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279 <div id="start-of-content" class="show-on-focus"></div>
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280
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281 <div id="js-flash-container">
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282 </div>
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284
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285
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286 <div role="main">
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287 <div itemscope itemtype="http://schema.org/SoftwareSourceCode">
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295 <div class="pagehead repohead instapaper_ignore readability-menu experiment-repo-nav ">
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301
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312 Watch
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334 <span class="select-menu-item-heading">Not watching</span>
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335 <span class="description">Be notified when participating or @mentioned.</span>
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336 <span class="js-select-button-text hidden-select-button-text">
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337 <svg aria-hidden="true" class="octicon octicon-eye" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M8.06 2C3 2 0 8 0 8s3 6 8.06 6C13 14 16 8 16 8s-3-6-7.94-6zM8 12c-2.2 0-4-1.78-4-4 0-2.2 1.8-4 4-4 2.22 0 4 1.8 4 4 0 2.22-1.78 4-4 4zm2-4c0 1.11-.89 2-2 2-1.11 0-2-.89-2-2 0-1.11.89-2 2-2 1.11 0 2 .89 2 2z"/></svg>
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349 <span class="js-select-button-text hidden-select-button-text">
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351 Unwatch
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352 </span>
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355
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356 <div class="select-menu-item js-navigation-item " role="menuitem" tabindex="0">
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360 <span class="select-menu-item-heading">Ignoring</span>
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361 <span class="description">Never be notified.</span>
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362 <span class="js-select-button-text hidden-select-button-text">
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364 Stop ignoring
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368
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369 </div>
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370
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371 </div>
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372 </div>
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374 </form>
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376
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377 <li>
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378
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379 <div class="js-toggler-container js-social-container starring-container ">
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382 type="submit"
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387 Unstar
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390 aria-label="6 users starred this repository">
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404 aria-label="6 users starred this repository">
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420 Fork
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426 </a>
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429
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430 <h1 class="public ">
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460
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468
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471 Projects
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565 <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring">
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580 data-pjax
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582 Find file
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583 </a>
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584 <button aria-label="Copy file path to clipboard" class="js-zeroclipboard btn btn-sm BtnGroup-item tooltipped tooltipped-s" data-copied-hint="Copied!" type="button">Copy path</button>
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585 </div>
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588 </div>
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589 </div>
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591
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592
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593 <div class="commit-tease">
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594 <span class="float-right">
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595 <a class="commit-tease-sha" href="/najoshi/ucd-biocore-galaxy/commit/2ba3ca1e6b00cdc3727008ecfe6b2e7b7209c9b7" data-pjax>
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596 2ba3ca1
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597 </a>
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598 <relative-time datetime="2014-12-09T10:28:05Z">Dec 9, 2014</relative-time>
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599 </span>
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600 <div>
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601 <img alt="@najoshi" class="avatar" height="20" src="https://avatars3.githubusercontent.com/u/607905?v=4&s=40" width="20" />
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602 <a href="/najoshi" class="user-mention" rel="author">najoshi</a>
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603 <a href="/najoshi/ucd-biocore-galaxy/commit/2ba3ca1e6b00cdc3727008ecfe6b2e7b7209c9b7" class="message" data-pjax="true" title="removed software from galaxy listing that we do not have for galaxy, added indexes for chr20 on hg19, updated versions in XML for all non-built-in software">removed software from galaxy listing that we do not have for galaxy, โฆ</a>
