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V2.1.0 #97
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V2.1.0 #97
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48fce09
app.py dropdown
kristinelacek 6efd500
comma bug
kristinelacek 1ce057c
artic dropdown
kristinelacek f762dec
add new AUS primers
kristinelacek 227abe5
version update for staging
kristinelacek e2b391c
reconstruct image as bookworm
rchau88 2fab14c
fix vulnerbilities
rchau88 7ecec6a
Merge pull request #98 from CDCgov/fix_vulnerabilities
kristinelacek e1c399b
Merge pull request #99 from CDCgov/s-gene-illumina
kristinelacek 92f80ea
s gene illumina primer arg
kristinelacek 9902096
hyperlink FDA recs
kristinelacek 93a99d0
pointed url to repo instead of website
nbx0 1bfd519
added CVV reference table
nbx0 eb1417e
init podman desktop docs
nbx0 49d0801
podman docs
nbx0 f82daf0
menu updates
nbx0 b6f75f6
Update DESCRIPTION
rchau88 67d4a06
documentation for CVVs and new SC2 primer scheme
kristinelacek 3b3d39b
comma error
kristinelacek 339edf6
Merge pull request #101 from CDCgov/expand-dais-refs
kristinelacek d3073ca
release notes
kristinelacek 54d022d
typo
kristinelacek d356aa8
+Mandy, amend title
kristinelacek 1558fa5
missing .
kristinelacek a356639
Merge pull request #100 from CDCgov/podman-docs
kristinelacek 7d994d5
Expand upgrading MIRA page to have both container removal and re-runn…
kristinelacek 34ab4a3
update inst.citation
kristinelacek b440752
Update title in mac-podman-setup.Rmd to specify "M-chip" Mac
nbx0 e0bcc29
Add release email for MIRA v2.1.0
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,126 @@ | ||
| Subject: e(draft) MIRA v2.1.0 Released! | ||
| Content-type: text/html | ||
| Bcc: "Ben gmail" <b.rambomartin@gmail.com>, "Ben" <nbx0@cdc.gov>, "Kristine" <qgx6@cdc.gov> | ||
| From: idseqsupport@cdc.gov | ||
|
|
||
| <html> | ||
|
|
||
| <head> | ||
| <meta charset="UTF-8"> | ||
| <title>MIRA v2.1.0 Released!</title> | ||
| <style> | ||
| body { | ||
| font-family: "Segoe UI", "Roboto", "Helvetica Neue", Arial, "Liberation Sans", sans-serif; | ||
| color: #222; | ||
| background: #fff; | ||
| } | ||
|
|
||
| .container { | ||
| max-width: 700px; | ||
| margin: 0 auto; | ||
| background: #f1f1f1; | ||
| padding: 32px 40px; | ||
| border-radius: 10px; | ||
| border: 1px solid #e0e0e0; | ||
| } | ||
|
|
||
| h1 { | ||
| color: #005ea2; | ||
| font-size: 1.6em; | ||
| margin-bottom: 0.5em; | ||
| } | ||
|
|
||
| ul, | ||
| ol { | ||
| margin: 0 0 1em 1.5em; | ||
| } | ||
|
|
||
| li { | ||
| margin-bottom: 0.6em; | ||
| } | ||
|
|
||
| .signature { | ||
| margin-top: 2em; | ||
| } | ||
|
|
||
| .footer { | ||
| color: #888; | ||
| font-size: 0.95em; | ||
| margin-top: 2em; | ||
| } | ||
|
|
||
| .section-title { | ||
| font-weight: bold; | ||
| font-size: large; | ||
| margin-top: 1.5em; | ||
| } | ||
| </style> | ||
| </head> | ||
|
|
||
| <body> | ||
| <div class="container"> | ||
| <img src="https://cdcgov.github.io/MIRA/logo.png" alt="MIRA Logo" style="width:200px;height:auto;"> | ||
| <p>Dear MIRA users,</p> | ||
| <p>Due to your ongoing sequencing efforts, GISAID sequences assembled with MIRA now total over <b>14,000 samples | ||
| from 47 countries</b>!</p> | ||
| <h1>MIRA v2.1.0</h1> | ||
