Merge pull request #345 from MoTrPAC/342_JZ_Publication_Screenshots

Connects to #342. Connects to #344. Published paper screenshots. PreCAWG onboarding info update.

src/LandingPage/landingPage.jsx

@@ -15,6 +15,7 @@ import BackgroundVideoImage from '../assets/LandingPageGraphics/background_video
 import LayerRunner from '../assets/LandingPageGraphics/Data_Layer_Runner.png';
 import RatFigurePaass1b from '../assets/LandingPageGraphics/rat-figure-pass1b.svg';
 import LandscapeAbstract from '../assets/LandingPageGraphics/landscape_abstract.gif';
+import NatureIssueCover from '../assets/LandingPageGraphics/nature_issue_cover.jpg';
 import BackgroundVideo from './components/backgroundVideo';
 import Figure1C from './components/figure1c';
 
@@ -163,7 +164,7 @@ export function LandingPage({ isAuthenticated, profile }) {
   }, [networkNodes]);
 
   const goToExternalLink = useCallback(() => {
-    window.open('https://www.nature.com/articles/s41586-023-06877-w', '_blank');
+    window.open('https://www.nature.com/nature/volumes/629/issues/8010', '_blank');
   }, []);
 
   // Redirect authenticated users to protected route
@@ -261,7 +262,7 @@ export function LandingPage({ isAuthenticated, profile }) {
       <section className="fifth">
         <div className="w-100 h-100 d-flex align-items-center">
           <div className="section-content-container container text-center">
-            <div className="row content-landscape-preprint d-flex align-items-center">
+            <div className="row content-landscape-paper d-flex align-items-center">
               <div className="content col-12 col-md-6">
                 <h1>
                   MoTrPAC animal endurance training exercise study paper now published in
@@ -278,15 +279,15 @@ export function LandingPage({ isAuthenticated, profile }) {
                   LEARN MORE
                 </a>
               </div>
-              <div
-                className="feature-image col-12 col-md-6 mx-auto"
-                onClick={goToExternalLink}
-              >
-                <img
-                  src={LandscapeAbstract}
-                  className="img-fluid lanascape-paper-abstract"
-                  alt="Landscape Paper Abstract"
-                />
+              <div className="feature-image-content-container col-12 col-md-6 mx-auto">
+                <div className="feature-image" onClick={goToExternalLink}>
+                  <img
+                    src={NatureIssueCover}
+                    className="img-fluid lanascape-paper-abstract"
+                    alt="Landscape Paper Abstract"
+                  />
+                </div>
+                <div className="feature-image-attribution mt-1">Cover image by Nik Spencer/Nature</div>
               </div>
             </div>
           </div>

src/MultiOmicsWorkingGroups/preCAWG.jsx

@@ -557,15 +557,17 @@ function PreCAWG() {
             below).
           </li>
           <li>
-            Download and install the{' '}
+            Download and install the
+            {' '}
             <a
-              href="https://cloud.google.com/sdk/?hl=en"
+              href="https://cloud.google.com/sdk/docs/install"
               target="_blank"
               rel="noreferrer"
             >
               Google Command Line Tools
             </a>{' '}
-            on your preferred work computer.
+            on your preferred work computer and connect them to the institutional
+            Google account you created (See Google CLI instructions).
           </li>
           <li>
             Set up a{' '}
@@ -666,7 +668,8 @@ function PreCAWG() {
               rel="noreferrer"
             >
               [email protected]
-            </a>{' '}
+            </a>
+            {' '}
             and <b>your local site PI</b> with a written request for the
             following access permissions:
             <ol className="nested-order-list">
@@ -713,6 +716,19 @@ function PreCAWG() {
               </li>
             </ol>
           </li>
+          <li>
+            Once this is done, you should be able to open a PowerShell (Windows) or
+            Terminal (Mac) and run the command
+            {' '}
+            <code>gsutil ls gs://motrpac-data-hub</code>
+            . If you can, that means your Google Cloud CLI is set up and your GCP
+            access is working correctly. If this fails, but you think you have access,
+            check that
+            {' '}
+            <code>gsutil</code>
+            {' '}
+            is in your PATH.
+          </li>
           <li>
             Clone the following two GitHub repositories once you are granted
             access:
@@ -738,45 +754,88 @@ function PreCAWG() {
             </ol>
           </li>
           <li>
-            Install the{' '}
+            Install the
+            {' '}
             <a
               href="https://github.com/MoTrPAC/MotrpacHumanPreSuspension"
               target="_blank"
               rel="noreferrer"
             >
               MoTrPAC/MotrpacHumanPreSuspension
-            </a>{' '}
+            </a>
+            {' '}
             package - this package gives you programmatic access to the PreCAWG
-            data. Also review the <code>README.md</code>
+            data. Also review the
+            {' '}
+            <code>README.md</code>
+            {' '}
+            which explains how to install from the local clone of the repo. This
+            package cannot be installed directly from GitHub.com.
           </li>
           <li>
-            Read the{' '}
+            Read the
+            {' '}
             <a
               href="https://github.com/MoTrPAC/precovid-analyses"
               target="_blank"
               rel="noreferrer"
             >
               MoTrPAC/precovid-analyses
-            </a>{' '}
-            <code>README.md</code> - this repo is where novel analysis code must
+            </a>
+            {' '}
+            <code>README.md</code>
+            {' '}
+            - this repo is where novel analysis code must
             be stored
           </li>
           <li>
-            Set up your <code>motrpac_config.json</code> configuration file
+            Set up your
+            {' '}
+            <code>motrpac_config.json</code>
+            {' '}
+            configuration file as described in the
+            {' '}
+            <a
+              href="https://github.com/MoTrPAC/precovid-analyses"
+              target="_blank"
+              rel="noreferrer"
+            >
+              MoTrPAC/precovid-analyses
+            </a>
+            {' '}
+            <code>README.md</code>
           </li>
           <li>
-            Open Rstudio and attempt to run{' '}
+            Open Rstudio and attempt to run
+            {' '}
             <code>
               human-precovid-sed-adu_t07-adipose_prot-ph_metadata_qc-report_v1.Rmd
-            </code>{' '}
-            (after pointing to your <code>motrpac_config.json</code> file.
+            </code>
+            {' '}
+            (after pointing to your
+            {' '}
+            <code>motrpac_config.json</code>
+            {' '}
+            file). This R markdown file is in the
+            {' '}
+            <a
+              href="https://github.com/MoTrPAC/precovid-analyses"
+              target="_blank"
+              rel="noreferrer"
+            >
+              MoTrPAC/precovid-analyses
+            </a>
+            {' '}
+            repo in the QC folder.
           </li>
           <li>
-            Then ensure that{' '}
-            <code>MotrpacHumanPreSuspension::load_differential_analysis</code>{' '}
+            Then ensure that
+            {' '}
+            <code>MotrpacHumanPreSuspension::load_differential_analysis</code>
+            {' '}
             runs for you.
           </li>
-          <li>If #13 and #15 are running, you are ready to go!</li>
+          <li>If #13 and #14 are running, you are ready to go!</li>
         </ol>
       </div>
     </div>