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604 </div>
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605
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606 <div class="commit-tease-contributors">
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607 <button type="button" class="btn-link muted-link contributors-toggle" data-facebox="#blob_contributors_box">
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608 <strong>1</strong>
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609 contributor
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610 </button>
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611
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612 </div>
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613
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614 <div id="blob_contributors_box" style="display:none">
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615 <h2 class="facebox-header" data-facebox-id="facebox-header">Users who have contributed to this file</h2>
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616 <ul class="facebox-user-list" data-facebox-id="facebox-description">
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617 <li class="facebox-user-list-item">
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618 <img alt="@najoshi" height="24" src="https://avatars1.githubusercontent.com/u/607905?v=4&s=48" width="24" />
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619 <a href="/najoshi">najoshi</a>
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620 </li>
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621 </ul>
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622 </div>
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624
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625
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626 <div class="file">
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627 <div class="file-header">
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628 <div class="file-actions">
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629
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630 <div class="BtnGroup">
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631 <a href="/najoshi/ucd-biocore-galaxy/raw/master/tool-data/bwa_index.loc" class="btn btn-sm BtnGroup-item" id="raw-url">Raw</a>
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632 <a href="/najoshi/ucd-biocore-galaxy/blame/master/tool-data/bwa_index.loc" class="btn btn-sm js-update-url-with-hash BtnGroup-item" data-hotkey="b">Blame</a>
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633 <a href="/najoshi/ucd-biocore-galaxy/commits/master/tool-data/bwa_index.loc" class="btn btn-sm BtnGroup-item" rel="nofollow">History</a>
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634 </div>
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635
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636
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637 <!-- '"` --><!-- </textarea></xmp> --></option></form><form accept-charset="UTF-8" action="/najoshi/ucd-biocore-galaxy/edit/master/tool-data/bwa_index.loc" class="inline-form js-update-url-with-hash" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="uNXaP8A9g4c3DroAPwIiSttcfNFSLnLXybaRGLtxHXYRYvz25OtL+cTPq4C0ROVBugzsrojxKkR1ccGozObx5g==" /></div>
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638 <button class="btn-octicon tooltipped tooltipped-nw" type="submit"
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639 aria-label="Fork this project and edit the file" data-hotkey="e" data-disable-with>
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640 <svg aria-hidden="true" class="octicon octicon-pencil" height="16" version="1.1" viewBox="0 0 14 16" width="14"><path fill-rule="evenodd" d="M0 12v3h3l8-8-3-3-8 8zm3 2H1v-2h1v1h1v1zm10.3-9.3L12 6 9 3l1.3-1.3a.996.996 0 0 1 1.41 0l1.59 1.59c.39.39.39 1.02 0 1.41z"/></svg>
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641 </button>
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642 </form> <!-- '"` --><!-- </textarea></xmp> --></option></form><form accept-charset="UTF-8" action="/najoshi/ucd-biocore-galaxy/delete/master/tool-data/bwa_index.loc" class="inline-form" method="post"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /><input name="authenticity_token" type="hidden" value="Nr1qDS2fGXMfBgjrpjq7LQQBAOF4FKnkWNwFPiRHp3fjBi9K9L0PIj03Yy+nu1Z1nNTAUxM+ejwgvgB31MzJPw==" /></div>
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643 <button class="btn-octicon btn-octicon-danger tooltipped tooltipped-nw" type="submit"
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644 aria-label="Fork this project and delete the file" data-disable-with>
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645 <svg aria-hidden="true" class="octicon octicon-trashcan" height="16" version="1.1" viewBox="0 0 12 16" width="12"><path fill-rule="evenodd" d="M11 2H9c0-.55-.45-1-1-1H5c-.55 0-1 .45-1 1H2c-.55 0-1 .45-1 1v1c0 .55.45 1 1 1v9c0 .55.45 1 1 1h7c.55 0 1-.45 1-1V5c.55 0 1-.45 1-1V3c0-.55-.45-1-1-1zm-1 12H3V5h1v8h1V5h1v8h1V5h1v8h1V5h1v9zm1-10H2V3h9v1z"/></svg>
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646 </button>
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647 </form> </div>
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648
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649 <div class="file-info">
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650 42 lines (40 sloc)
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651 <span class="file-info-divider"></span>
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652 1.92 KB
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653 </div>
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654 </div>
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655
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656
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657
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658 <div itemprop="text" class="blob-wrapper data type-text">
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659 <table class="highlight tab-size js-file-line-container" data-tab-size="8">
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660 <tr>
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661 <td id="L1" class="blob-num js-line-number" data-line-number="1"></td>
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662 <td id="LC1" class="blob-code blob-code-inner js-file-line">#This is a sample file distributed with Galaxy that enables tools</td>
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663 </tr>
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664 <tr>
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665 <td id="L2" class="blob-num js-line-number" data-line-number="2"></td>
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666 <td id="LC2" class="blob-code blob-code-inner js-file-line">#to use a directory of BWA indexed sequences data files. You will need</td>
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667 </tr>
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668 <tr>
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669 <td id="L3" class="blob-num js-line-number" data-line-number="3"></td>
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670 <td id="LC3" class="blob-code blob-code-inner js-file-line">#to create these data files and then create a bwa_index.loc file</td>
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671 </tr>
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672 <tr>
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673 <td id="L4" class="blob-num js-line-number" data-line-number="4"></td>
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674 <td id="LC4" class="blob-code blob-code-inner js-file-line">#similar to this one (store it in this directory) that points to</td>
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675 </tr>
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676 <tr>
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677 <td id="L5" class="blob-num js-line-number" data-line-number="5"></td>
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678 <td id="LC5" class="blob-code blob-code-inner js-file-line">#the directories in which those files are stored. The bwa_index.loc</td>
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679 </tr>
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680 <tr>
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681 <td id="L6" class="blob-num js-line-number" data-line-number="6"></td>
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682 <td id="LC6" class="blob-code blob-code-inner js-file-line">#file has this format (longer white space characters are TAB characters):</td>
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683 </tr>
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684 <tr>
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685 <td id="L7" class="blob-num js-line-number" data-line-number="7"></td>
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686 <td id="LC7" class="blob-code blob-code-inner js-file-line">#</td>
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687 </tr>
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688 <tr>
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689 <td id="L8" class="blob-num js-line-number" data-line-number="8"></td>
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690 <td id="LC8" class="blob-code blob-code-inner js-file-line">#<unique_build_id> <dbkey> <display_name> <file_path></td>
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691 </tr>
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692 <tr>
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693 <td id="L9" class="blob-num js-line-number" data-line-number="9"></td>
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694 <td id="LC9" class="blob-code blob-code-inner js-file-line">#</td>
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695 </tr>
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696 <tr>
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697 <td id="L10" class="blob-num js-line-number" data-line-number="10"></td>
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698 <td id="LC10" class="blob-code blob-code-inner js-file-line">#So, for example, if you had phiX indexed stored in </td>
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699 </tr>
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700 <tr>
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701 <td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
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702 <td id="LC11" class="blob-code blob-code-inner js-file-line">#/depot/data2/galaxy/phiX/base/, </td>
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703 </tr>
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704 <tr>
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705 <td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
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706 <td id="LC12" class="blob-code blob-code-inner js-file-line">#then the bwa_index.loc entry would look like this:</td>
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707 </tr>
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708 <tr>
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709 <td id="L13" class="blob-num js-line-number" data-line-number="13"></td>
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710 <td id="LC13" class="blob-code blob-code-inner js-file-line">#</td>
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711 </tr>
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712 <tr>
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713 <td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
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714 <td id="LC14" class="blob-code blob-code-inner js-file-line">#phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa</td>
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715 </tr>
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716 <tr>
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717 <td id="L15" class="blob-num js-line-number" data-line-number="15"></td>
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718 <td id="LC15" class="blob-code blob-code-inner js-file-line">#</td>
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719 </tr>
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720 <tr>