| <p>We are delighted to announce the release of <b>MIRA v2.1.0</b>! Please be sure to upgrade your installation | ||
| following these <a href="https://cdcgov.github.io/MIRA/articles/upgrading-mira-dd.html" target="_blank">these | ||
| instructions our website.</a> For Mac users who have experienced problems with Docker, we now | ||
| recommend using Podman and have <a href="https://cdcgov.github.io/MIRA/articles/mac-podman-setup.html" | ||
| target="_blank"> | ||
| instructions here.</a></p> | ||
| <div class="section-title">Notable additions to this version include:</div> | ||
| <ul> | ||
| <li><b>Influenza</b> | ||
| <ul> | ||
| <li>Amino acid mutations called against <a | ||
| href="https://www.who.int/publications/m/item/recommended-composition-of-influenza-virus-vaccines-for-use-in-the-2025-2026-nh-influenza-season" | ||
| target="_blank">contemporary seasonal vaccine recommendations</a> and <a | ||
| href="https://aspr.hhs.gov/legal/Pandemic-Influenza-Strategy/Pages/Objective-1.aspx" | ||
| target="_blank">zoonotic CVVs.</a></li> | ||
| </ul> | ||
| </li> | ||
| <li><b>SARS-CoV-2</b> | ||
| <ul> | ||
| <li>SC2-Spike Illumina module</li> | ||
| <li>Artic V5.4.2 primers for SARS-CoV-2 whole genome Illumina sequencing</li> | ||
| </ul> | ||
| </li> | ||
| <li><b>RSV</b> | ||
| <ul> | ||
| <li>Artic V1.0 and updated VIDRL primers</li> | ||
| </ul> | ||
| </li> | ||
| </ul> | ||
| <div class="section-title">GISAID Submissions</div> | ||
| <p>GISAID Influenza submissions now allow you to include <b>"Assembly Method"</b> in the sample metadata, please | ||
| be | ||
| sure to denote <b>MIRA</b> here.</p> | ||
| <img | ||
| src="https://github.com/CDCgov/MIRA/blob/v2.1.0/images/gisaid_assembly_method_mira.png?raw=true" alt="Select MIRA as the assembler when submitting to GISAID" style="width:400px;height:auto;"> | ||
| <p>If you are submitting MIRA sequences to GISAID and have not been receiving monthly clade and mutation reports | ||
| from us, please reply to this email.</p> | ||
| <div class="section-title">HPC Support</div> | ||
| <p>If your laboratory utilizes a High-Performance Computing Cluster (HPC), we can assist | ||
| your bioinformatics personnel with setting up <b>MIRA-NF</b>, which leverages a Nextflow framework to run MIRA | ||
| without the GUI on a computing cluster.</p> | ||
| <hr> | ||
| <p>CDC's Influenza Division remains committed to providing technical support to the laboratories that we have | ||
| trained. Thank you for your ongoing collaboration and we are eager to assist with any future questions you may | ||
| have.</p> | ||
| <hr> | ||
| <div class="signature"> | ||
| Most sincerely,<br><br> | ||
| Ben, Kristine, Reina, and Mandy<br> | ||
| <span>Bioinformatics Infrastructure Activity<br> | ||
| Influenza Division<br> | ||
| United States CDC</span> | ||
| <br> | ||
| <img src="https://www.cdc.gov/TemplatePackage/5.0/img/logo/cdc-logo-tag-right.svg" alt="CDC Logo" | ||
| style="width:300px;height:auto;"> | ||
| </div> | ||
| </div> | ||
| </body> | ||
|
|
||
| </html> |
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[nitpick] The repeated comments and individual COPY/RUN blocks increase layer count; consider combining related steps into fewer RUN/COPY instructions to optimize the image.