Wong Foo Lam wrote:

Dear Support

We have users who are using Galaxy and would like to have this application installed on our compute cluster. I read through the documentation for using Galaxy both on a web browser and on a compute cluster. The document states that a qsub command line can be submitted when using on a cluster.

Currently the info documented on this weblink: http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster mentions the qsub -I command. Does this mode sets a platform for user to launch the interactive web browser? I am looking at the option of not launching the web browser where we launch the task with an input file and then the output files are appended to a designated folder.

Hi,

qsub -I was just used as an example to show successful operation of the cluster resource manager. Galaxy does not run interactive cluster jobs, it runs background (batch) jobs.

Is it possible to know whether Galaxy software can be installed as a standalone without launching a web browser to submit & run sequencing tasks. Or the interactive web browser is a mandatory interface for running this application regardless of local system or on a compute cluster.

It's possible to run Galaxy's command line tools without Galaxy. For the Python tools this generally means setting $PYTHONPATH to Galaxy's lib/ directory and then executing as usual. This would require you to run them through the cluster scheduler manually, however.

Galaxy also has an API that will eventually allow you to run jobs. Unfortunately, job/workflow running is not yet available via the API.

--nate

Looking forward to hearing from you soon.

Regards Foo Lam

[cid:image001.gif@01CB80BC.219AC830]

WONG Foo Lam (Mr) | Senior HPC Application Engineer | High Performance Computing Centre | Nanyang Technological University 50 Nanyang Avenue, North Spine, Block NS4-04-25 Singapore 639798 Tel: (65) 6592 2414 GMT+8h | Email: foo-lam.wong@ntu.edu.sgmailto:foo-lam.wong@ntu.edu.sg | Web: www.hpc.ntu.edu.sghttp://www.ntu.edu.sg/

---

CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its content. Thank you.

Towards A Sustainable Earth: Print Only When Necessary

---

galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev

Nicolas Delhomme wrote:

Hi Nate,

I wasn't aware of the Galaxy API. Do you have any more information about it, i.e. is there a page on the wiki? What I'd like to do is actually what you say is missing (adding jobs through the command line) and I'd be willing to contribute code for that. Just let me know if you're interested (pointers to start would be welcome, then :-)).

Hi Nico,

No documentation, unfortunately, but there is example client code in scripts/api/. The methods which the API acceses are under lib/galaxy/web/api/ and are mostly just wrappers around their regular web counterparts in lib/galaxy/web/controllers/.

--nate

Keep on the good work!

Cheers,

Nico

---

Nicolas Delhomme

High Throughput Functional Genomics Center

European Molecular Biology Laboratory

Tel: +49 6221 387 8310 Email: nicolas.delhomme@embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany

---

On 10 Nov 2010, at 15:34, Nate Coraor wrote:

...

Wong Foo Lam wrote:

...

Dear Support

We have users who are using Galaxy and would like to have this application installed on our compute cluster. I read through the documentation for using Galaxy both on a web browser and on a compute cluster. The document states that a qsub command line can be submitted when using on a cluster.

Currently the info documented on this weblink: http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster mentions the qsub -I command. Does this mode sets a platform for user to launch the interactive web browser? I am looking at the option of not launching the web browser where we launch the task with an input file and then the output files are appended to a designated folder.

Hi,

qsub -I was just used as an example to show successful operation of the cluster resource manager. Galaxy does not run interactive cluster jobs, it runs background (batch) jobs.

...

Is it possible to know whether Galaxy software can be installed as a standalone without launching a web browser to submit & run sequencing tasks. Or the interactive web browser is a mandatory interface for running this application regardless of local system or on a compute cluster.

It's possible to run Galaxy's command line tools without Galaxy. For the Python tools this generally means setting $PYTHONPATH to Galaxy's lib/ directory and then executing as usual. This would require you to run them through the cluster scheduler manually, however.

Galaxy also has an API that will eventually allow you to run jobs. Unfortunately, job/workflow running is not yet available via the API.

--nate

...

Looking forward to hearing from you soon.

Regards Foo Lam

[cid:image001.gif@01CB80BC.219AC830]

WONG Foo Lam (Mr) | Senior HPC Application Engineer | High Performance Computing Centre | Nanyang Technological University 50 Nanyang Avenue, North Spine, Block NS4-04-25 Singapore 639798 Tel: (65) 6592 2414 GMT+8h | Email: foo-lam.wong@ntu.edu.sgmailto:foo-lam.wong@ntu.edu.sg | Web: www.hpc.ntu.edu.sghttp://www.ntu.edu.sg/

---

CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its content. Thank you.

Towards A Sustainable Earth: Print Only When Necessary

...

---

galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev

---

galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev