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biocore / qiime

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
GNU General Public License v2.0
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Openstack compatible QIIME image #1485

Open smaffiol opened 10 years ago

smaffiol commented 10 years ago

Hi we are panning to support QIIME on our Openstack-based infrastructure would it be possible to release, together with the VirtualBox and AWS images an Openstack compatible one ? (like in qcow2 format for example) ?

It would also be nice to have two type of images:

Alternatively, would you be willing to share the procedures you use to create both the VirtualBox and the AWS images ?

thanks Sergio Maffioletti Project director Swiss Academic Compute Cloud project http://www.swing-grid.ch/SwissACC University of Zurich

antgonza commented 10 years ago

Hi Sergio,

Thanks for your interest. I think the easiest will be for you to convert the vdi that we create to whatever format you need, see http://docs.openstack.org/image-guide/content/ch_converting.html. Now for the GUI you can use the latest here: ftp://thebeast.colorado.edu/pub/qiime-release-VMs/ and for the minimum this other one: ftp://thebeast.colorado.edu/pub/evident-snapshop-VMs/.

A few notes:

Hope this helps.

rob-knight commented 10 years ago

I added Dmitry and Jeff to this in case they are not on the mailing list but interested in helping.

Rob

On Apr 3, 2014, at 7:10 AM, Antonio Gonzalez notifications@github.com<mailto:notifications@github.com> wrote:

Hi Sergio,

Thanks for your interest. I think the easiest will be for you to convert the vdi that we create to whatever format you need, see http://docs.openstack.org/image-guide/content/ch_converting.html. Now for the GUI you can use the latest here: ftp://thebeast.colorado.edu/pub/qiime-release-VMs/ and for the minimum this other one: ftp://thebeast.colorado.edu/pub/evident-snapshop-VMs/.

A few notes:

Hope this helps.

— Reply to this email directly or view it on GitHubhttps://github.com/biocore/qiime/issues/1485#issuecomment-39448547.

smaffiol commented 10 years ago

Hi Antonio

thanks so much for your prompt reply

quick question back:

in terms of support that you provide, would you support a custom image (say Ubuntu, SuSe, Gentoo) built with qiime-deploy script ?

if I understand correctly your process for creating new images, we would follow pretty much the same procedure if we would run qiime-deploy starting from an already available Openstack image, is that right ?

do you have standard regression and/or verification tests you normally run when producing a new image ?

thanks Sergio :)

---------- Forwarded message ---------- From: Antonio Gonzalez notifications@github.com Date: 2014-04-03 15:10 GMT+02:00 Subject: Re: [qiime] Openstack compatible QIIME image (#1485) To: biocore/qiime qiime@noreply.github.com Cc: smaffiol sergio.maffioletti@gc3.uzh.ch

Hi Sergio,

Thanks for your interest. I think the easiest will be for you to convert the vdi that we create to whatever format you need, see http://docs.openstack.org/image-guide/content/ch_converting.html. Now for the GUI you can use the latest here: ftp://thebeast.colorado.edu/pub/qiime-release-VMs/ and for the minimum this other one: ftp://thebeast.colorado.edu/pub/evident-snapshop-VMs/.

A few notes:

Hope this helps.

Reply to this email directly or view it on GitHubhttps://github.com/biocore/qiime/issues/1485#issuecomment-39448547 .

sergio.maffioletti@gc3.uzh.ch GC3: Grid Computing Competence Center http://www.gc3.uzh.ch/ University of Zurich Winterthurerstrasse 190 CH-8057 Zurich Switzerland Tel: +41 44 635 4222 Fax: +41 44 635 6888

smaffiol commented 10 years ago

thanks

here's the reply I sent to Antonio:

Hi Antonio

thanks so much for your prompt reply

quick question back:

in terms of support that you provide, would you support a custom image (say Ubuntu, SuSe, Gentoo) built with qiime-deploy script ?

if I understand correctly your process for creating new images, we would follow pretty much the same procedure if we would run qiime-deploy starting from an already available Openstack image, is that right ?

do you have standard regression and/or verification tests you normally run when producing a new image ?

thanks Sergio :)

2014-04-03 15:13 GMT+02:00 Rob Knight notifications@github.com:

I added Dmitry and Jeff to this in case they are not on the mailing list but interested in helping.

Rob

On Apr 3, 2014, at 7:10 AM, Antonio Gonzalez <notifications@github.com mailto:notifications@github.com> wrote:

Hi Sergio,

Thanks for your interest. I think the easiest will be for you to convert the vdi that we create to whatever format you need, see http://docs.openstack.org/image-guide/content/ch_converting.html. Now for the GUI you can use the latest here: ftp://thebeast.colorado.edu/pub/qiime-release-VMs/ and for the minimum this other one: ftp://thebeast.colorado.edu/pub/evident-snapshop-VMs/.

