Add single-end and ONT support, add GitHub Actions, update readme

[rpetit3]

Here's the fork: https://github.com/rpetit3/shigatyper

Added

• single-end and ONT support
• Github Action for testing
• two outputs, the serotype and hits

Fixed

• missing heparinase gene in the reference

  I also cleaned up a little, mostly just removed comments related to ipython (i think)

I can also create a tempory install on my personal conda channel if you have a test set you want to run them through

Address:

• https://github.com/CFSAN-Biostatistics/shigatyper/issues/2
• https://github.com/CFSAN-Biostatistics/shigatyper/issues/3
• https://github.com/CFSAN-Biostatistics/shigatyper/issues/6
• https://github.com/CFSAN-Biostatistics/shigatyper/issues/7

[florathecat]

Really appreciate it Robert!!

Crashfrog will get to it.

Yun

On Feb 11, 2022, at 12:51 PM, Robert A. Petit III @.***> wrote:

 Here's the fork: https://github.com/rpetit3/shigatyper

Added

single-end and ONT support Github Action for testing two outputs, the serotype and hits Fixed

missing heparinase gene in the reference I also cleaned up a little, mostly just removed comments related to ipython (i think)

I can also create a tempory install on my personal conda channel if you have a test set you want to run them through

You can view, comment on, or merge this pull request online at:

https://github.com/CFSAN-Biostatistics/shigatyper/pull/9

Commit Summary

3469c40 add license that matches other FDA tools 6cd354a cleanup code, add single end and nanopore support 62b8f79 update readme 836262b add heparinase to the reference fasta ccf0b41 tweaks and update readme a1a1bc1 missed some dependencies 465197d Update README.md b1a0d6c Add github action workflow 801bf11 one more cleanup on ci File Changes (6 files) A .github/workflows/test-shigatyper.yml (57) A LICENSE (30) M README.md (134) M setup.py (35) M shigatyper/resources/ShigellaRef5.fasta (28) M shigatyper/shigatyper.py (403) Patch Links:

https://github.com/CFSAN-Biostatistics/shigatyper/pull/9.patch https://github.com/CFSAN-Biostatistics/shigatyper/pull/9.diff — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you are subscribed to this thread.

[rpetit3]

@crashfrog wonder if we could get your thoughts on this? Thank you!

[hughrandFDA]

Hi Robert, Sorry, long story, but Justin is currently in Thailand (with his wife who is on a military tour of duty) and not allowed to work remotely until the FDA gets its act together with paperwork to authorize his working remotely. I’ll try and see what alternative resources we can drum up here to act on this. H

From: Robert A. Petit III @.> Sent: Saturday, February 19, 2022 1:22 PM To: CFSAN-Biostatistics/shigatyper @.> Cc: Subscribed @.***> Subject: [EXTERNAL] Re: [CFSAN-Biostatistics/shigatyper] Add single-end and ONT support, add GitHub Actions, update readme (PR #9)

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@crashfroghttps://github.com/crashfrog wonder if we could get your thoughts on this? Thank you!

— Reply to this email directly, view it on GitHubhttps://github.com/CFSAN-Biostatistics/shigatyper/pull/9#issuecomment-1046076948, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AB2BAG3Q4SWRTI2WQTTMJ2DU37NVHANCNFSM5OE56HZQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you are subscribed to this thread.Message ID: @.**@.>>

[rpetit3]

Thank you @hughrandFDA

Let me know what I can do to help. If it makes things easier I can create bioconda install on my personal channel to make testing easier

[rpetit3]

Thank you! One final request, could a new version be released so that it'll be reflected on Bioconda?

I bumped the version to v2.0.0, since there were some changes that were no longer backwards compatible

[florathecat]

Thank you Hugh and Charles for stepping up. I defer to CFSAN for whatever you see fit best for the tool. Please let me know if there is anything that I can help and I’ll do my best.

Yun

On Mar 3, 2022, at 12:01 PM, Robert A. Petit III @.***> wrote:

 Thank you! One final request, could a new version be released so that it'll be reflected on Bioconda?

