner
> 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/
[hidden email]


On Wed, Jun 5, 2013 at 11:22 AM, Nicholas Kline <[hidden email]> 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/
>
> 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/