A few notes:

  • forum.qiime.orghttp://forum.qiime.org is the best place for general Qiime questions.
  • We have tried different automatic recipes tools to generate the VMs and we are not happy with anyone; thus, we just update the previous version using https://github.com/qiime/qiime-deploy, you should check it out.
  • The Qiime (GUI) VM gets updated every Qiime release, ~6 months, and the Evident (CLI) every Evident release, ~12 months.

Hope this helps.

Reply to this email directly or view it on GitHub< https://github.com/biocore/qiime/issues/1485#issuecomment-39448547>.

Reply to this email directly or view it on GitHubhttps://github.com/biocore/qiime/issues/1485#issuecomment-39448888 .

sergio.maffioletti@gc3.uzh.ch GC3: Grid Computing Competence Center http://www.gc3.uzh.ch/ University of Zurich Winterthurerstrasse 190 CH-8057 Zurich Switzerland Tel: +41 44 635 4222 Fax: +41 44 635 6888

antgonza commented 10 years ago

For the time being we have our hands full with the 2 (EC2, Vbox) images that we create but we can help you set it up, if you are interested. We do that for example with http://www.wernerlab.org/software/macqiime.

Correct about the qiime-deploy.

Yes, we have print_qiime_config.py that tested the basic installation and then code and script level test to verify the rest, you can check our automatic testing framework for more info: http://ci.qiime.org/job/qiime-github-pr/

smaffiol commented 10 years ago

we have created an Openstack QIIME image starting from a vanilla Ubuntu 12.04 using the qiime-deploy ( that was back in July 2013 )

at that time I did just print_qiime_config.py

I just upgraded that image to QIIME 1.8 using the qiime-deploy script (worked pretty smoothly)

but when I run the nosetest I got the following failures:

ERROR: Runs a Mantel test on all pairs of distance matrices.

Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest self.test(_self.arg) File "/usr/lib/python2.7/dist-packages/nose/util.py", line 622, in newfunc return func(_arg, **kw) TypeError: run_mantel_test() takes at least 6 arguments (0 given)

ERROR: Perform two-sample t-test on all pairs of grouped distances.

Traceback (most recent call last): File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest self.test(_self.arg) File "/usr/lib/python2.7/dist-packages/nose/util.py", line 622, in newfunc return func(_arg, **kw) TypeError: all_pairs_t_test() takes at least 2 arguments (0 given)

FAIL: setup_server opens a port and listens

Traceback (most recent call last): File "/apps/qiime_software/qiime-1.8.0-release/tests/test_denoiser/test_cluster_util.py", line 186, in test_setup_server self.assertRaises(error, setup_server, 80) AssertionError: error not raised

FAIL: get_histogram_scale should return correct result.

Traceback (most recent call last): File "/apps/qiime_software/qiime-1.8.0-release/tests/test_make_distance_histograms.py", line 263, in test_get_histogram_scale self.assertFloatEqual(xscale_obs,xscale_exp) File "/apps/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages/cogent/util/unit_test.py", line 287, in assertFloatEqual self.assertFloatEqualRel(observed, expected, rel_eps) File "/apps/qiime_software/pycogent-1.5.3-release/lib/python2.7/site-packages/cogent/util/unit_test.py", line 205, in assertFloatEqualRel (observed, expected, diff)) AssertionError: Got 0.5, but expected 0.55 (diff was -0.050000000000000044)

I did not installed nor usearch nor sffinfo/sfffile packages

is this something I should check further ?

thanks

Sergio :)

2014-04-03 15:26 GMT+02:00 Antonio Gonzalez notifications@github.com:

For the time being we have our hands full with the 2 (EC2, Vbox) images that we create but we can help you set it up, if you are interested. We do that for example with http://www.wernerlab.org/software/macqiime.

Correct about the qiime-deploy.

Yes, we have print_qiime_config.py that tested the basic installation and then code and script level test to verify the rest, you can check our automatic testing framework for more info: http://ci.qiime.org/job/qiime-github-pr/

Reply to this email directly or view it on GitHubhttps://github.com/biocore/qiime/issues/1485#issuecomment-39450256 .

sergio.maffioletti@gc3.uzh.ch GC3: Grid Computing Competence Center http://www.gc3.uzh.ch/ University of Zurich Winterthurerstrasse 190 CH-8057 Zurich Switzerland Tel: +41 44 635 4222 Fax: +41 44 635 6888