Galaxy and Torque

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Galaxy and Torque

Yip, Miu ki
Hi all,

Is Torque still supported as a resource manager?

This page ( https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ) mentioned the usage of Torque and how to set it up. However, the setup instructions refer to a /script/scramble.py file which I assume interfaces with eggs. If I recall correctly, eggs were upgraded to wheels. Does this mean there are upgraded scripts in place of scramble.py and the eggs.ini?

I saw this page ( https://biostar.usegalaxy.org/p/20470/ ) and it looks like nobody has a solution to this.

Thanks!
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Re: Galaxy and Torque

cganote@iu.edu
Hi Miuki,

There's definitely a bit of out of date info on Torque integration. Here's what I've done most recently.

Torque
Which version do you have? Try:

rpm -qi torque
Name        : torque                       Relocations: /usr
Version     : 6.0.2                             Vendor: redhat
Release     : 1.adaptive.el6                Build Date: Mon 05 Dec 2016 09:33:30 PM EST

~ If that doesn't work, do: ~
/usr/bin/qsub --version
Version: 6.0.2

Where are your Torque libraries?
which qsub
/usr/bin

ldd /usr/bin/qsub
libtorque.so.2 => /usr/lib64/libtorque.so.2 (0x00007f58b8f18000)

~ or ~
rpm -ql torque | grep "\.so"
/usr/lib64/libtorque.so
rpm -ql torque-drmaa | grep "\.so"
/usr/lib64/libdrmaa.so

Environment variables
Use  the information gained above to set your environment to point to the right libraries
export DRMAA_LIBRARY_PATH=/usr/lib64/libdrmaa.so
export LD_LIBRARY_PATH=/usr/lib64:LD_LIBRARY_PATH
export LIBTORQUE_DIR=/usr/lib64

I think the libdrmaa.so is working ok now for Torque 6, so I'll use it instead of getting another libdrmaa.

Python 
This will be a lot easier on you if you are using a virtualenv for Galaxy. This is the default behavior on recent Galaxy builds. To use, make sure your above environment variables are set, and then do:
cd galaxy
source .venv/bin/activate
pip install drmaa-python
deactivate

Now give Galaxy a kick and see if it works!

-Carrie


From: "Yip, Miu ki" <[hidden email]>
Date: Monday, February 27, 2017 at 12:26 PM
To: "[hidden email]" <[hidden email]>
Subject: [galaxy-dev] Galaxy and Torque

Hi all,

Is Torque still supported as a resource manager?

This page ( https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster ) mentioned the usage of Torque and how to set it up. However, the setup instructions refer to a /script/scramble.py file which I assume interfaces with eggs. If I recall correctly, eggs were upgraded to wheels. Does this mean there are upgraded scripts in place of scramble.py and the eggs.ini?

I saw this page ( https://biostar.usegalaxy.org/p/20470/ ) and it looks like nobody has a solution to this.

Thanks!


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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:
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To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/