I bumped the version to v2.0.0, since there were some changes that were no longer backwards compatible

— Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you commented.

[charesredhat]

Yes we will work on getting a new version released.

Charles

[rpetit3]

Ok, once new release is created, the Bioconda Bot will create a new pull request over at https://github.com/bioconda/bioconda-recipes

I can handle updates to the recipe from there.

Thanks again!

[hughrandFDA]

Sounds like Charles got this under control. Holler if something seems to go off the rails. H

From: Robert A. Petit III @.> Sent: Thursday, March 3, 2022 12:17 PM To: CFSAN-Biostatistics/shigatyper @.> Cc: Rand, Hugh @.>; Mention @.> Subject: [EXTERNAL] Re: [CFSAN-Biostatistics/shigatyper] Add single-end and ONT support, add GitHub Actions, update readme (PR #9)

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.

Ok, once new release is created, the Bioconda Bot will create a new pull request over at https://github.com/bioconda/bioconda-recipes

I can handle updates to the recipe from there.

Thanks again!

— Reply to this email directly, view it on GitHubhttps://github.com/CFSAN-Biostatistics/shigatyper/pull/9#issuecomment-1058282855, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AB2BAG4KQPPCX7MCFL5IFY3U6DXYFANCNFSM5OE56HZQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you were mentioned.Message ID: @.**@.>>

[rpetit3]

Hello, following up on a timeline for a new release, so I can get things updated on the Bioconda side.

If there's an internal clearance process for CFSAN that's understandable, just trying to get a timeframe in my mind.

Thank you!

[hughrandFDA]

I just did it; once the Bioconda group accepts the PR there should be a new conda package (version 1.0.8.) Once that's out, I can update the package in GalaxyTrakr, too.

Justin

On Fri, Mar 11, 2022 at 2:27 AM Rand, Hugh @.***> wrote:

Good news. We got Justin authorization to work from Thailand, so he can help.

Justin – can you circle round with Charles and come up with a timeline on this. Thx.

From: Robert A. Petit III @.> Sent: Thursday, March 10, 2022 12:44 PM To: CFSAN-Biostatistics/shigatyper @.> Cc: Rand, Hugh @.>; Mention < @.> Subject: [EXTERNAL] Re: [CFSAN-Biostatistics/shigatyper] Add single-end and ONT support, add GitHub Actions, update readme (PR #9)

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.

Hello, following up on a timeline for a new release, so I can get things updated on the Bioconda side.

If there's an internal clearance process for CFSAN that's understandable, just trying to get a timeframe in my mind.

Thank you!

— Reply to this email directly, view it on GitHub https://github.com/CFSAN-Biostatistics/shigatyper/pull/9#issuecomment-1064328616, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB2BAG72YPTFUH2KMB7GAA3U7IYFBANCNFSM5OE56HZQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

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[rpetit3]

Thank you! Just a heads up, you're going to have a version mismatch https://github.com/CFSAN-Biostatistics/shigatyper/blob/master/setup.py#L6

[hughrandFDA]

Good news. We got Justin authorization to work from Thailand, so he can help.

Justin – can you circle round with Charles and come up with a timeline on this. Thx.

From: Robert A. Petit III @.> Sent: Thursday, March 10, 2022 12:44 PM To: CFSAN-Biostatistics/shigatyper @.> Cc: Rand, Hugh @.>; Mention @.> Subject: [EXTERNAL] Re: [CFSAN-Biostatistics/shigatyper] Add single-end and ONT support, add GitHub Actions, update readme (PR #9)

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.

Hello, following up on a timeline for a new release, so I can get things updated on the Bioconda side.

If there's an internal clearance process for CFSAN that's understandable, just trying to get a timeframe in my mind.

Thank you!

— Reply to this email directly, view it on GitHubhttps://github.com/CFSAN-Biostatistics/shigatyper/pull/9#issuecomment-1064328616, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AB2BAG72YPTFUH2KMB7GAA3U7IYFBANCNFSM5OE56HZQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you were mentioned.Message ID: @.**@.>>