Can I Create Sub Workflows In Galaxy?

Question: Can I Create Sub Workflows In Galaxy?

7.9 years ago by

Sonali Amonkar • 150 wrote:

Hi, Am a newbie to Galaxy and was looking for some basic answers about Galaxy's offerings till date: 1. Is there any way that I can plug in a small work flow inside another work flow (sub work flow) in Galaxy? 2. Is there any step wise process documented somewhere to install Galaxy on Windows? 3. Does Galaxy have any commercial support offered? 4. Which languages can the Galaxy tools be built in? (Java, C, C++, etc) ? 5. Does Galaxy have any monitoring tools to keep a check on the process and the statistics at run time? Answers to any questions above will be greatly appreciated. Thank you, Sonali Amonkar DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.

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modified 7.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.9 years ago by Sonali Amonkar • 150

7.9 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Sonali, Please see below for our replies per question. Thanks! Jen Galaxy team Not at this time. Galaxy does not run on Windows. As a work-around, we recommend using VirtualBox or another virtualization product and running Linux in it. Not at this time. Any language is OK, if the following conditions are met: 1. All parameters, including inputs and outputs, need to be able to be specified on the command line or in a dynamically-generated config file. 2. The program doesn't write anything to STDERR unless it's really an error. If either of these are untrue, you may need a wrapper, but it can be written in anything. There's a script at galaxy-dist/scripts/check_galaxy.py that can be used to check that a Galaxy server is up and able to run jobs. It is invoked with: % python ./scripts/check_galaxy.py <server> On first run, it will explain how to store the email and password of the Galaxy account to use. There's also a script at galaxy-dist/cron/check_galaxy.sh which is a wrapper for the python script which can be used with cron. -- Jennifer Jackson http://usegalaxy.org

ADD COMMENT • link written 7.9 years ago by Jennifer Hillman Jackson ♦ 25k

Thank you for your time. I got what I was looking for here. Regards, Sonali Amonkar ________________________________________ To: Sonali Amonkar Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Can I create sub workflows in Galaxy? Hello Sonali, Please see below for our replies per question. Thanks! Jen Galaxy team Not at this time. Galaxy does not run on Windows. As a work-around, we recommend using VirtualBox or another virtualization product and running Linux in it. Not at this time. Any language is OK, if the following conditions are met: 1. All parameters, including inputs and outputs, need to be able to be specified on the command line or in a dynamically-generated config file. 2. The program doesn't write anything to STDERR unless it's really an error. If either of these are untrue, you may need a wrapper, but it can be written in anything. There's a script at galaxy-dist/scripts/check_galaxy.py that can be used to check that a Galaxy server is up and able to run jobs. It is invoked with: % python ./scripts/check_galaxy.py <server> On first run, it will explain how to store the email and password of the Galaxy account to use. There's also a script at galaxy-dist/cron/check_galaxy.sh which is a wrapper for the python script which can be used with cron. -- Jennifer Jackson http://usegalaxy.org DISCLAIMER ========== This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails.

ADD REPLY • link written 7.9 years ago by Sonali Amonkar • 150

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