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721 <td id="L16" class="blob-num js-line-number" data-line-number="16"></td>
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722 <td id="LC16" class="blob-code blob-code-inner js-file-line">#and your /depot/data2/galaxy/phiX/base/ directory</td>
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723 </tr>
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724 <tr>
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725 <td id="L17" class="blob-num js-line-number" data-line-number="17"></td>
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726 <td id="LC17" class="blob-code blob-code-inner js-file-line">#would contain phiX.fa.* files:</td>
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727 </tr>
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728 <tr>
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729 <td id="L18" class="blob-num js-line-number" data-line-number="18"></td>
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730 <td id="LC18" class="blob-code blob-code-inner js-file-line">#</td>
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731 </tr>
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732 <tr>
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733 <td id="L19" class="blob-num js-line-number" data-line-number="19"></td>
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734 <td id="LC19" class="blob-code blob-code-inner js-file-line">#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb</td>
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735 </tr>
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736 <tr>
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737 <td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
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738 <td id="LC20" class="blob-code blob-code-inner js-file-line">#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann</td>
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739 </tr>
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740 <tr>
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741 <td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
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742 <td id="LC21" class="blob-code blob-code-inner js-file-line">#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt</td>
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743 </tr>
|
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744 <tr>
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745 <td id="L22" class="blob-num js-line-number" data-line-number="22"></td>
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746 <td id="LC22" class="blob-code blob-code-inner js-file-line">#...etc...</td>
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747 </tr>
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748 <tr>
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749 <td id="L23" class="blob-num js-line-number" data-line-number="23"></td>
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750 <td id="LC23" class="blob-code blob-code-inner js-file-line">#</td>
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751 </tr>
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752 <tr>
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753 <td id="L24" class="blob-num js-line-number" data-line-number="24"></td>
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754 <td id="LC24" class="blob-code blob-code-inner js-file-line">#Your bwa_index.loc file should include an entry per line for each</td>
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755 </tr>
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756 <tr>
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757 <td id="L25" class="blob-num js-line-number" data-line-number="25"></td>
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758 <td id="LC25" class="blob-code blob-code-inner js-file-line">#index set you have stored. The "file" in the path does not actually</td>
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759 </tr>
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760 <tr>
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761 <td id="L26" class="blob-num js-line-number" data-line-number="26"></td>
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762 <td id="LC26" class="blob-code blob-code-inner js-file-line">#exist, but it is the prefix for the actual index files. For example:</td>
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763 </tr>
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764 <tr>
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765 <td id="L27" class="blob-num js-line-number" data-line-number="27"></td>
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766 <td id="LC27" class="blob-code blob-code-inner js-file-line">#</td>
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767 </tr>
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768 <tr>
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769 <td id="L28" class="blob-num js-line-number" data-line-number="28"></td>
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|
770 <td id="LC28" class="blob-code blob-code-inner js-file-line">#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa</td>
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|
771 </tr>
|
|
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772 <tr>
|
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|
773 <td id="L29" class="blob-num js-line-number" data-line-number="29"></td>
|
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|
774 <td id="LC29" class="blob-code blob-code-inner js-file-line">#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa</td>
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775 </tr>
|
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|
776 <tr>
|
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777 <td id="L30" class="blob-num js-line-number" data-line-number="30"></td>
|
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|
778 <td id="LC30" class="blob-code blob-code-inner js-file-line">#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa</td>
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779 </tr>
|
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780 <tr>
