changeset 6:a4e5c90cf6cb draft

Uploaded
author lz_hust
date Sat, 01 Jun 2019 07:03:27 -0400
parents e0a6b2ba8bd3
children 5312036ae97e
files gatk-tools
diffstat 1 files changed, 1188 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gatk-tools	Sat Jun 01 07:03:27 2019 -0400
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+                    </ul>
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+                    <h4 class="text-gray-light text-normal text-mono f5 mb-2  border-top pt-3">Connect with others</h4>
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+            <a rel="nofollow" class="get-repo-btn btn btn-outline" style="width: 50%" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;download popover&quot;,&quot;repository_id&quot;:189599350,&quot;auth_type&quot;:&quot;LOG_IN&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;9296:3F63:B1FBFC:1321364:5CF25B7F&quot;,&quot;originating_url&quot;:&quot;https://github.com/huster16/gatk-tools&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="cb61463cc7655c64c1c248161ce77d7b3d3c314ea70146f402f8c7d75b0680e3" href="/login?return_to=https%3A%2F%2Fgithub.com%2Fhuster16%2Fgatk-tools">Sign in</a>
+            <a rel="nofollow" class="get-repo-btn btn btn-primary" style="width: 50%" data-hydro-click="{&quot;event_type&quot;:&quot;authentication.click&quot;,&quot;payload&quot;:{&quot;location_in_page&quot;:&quot;download popover&quot;,&quot;repository_id&quot;:189599350,&quot;auth_type&quot;:&quot;SIGN_UP&quot;,&quot;client_id&quot;:null,&quot;originating_request_id&quot;:&quot;9296:3F63:B1FBFC:1321364:5CF25B7F&quot;,&quot;originating_url&quot;:&quot;https://github.com/huster16/gatk-tools&quot;,&quot;referrer&quot;:null,&quot;user_id&quot;:null}}" data-hydro-click-hmac="4de2cd77e5bd2d2867a7b2d5a861644713963b0a7cf6f57303dd2946291b114e" href="/join?return_to=%2Fhuster16%2Fgatk-tools">Sign up</a>
+          </div>
+        </div>
+
+      <div class="js-modal-download-mac py-2 px-3 d-none">
+        <h4 class="lh-condensed mb-3">Launching GitHub Desktop<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4>
+        <p class="text-gray">If nothing happens, <a href="https://desktop.github.com/">download GitHub Desktop</a> and try again.</p>
+        <p><button class="btn-link js-get-repo-modal-download-back">Go back</button></p>
+      </div>
+
+      <div class="js-modal-download-windows py-2 px-3 d-none">
+        <h4 class="lh-condensed mb-3">Launching GitHub Desktop<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4>
+        <p class="text-gray">If nothing happens, <a href="https://desktop.github.com/">download GitHub Desktop</a> and try again.</p>
+        <p><button class="btn-link js-get-repo-modal-download-back">Go back</button></p>
+      </div>
+
+      <div class="js-modal-download-xcode py-2 px-3 d-none">
+        <h4 class="lh-condensed mb-3">Launching Xcode<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4>
+        <p class="text-gray">If nothing happens, <a href="https://developer.apple.com/xcode/">download Xcode</a> and try again.</p>
+        <p><button class="btn-link js-get-repo-modal-download-back">Go back</button></p>
+      </div>
+
+      <div class="js-modal-download-visual-studio py-2 px-3 d-none">
+        <h4 class="lh-condensed mb-3">Launching Visual Studio<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4>
+        <p class="text-gray">If nothing happens, <a href="https://visualstudio.github.com/">download the GitHub extension for Visual Studio</a> and try again.</p>
+        <p><button class="btn-link js-get-repo-modal-download-back">Go back</button></p>
+      </div>
+
+    </div>
+  </div>
+</details>
+
+</div>
+
+
+  
+
+<include-fragment src="/huster16/gatk-tools/tree-commit/8396208ba320ef1f0cd4b6b02607a2d2aae5f760" class="commit-tease commit-loader">
+  <div class="blank loader-loading">
+      <img alt="" class="loader" src="https://github.githubassets.com/images/spinners/octocat-spinner-32-EAF2F5.gif" width="16" height="16" />
+      Fetching latest commit…
+  </div>
+  <div class="loader-error">
+    Cannot retrieve the latest commit at this time.
+  </div>
+</include-fragment>
+
+
+<include-fragment class="file-wrap" src="/huster16/gatk-tools/file-list/master">
+  <a class="d-none js-permalink-shortcut" data-hotkey="y" href="/huster16/gatk-tools/tree/8396208ba320ef1f0cd4b6b02607a2d2aae5f760">Permalink</a>
+
+  <table class="files js-navigation-container js-active-navigation-container" data-pjax>
+    <thead>
+      <tr>
+        <th><span class="sr-only">Type</span></th>
+        <th><span class="sr-only">Name</span></th>
+        <th><span class="sr-only">Latest commit message</span></th>
+        <th><span class="sr-only">Commit time</span></th>
+      </tr>
+    </thead>
+
+
+    <tbody>
+      <tr class="warning include-fragment-error">
+        <td class="icon"><svg class="octicon octicon-alert" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M8.893 1.5c-.183-.31-.52-.5-.887-.5s-.703.19-.886.5L.138 13.499a.98.98 0 0 0 0 1.001c.193.31.53.501.886.501h13.964c.367 0 .704-.19.877-.5a1.03 1.03 0 0 0 .01-1.002L8.893 1.5zm.133 11.497H6.987v-2.003h2.039v2.003zm0-3.004H6.987V5.987h2.039v4.006z"/></svg></td>
+        <td class="content" colspan="3">Failed to load latest commit information.</td>
+      </tr>
+
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <svg aria-label="directory" class="octicon octicon-file-directory" viewBox="0 0 14 16" version="1.1" width="14" height="16" role="img"><path fill-rule="evenodd" d="M13 4H7V3c0-.66-.31-1-1-1H1c-.55 0-1 .45-1 1v10c0 .55.45 1 1 1h12c.55 0 1-.45 1-1V5c0-.55-.45-1-1-1zM6 4H1V3h5v1z"/></svg>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="generation" id="9cb9ce5bd9e807867d42a740c9633fc7-3625a25873af83c0541afd8f95fc07be91aabe3a" href="/huster16/gatk-tools/tree/master/generation">generation</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <svg aria-label="directory" class="octicon octicon-file-directory" viewBox="0 0 14 16" version="1.1" width="14" height="16" role="img"><path fill-rule="evenodd" d="M13 4H7V3c0-.66-.31-1-1-1H1c-.55 0-1 .45-1 1v10c0 .55.45 1 1 1h12c.55 0 1-.45 1-1V5c0-.55-.45-1-1-1zM6 4H1V3h5v1z"/></svg>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="tool-data" id="cacc76c3f8e5d46af3e9a108d7a64298-a54d24bc89b721726d1816c1d84b612e87530b2c" href="/huster16/gatk-tools/tree/master/tool-data">tool-data</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title=".shed.yml" id="cdcc89357908fc034bde629890b000b5-2325e6cb39480ba78f39c79f6c003dbd1e31d57f" href="/huster16/gatk-tools/blob/master/.shed.yml">.shed.yml</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="LICENSE" id="9879d6db96fd29134fc802214163b95a-261eeb9e9f8b2b4b0d119366dda99c6fd7d35c64" itemprop="license" href="/huster16/gatk-tools/blob/master/LICENSE">LICENSE</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="README" id="c47c7c7383225ab55ff591cb59c41e6b-a8addefe468edbe7d68593ece5e8aa412b4899ff" href="/huster16/gatk-tools/blob/master/README">README</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="analyze_covariates.xml" id="59610722be95a0212262688dcbf7c239-2e2bbaf59e3a3ca897dbc81ce2bd795b9d42325f" href="/huster16/gatk-tools/blob/master/analyze_covariates.xml">analyze_covariates.xml</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="base_recalibrator.xml" id="48bdf74141faebe19e0066be8cd87dd5-7317df4b6cf2302f9127fd576bc4ae33f4492009" href="/huster16/gatk-tools/blob/master/base_recalibrator.xml">base_recalibrator.xml</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="combine_gvcfs.xml" id="5a42bf8ebd8f0473dfab105bce4454bd-8f5dab6ecfcf6eecdc49559973a0f517c7ce51fe" href="/huster16/gatk-tools/blob/master/combine_gvcfs.xml">combine_gvcfs.xml</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="combine_variants.xml" id="27122924aa0d6acdcda3d1a0fdd0ca79-9f7532b3fd7b7bc45137cdb66ad4deadbf2637be" href="/huster16/gatk-tools/blob/master/combine_variants.xml">combine_variants.xml</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="gatk.xml" id="6aeaf5662a51985b4f74c250a5ccefa2-715530fdb731605326741b7f0e5da00bfaea2c70" href="/huster16/gatk-tools/blob/master/gatk.xml">gatk.xml</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="gatk_macros.xml" id="e86fbc71297931c373dc3c1ebbc5aa9b-0edfc715939f63ad66fd7e4555ecac6bc3623748" href="/huster16/gatk-tools/blob/master/gatk_macros.xml">gatk_macros.xml</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="genotype_gvcfs.xml" id="0372ebae7a90c232ee5e7536d5fc3d71-18e615ecb169da998a8246b66159d1c6819ef222" href="/huster16/gatk-tools/blob/master/genotype_gvcfs.xml">genotype_gvcfs.xml</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="haplotype_caller.xml" id="3ba21ca32b06283a30eaa19f3d2aacb7-0fddf817930f1bfbd2c286514af781a06edf1fe0" href="/huster16/gatk-tools/blob/master/haplotype_caller.xml">haplotype_caller.xml</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="indel_realigner.xml" id="e7b986d614bb6b302bf2fc4aa93817d0-6c46b5cf10b2b57e641689d5474b80f538bc11bc" href="/huster16/gatk-tools/blob/master/indel_realigner.xml">indel_realigner.xml</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="print_reads.xml" id="084bb1c569888ece53345b6d80b919d7-19269244ac276c5ac4c3ea35d88a0faa1c63dbf1" href="/huster16/gatk-tools/blob/master/print_reads.xml">print_reads.xml</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="realigner_target_creator.xml" id="00d1312b6f84e2192f19921c8e5e53d7-86621b8b4cbbf521fa5741f6fecc16f87c810c1d" href="/huster16/gatk-tools/blob/master/realigner_target_creator.xml">realigner_target_creator.xml</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="tool_data_table_conf.xml.sample" id="60160a6e4efd651b475bcbf960abcc2d-b0e4b46b92ceb44e50c9abf01cf31db95628ac93" href="/huster16/gatk-tools/blob/master/tool_data_table_conf.xml.sample">tool_data_table_conf.xml.sample</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"></span>
+          </td>
+        </tr>
+        <tr class="js-navigation-item">
+          <td class="icon">
+            <svg aria-label="file" class="octicon octicon-file" viewBox="0 0 12 16" version="1.1" width="12" height="16" role="img"><path fill-rule="evenodd" d="M6 5H2V4h4v1zM2 8h7V7H2v1zm0 2h7V9H2v1zm0 2h7v-1H2v1zm10-7.5V14c0 .55-.45 1-1 1H1c-.55 0-1-.45-1-1V2c0-.55.45-1 1-1h7.5L12 4.5zM11 5L8 2H1v12h10V5z"/></svg>
+            <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a class="js-navigation-open" title="tool_dependencies.xml" id="1f1e2fcbf1ddc07a88bc59ca246c9a90-3ac9ffc6df38d4633e8022ed0b78e3c95e586b10" href="/huster16/gatk-tools/blob/master/tool_dependencies.xml">tool_dependencies.xml</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"></span>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+</include-fragment>
+
+
+
+  <div id="readme" class="Box Box--condensed instapaper_body  js-code-block-container">
+    <div class="Box-header d-flex flex-items-center flex-justify-between px-2">
+      <h3 class="Box-title pr-3">
+        <svg class="octicon octicon-book" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M3 5h4v1H3V5zm0 3h4V7H3v1zm0 2h4V9H3v1zm11-5h-4v1h4V5zm0 2h-4v1h4V7zm0 2h-4v1h4V9zm2-6v9c0 .55-.45 1-1 1H9.5l-1 1-1-1H2c-.55 0-1-.45-1-1V3c0-.55.45-1 1-1h5.5l1 1 1-1H15c.55 0 1 .45 1 1zm-8 .5L7.5 3H2v9h6V3.5zm7-.5H9.5l-.5.5V12h6V3z"/></svg>
+        README
+      </h3>
+    </div>
+      <div class="Box-body">
+        <div class="plain"><pre style="white-space: pre-wrap">Installation note:
+A GATK license needs to be obtained separately from the Broad Institute (<a href="https://www.broadinstitute.org/gatk/" rel="nofollow">https://www.broadinstitute.org/gatk/</a>)
+to be able to use this tool. Once the license is obtained, the GATK Jar file must then be downloaded and moved 
+to /mnt/galaxy/tools/GATK/x.x-x on the server. Substitute the appropriate version number in the file path. 
+Be sure to download the correct version of the Jar file for the toolshed version installed.
+</pre></div>
+      </div>
+  </div>
+
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+  <div class="d-flex flex-justify-center pb-6">
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+    You can’t perform that action at this time.
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+    <script crossorigin="anonymous" integrity="sha512-EPrD+nddbyhpiLL8l3M8VfJpZr4J2EWQLaPXZ+6A3VDJKzS5HeZ3dkMVieHSdvIPHsMbWPyVlY42SWKoS4XTfA==" type="application/javascript" src="https://github.githubassets.com/assets/compat-bootstrap-831f12d4.js"></script>
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+  <template id="site-details-dialog">
+  <details class="details-reset details-overlay details-overlay-dark lh-default text-gray-dark hx_rsm" open>
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+        <svg class="octicon octicon-x" viewBox="0 0 12 16" version="1.1" width="12" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.48 8l3.75 3.75-1.48 1.48L6 9.48l-3.75 3.75-1.48-1.48L4.52 8 .77 4.25l1.48-1.48L6 6.52l3.75-3.75 1.48 1.48L7.48 8z"/></svg>
+      </button>
+      <div class="octocat-spinner my-6 js-details-dialog-spinner"></div>
+    </details-dialog>
+  </details>
+</template>
+
+  <div class="Popover js-hovercard-content position-absolute" style="display: none; outline: none;" tabindex="0">
+  <div class="Popover-message Popover-message--bottom-left Popover-message--large Box box-shadow-large" style="width:360px;">
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