Confusion over which AMI to use

[collinstorlie]

G'day, I am planning to teach the DataCarpentry Genomics Workshop to a group of research students and staff in a few weeks time. In the course of preparing for the workshop, I noted a few inconsistencies w/in the material that I would like to point out / receive clarification about.

First, there are two AMI's referenced in the material. One of which, ami-3c1c3454, doesn't seem to exist w/in the Community AMI's. I tried following Jason Williams updated instructions (found here https://jasonjwilliamsny.github.io/cloud-genomics/logging-onto-cloud.html), and encountered a similar problem locating ami-07b4456a.

The image I could locate and run as an instance (ami-6516b30e) doesn't seem to contain all of the .fastq data described in the rest of the lesson.

So, I guess my questions are two:

1) Is there a single AMI for these lessons, if so, how can I access it?

2) Is the difference between the AMI's referred to just the data present? If so, could I use the SRA Toolkit prefetch command to add the necessary data to ami-6516b30e and run the workshop with that?

Attached are some screenshots of the portions of the lessons which reference the AMI's I couldn't find. Thanks in advance for your time and help with my enquiry.

Kind Regards,

Collin

[maneesha]

+1 I came here to post the same issue.

If you begin at http://www.datacarpentry.org/lessons/ and click on "More Workshop Details" under Genomics workshop it takes you to http://www.datacarpentry.org/genomics-workshop/. From there clicking on "Module 3: Using cloud computing for genomics" takes you to https://jasonjwilliamsny.github.io/cloud-genomics. From there the instructions on "launching cloud instances on your own" takes you to https://jasonjwilliamsny.github.io/cloud-genomics/logging-onto-cloud.html which tells you to use image ami-07b4456a.

However If you begin at http://www.datacarpentry.org/lessons/ and click on the "Site" icon for "Introduction to cloud computing for genomics" it takes you to this github repo: https://github.com/datacarpentry/cloud-genomics/tree/gh-pages/lessons. From there clicking on "1.logging-onto-cloud.md" tells you to use image ami-6516b30e

[collinstorlie]

Maneesha,

I had a nice e-mail chat to Tracy Teal and she has provided me some clarity around lesson organisation. In a nutshell, the repos referenced at http://www.datacarpentry.org/lessons/ are deprecated. However, if you link to the lessons from http://www.datacarpentry.org/genomics-workshop/ then the lesson materials corresponds to the file structure and data on the AMI 6516b30e. I'll be going over all of the lesson material tomorrow and will gladly point out any further inconsistencies or unclear bits I happen to find. Further, I'd like to also thank the DataCarpentry team for creating and providing this content for training purposes, even in a slightly disorganised state, it's still an excellent resource to be utilised.

Regards,

Collin

[maneesha]

Thanks @collinstorlie for brining this all to our attention. If the repos at http://www.datacarpentry.org/lessons/ are deprecated I'd like to ask lesson maintainers to make this clear and to note what we should be using instead. @tracykteal @JasonJWilliamsNY @devbioinfoguy

[devbioinfoguy]

Thanks, Collin & Maneesha. Both Tracy and I are in the process of updating / reorganizing / consolidating all the Cloud-Genomics repos, as there have been developments and usage that have been outside the repos here, as well as decisions that needed to be made in regards to what track these lessons will take.

Thanks for your support and your patience!

Best, Bob

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Bob Freeman, PhD Director, Research Technology Operations @ Research Computing Services Division of Research and Faculty Development HARVARD | BUSINESS | SCHOOL Baker Library & Bloomberg Center B96 25 Harvard Way, Boston, MA 02163

617.496.6612, phone @DevBizInfoGuy http://bit.ly/whatAboutBob

For more information – RCS: http://intranet.hbs.edu/dept/research/ Software: http://intranet.hbs.edu/dept/research/software/ Rsrch Grid: http://grid.rcs.hbs.orghttp://grid.rcs.hbs.org/ Training: http://training.rcs.hbs.orghttp://training.rcs.hbs.org/

From: maneesha sane notifications@github.com Reply-To: datacarpentry/cloud-genomics reply@reply.github.com Date: Wednesday, March 22, 2017 at 9:18 AM To: datacarpentry/cloud-genomics cloud-genomics@noreply.github.com Cc: Robert Freeman rfreeman@hbs.edu, Mention mention@noreply.github.com Subject: Re: [datacarpentry/cloud-genomics] Confusion over which AMI to use (#33)

Thanks @collinstorliehttps://github.com/collinstorlie for brining this all to our attention. If the repos at http://www.datacarpentry.org/lessons/ are deprecated I'd like to ask lesson maintainers to make this clear and to note what we should be using instead. @tracyktealhttps://github.com/tracykteal @JasonJWilliamsNYhttps://github.com/JasonJWilliamsNY @devbioinfoguyhttps://github.com/devbioinfoguy

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/datacarpentry/cloud-genomics/issues/33#issuecomment-288395135, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AHO3gL5z1SnoiPg_CfjNua4ZzztLrzsbks5roR-ugaJpZM4MjY70.

[tracykteal]

Thanks @collinstorlie. The lessons at http://www.datacarpentry.org/lessons haven't been deprecated, just some of the particular files within lessons. Some of the links aren't correct though, so I'm going through and updating those, so that should add clarity.

[tracykteal]

Updated the data carpentry.org/lessons page with correct links https://github.com/datacarpentry/datacarpentry.github.io/pull/213

[JasonJWilliamsNY]

Hi everyone including @collinstorlie. I was away teaching when this thread occurred, but went through a bunch of things with Maneesha. ami-aab445c7 is the definitive image so far as I know. In the Data Carpentry AWS account there are only three images and this is the latest one, and the one we have used on several occasions. As far as I know, the lessons on http://www.datacarpentry.org/genomics-workshop/ are very out of date, but I know we have been disorganized. I have taught the genomics lessons about 5 times now, ultimately following this schedule (http://www.datacarpentry.org/2016-05-26-NIH/). I am still personally confused because my own lesson refers to yet another AMI (https://jasonjwilliamsny.github.io/cloud-genomics/logging-onto-cloud.html), but in any case after testing I am sure ami-aab445c7 is the one.

[devbioinfoguy]

Sorry about that @collinstorlie & Jason. Both Tracy and I are trying to make efforts on this and have been pulled away. My schedule clears after Thursday, so we'll make headway on this quickly enough.

Cannot say with certainty which is correct:

· ami-6516b30e was reference in another issue.

· ami-5bc63136 was used for recent workshops at Tufts.

-Bob

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Bob Freeman, PhD Director, Research Technology Operations @ Research Computing Services Division of Research and Faculty Development HARVARD | BUSINESS | SCHOOL Baker Library & Bloomberg Center B96 25 Harvard Way, Boston, MA 02163

617.496.6612, phone @DevBizInfoGuy http://bit.ly/whatAboutBob

For more information – RCS: http://intranet.hbs.edu/dept/research/ Software: http://intranet.hbs.edu/dept/research/software/ Rsrch Grid: http://grid.rcs.hbs.orghttp://grid.rcs.hbs.org/ Training: http://training.rcs.hbs.orghttp://training.rcs.hbs.org/

From: Jason Williams notifications@github.com Reply-To: datacarpentry/cloud-genomics reply@reply.github.com Date: Tuesday, March 28, 2017 at 1:36 PM To: datacarpentry/cloud-genomics cloud-genomics@noreply.github.com Cc: Robert Freeman rfreeman@hbs.edu, Mention mention@noreply.github.com Subject: Re: [datacarpentry/cloud-genomics] Confusion over which AMI to use (#33)

Hi everyone including @collinstorliehttps://github.com/collinstorlie. I was away teaching when this thread occurred, but went through a bunch of things with Maneesha. ami-aab445c7 is the definitive image so far as I know. In the Data Carpentry AWS account there are only three images and this is the latest one, and the one we have used on several occasions. As far as I know, the lessons on http://www.datacarpentry.org/genomics-workshop/ are very out of date, but I know we have been disorganized. I have taught the genomics lessons about 5 times now, ultimately following this schedule (http://www.datacarpentry.org/2016-05-26-NIH/). I am still personally confused because my own lesson refers to yet another AMI (https://jasonjwilliamsny.github.io/cloud-genomics/logging-onto-cloud.html), but in any case after testing I am sure ami-aab445c7 is the one.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/datacarpentry/cloud-genomics/issues/33#issuecomment-289846423, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AHO3gFYvynrc7idqH6fqqTXEMcnBvFgGks5rqUUBgaJpZM4MjY70.