[DOCKTESTERS] docker testing WG update

Mon Nov 28 10:48:22 EST 2016

Hi,
I just wanted to clarify a few things which should actually make things a bit easier.

1) Some reference data is about to be moved (has not been moved yet). When this occurs, I'll upload new test json and let this group know on a tool-by-tool basis.
In order to use the new site for reference data, if you're launching using the Dockstore CLI, you will need to update to 1.1 (already in production).

2) To expand on the sudo issue, the fix actually occurs inside the docker image for each CWL tool.
I'm hoping to time my work so that I can release a gosu+new reference data update for each tool that is affected at the same time so that we kill two birds with one stone.
Contact me if you think you are writing a docker image that is affected (you will be affected if you use sudo or if you use the "USER" instruction in a Dockerfile).

Thanks!

Denis Yuen
Bioinformatics Software Developer

Ontario Institute for Cancer Research
MaRS Centre
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Toronto, Ontario, Canada M5G 0A3

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________________________________
From: docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org [docktesters-bounces+denis.yuen=oicr.on.ca at lists.icgc.org] on behalf of Francis Ouellette [francis at oicr.on.ca]
Sent: November 28, 2016 10:33 AM
To: docktesters at lists.icgc.org
Subject: [DOCKTESTERS] docker testing WG update

Dear all,

This past week has been somewhat quiet on the docktesters mailing list, although
I understand from the PCAWG-tech conference call today that a number of things
are happening in the background.

Minutes/updates from today’s PCAWG-tech call are here: https://goo.gl/R0L6nN<redir.aspx?REF=9QXpWySocykQJqkoLU2KBe86pW9MjufmbeKzomQf9wVLsSKjpBfUCAFodHRwczovL2dvby5nbC9SMEw2bk4.>

This e-mail is to provide spme specific updates from those of you not on the call today
but of relevance to dockstore testing WG (and I invite those who were on the call to
correct anything I have wrong, or which could use more details).

  1.  (from Junjun & Denis): Some reference files which are now hosted on the dcc.icgc.org<redir.aspx?REF=2wVIfnaVEmEa9C4cUJEqKYFoNDMocy0dg7EbEVUqk8KlEyWjpBfUCAFodHRwOi8vZGNjLmljZ2Mub3Jn> portal were moved, and those docker containers that use these (human reference sequence) will need to be retested (I think this is all of the ones we have done to date!).
  2.  (From Denis): There is an issue for people who use docker on a shared instance with multiple users, and use the “sudo” command (e.g. the BWA-mem, Sanger and DKFZ pipelines), and for this a fix has been put in, and a new dockstore will be (has been?) deployed. Retesting will be necessary.
  3.  The Broad (Gordon Saksena <gsaksena at broadinstitute.org<redir.aspx?REF=Qj1LthAAC7CL2Elnqv23PbVnVqTVIxgCkHPfb5KLH3mlEyWjpBfUCAFtYWlsdG86Z3Nha3NlbmFAYnJvYWRpbnN0aXR1dGUub3Jn>>, who is on this mailman list) is asking for help to test some not quite yet deployed containers. Those of you who want to help (OHSU was mentioned :), probably best to contact Gordon directly, and CC list, to see what is needed to get this testing started. Denis made the good suggestion to have “test data” available asap to help expedite the testing process.

All: from: https://wiki.oicr.on.ca/pages/editpage.action?pageId=66309629<redir.aspx?REF=XVCTzt_btUDKhLbqqkVNO66FcLZRW0KQGvmLJjSBtpSlEyWjpBfUCAFodHRwczovL3dpa2kub2ljci5vbi5jYS9wYWdlcy9lZGl0cGFnZS5hY3Rpb24_cGFnZUlkPTY2MzA5NjI5>

I added a request to include time-stamps of when testing was done, so we know which dockstore was used, and that the right testing was done.

[cid:A2252A3F-7328-495B-91BE-6EB69D8222AC at oicr.on.ca]

I would also like to encourage all of you to get to pick one container this week, and test one workflow before next Friday (Dec 2).

If you want me to assign a specific pipeline to you, please let me know.

Thank you all,

francis

--
B.F. Francis Ouellette          http://oicr.on.ca/person/francis-ouellette<redir.aspx?REF=1dwl05V0xbRkOi9Sod434RvgzUbByPIThln30cQ4bQmlEyWjpBfUCAFodHRwOi8vb2ljci5vbi5jYS9wZXJzb24vZnJhbmNpcy1vdWVsbGV0dGU.>

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