Lesson 3 doesn't match Lesson 1

[mcdickenson]

Lesson 1 uses ami-6516b30e. Lesson 3 uses ami-3c1c3454 which has a different organization and contents (and also appears not to be available in the AWS Community Marketplace). I think the solution is for Lesson 3 to be updated according to the organization and contents of ami-6516b30e. Are there plans to do this? (This may be the same issue that's described in #5.)

[mkcor]

@mcdickenson I would think so too, considering the information under "Amazon instance for workshop" found at http://www.datacarpentry.org/genomics-workshop/ (Sat Feb 6 22:46:34 EST 2016): """ All the software and data used in the workshop is on an Amazon AMI.

If you want to run your instance of the server used for this workshop, launch a t2.medium instance with AMI ami-6516b30e, available under "Community AMIs" in the Amazon EC2 Managemant Console. """

[tmorrell]

I wanted to bump this issue, because the presence of different images is confusing. One potential problem changing the image names - lesson 3 uses the run SRR519926, and I'm not sure those files are in the ami-6516b30e image. The cyverse/iplant instructions also don't provide access to the lesson 3 files (at least as far as I can figure out).

[devbioinfoguy]

I'm going to have to pull in Tracy & Jason on these, as I don't have access to the images. Clearly we'd like to ensure that there's one set of files being used. Let's see what we can do to rectify this problem.

-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: Thomas Morrell notifications@github.com Reply-To: datacarpentry/cloud-genomics reply@reply.github.com Date: Thursday, February 23, 2017 at 4:04 PM To: datacarpentry/cloud-genomics cloud-genomics@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: Re: [datacarpentry/cloud-genomics] Lesson 3 doesn't match Lesson 1 (#11)

I wanted to bump this issue, because the presence of different images is confusing. One potential problem changing the image names - lesson 3 uses the run SRR519926, and I'm not sure those files are in the ami-6516b30e image. The cyverse/iplant instructions also don't provide access to the lesson 3 files (at least as far as I can figure out).

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/datacarpentry/cloud-genomics/issues/11#issuecomment-282120628, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AHO3gMCxsjSXUZuvi5dIqcFQ3M_Zbsesks5rffRtgaJpZM4HU9Y3.

[devbioinfoguy]

I can probably help, let me take a look at this issue; I think I can get to it tomorrow.

• Jason

On Feb 27, 2017, at 5:03 PM, Freeman, Bob (Robert) rfreeman@hbs.edu<mailto:rfreeman@hbs.edu> wrote:

I'm going to have to pull in Tracy & Jason on these, as I don't have access to the images. Clearly we'd like to ensure that there's one set of files being used. Let's see what we can do to rectify this problem.

-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: Thomas Morrell notifications@github.com<mailto:notifications@github.com> Reply-To: datacarpentry/cloud-genomics reply@reply.github.com<mailto:reply@reply.github.com> Date: Thursday, February 23, 2017 at 4:04 PM To: datacarpentry/cloud-genomics cloud-genomics@noreply.github.com<mailto:cloud-genomics@noreply.github.com> Cc: Subscribed subscribed@noreply.github.com<mailto:subscribed@noreply.github.com> Subject: Re: [datacarpentry/cloud-genomics] Lesson 3 doesn't match Lesson 1 (#11)

I wanted to bump this issue, because the presence of different images is confusing. One potential problem changing the image names - lesson 3 uses the run SRR519926, and I'm not sure those files are in the ami-6516b30e image. The cyverse/iplant instructions also don't provide access to the lesson 3 files (at least as far as I can figure out).

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/datacarpentry/cloud-genomics/issues/11#issuecomment-282120628, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AHO3gMCxsjSXUZuvi5dIqcFQ3M_Zbsesks5rffRtgaJpZM4HU9Y3.

[JasonJWilliamsNY]

Looking in the backend of AWS, the most recent image is ami-aab445c7 which I have just confirmed is public and searchable in community AMIs. Interestingly, the one mentioned in the 'Launching your own Instance' lesson is not to be found in our catalogue.

To my knowledge, the AMI should not be mentioned except outside of that lesson, and I think when we did a PR we may have pulled in lessons that we don't us (We, meaning me and following this workshop as my personal reference for what lessons to use: http://www.datacarpentry.org/2016-05-26-NIH/)

ami-aab445c7 is the latest instance

[tmorrell]

I sounds like the examples in lesson 3 are out of date. Is it worth updating the content/does anyone use it?

[devbioinfoguy]

Yes, this lesson (#3) is likely going to go away (pending approval from Jason and Tracy) as most of this content is in other parts of the DC-genomics lessons, as was done as an temporary lesson early on in the DC-genomics evolution.

[tracykteal]

Yes, thank you. This is something very important to update. We'll be resolving this, this week.