|
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781 <td id="L31" class="blob-num js-line-number" data-line-number="31"></td>
|
|
|
782 <td id="LC31" class="blob-code blob-code-inner js-file-line">#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa</td>
|
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|
783 </tr>
|
|
|
784 <tr>
|
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785 <td id="L32" class="blob-num js-line-number" data-line-number="32"></td>
|
|
|
786 <td id="LC32" class="blob-code blob-code-inner js-file-line">#...etc...</td>
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|
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787 </tr>
|
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788 <tr>
|
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|
789 <td id="L33" class="blob-num js-line-number" data-line-number="33"></td>
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|
790 <td id="LC33" class="blob-code blob-code-inner js-file-line">#</td>
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791 </tr>
|
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792 <tr>
|
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|
793 <td id="L34" class="blob-num js-line-number" data-line-number="34"></td>
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794 <td id="LC34" class="blob-code blob-code-inner js-file-line">#Note that for backwards compatibility with workflows, the unique ID of</td>
|
|
|
795 </tr>
|
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|
796 <tr>
|
|
|
797 <td id="L35" class="blob-num js-line-number" data-line-number="35"></td>
|
|
|
798 <td id="LC35" class="blob-code blob-code-inner js-file-line">#an entry must be the path that was in the original loc file, because that</td>
|
|
|
799 </tr>
|
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|
800 <tr>
|
|
|
801 <td id="L36" class="blob-num js-line-number" data-line-number="36"></td>
|
|
|
802 <td id="LC36" class="blob-code blob-code-inner js-file-line">#is the value stored in the workflow for that parameter. That is why the</td>
|
|
|
803 </tr>
|
|
|
804 <tr>
|
|
|
805 <td id="L37" class="blob-num js-line-number" data-line-number="37"></td>
|
|
|
806 <td id="LC37" class="blob-code blob-code-inner js-file-line">#hg19 entry above looks odd. New genomes can be better-looking.</td>
|
|
|
807 </tr>
|
|
|
808 <tr>
|
|
|
809 <td id="L38" class="blob-num js-line-number" data-line-number="38"></td>
|
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|
810 <td id="LC38" class="blob-code blob-code-inner js-file-line">#</td>
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|
|
811 </tr>
|
|
|
812 <tr>
|
|
|
813 <td id="L39" class="blob-num js-line-number" data-line-number="39"></td>
|
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|
814 <td id="LC39" class="blob-code blob-code-inner js-file-line">
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815 </td>
|
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|
816 </tr>
|
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817 <tr>
|
|
|
818 <td id="L40" class="blob-num js-line-number" data-line-number="40"></td>
|
|
|
819 <td id="LC40" class="blob-code blob-code-inner js-file-line">hg19_chr12 hg19_chr12 hg19_chr12 /data/refs/hg19/chr12.fa</td>
|
|
|
820 </tr>
|
|
|
821 <tr>
|
|
|
822 <td id="L41" class="blob-num js-line-number" data-line-number="41"></td>
|
|
|
823 <td id="LC41" class="blob-code blob-code-inner js-file-line">hg19_chr20 hg19_chr20 hg19_chr20 /data/refs/hg19/chr20.fa</td>
|
|
|
824 </tr>
|
|
|
825 </table>
|
|
|
826
|
|
|
827 <div class="BlobToolbar position-absolute js-file-line-actions dropdown js-menu-container js-select-menu d-none" aria-hidden="true">
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828 <button class="btn-octicon ml-0 px-2 p-0 bg-white border border-gray-dark rounded-1 dropdown-toggle js-menu-target" id="js-file-line-action-button" type="button" aria-expanded="false" aria-haspopup="true" aria-label="Inline file action toolbar" aria-controls="inline-file-actions">
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829 <svg aria-hidden="true" class="octicon" height="16" version="1.1" viewBox="0 0 13 4" width="14">
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830 <g stroke="none" stroke-width="1" fill-rule="evenodd">
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831 <g transform="translate(-1.000000, -6.000000)">
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832 <path d="M2.5,9.5 C1.67157288,9.5 1,8.82842712 1,8 C1,7.17157288 1.67157288,6.5 2.5,6.5 C3.32842712,6.5 4,7.17157288 4,8 C4,8.82842712 3.32842712,9.5 2.5,9.5 Z M7.5,9.5 C6.67157288,9.5 6,8.82842712 6,8 C6,7.17157288 6.67157288,6.5 7.5,6.5 C8.32842712,6.5 9,7.17157288 9,8 C9,8.82842712 8.32842712,9.5 7.5,9.5 Z M12.5,9.5 C11.6715729,9.5 11,8.82842712 11,8 C11,7.17157288 11.6715729,6.5 12.5,6.5 C13.3284271,6.5 14,7.17157288 14,8 C14,8.82842712 13.3284271,9.5 12.5,9.5 Z"></path>
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833 </g>
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834 </g>
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835 </svg>
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836 </button>
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837 <div class="dropdown-menu-content js-menu-content" id="inline-file-actions">
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838 <ul class="BlobToolbar-dropdown dropdown-menu dropdown-menu-se mt-2">
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839 <li><a class="js-zeroclipboard dropdown-item" style="cursor:pointer;" id="js-copy-lines" data-original-text="Copy lines">Copy lines</a></li>
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840 <li><a class="js-zeroclipboard dropdown-item" id= "js-copy-permalink" style="cursor:pointer;" data-original-text="Copy permalink">Copy permalink</a></li>
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841 <li><a href="/najoshi/ucd-biocore-galaxy/blame/6d4781d7537c675590060898e98c3328d2b6f249/tool-data/bwa_index.loc" class="dropdown-item js-update-url-with-hash" id="js-view-git-blame">View git blame</a></li>
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842 <li><a href="/najoshi/ucd-biocore-galaxy/issues/new" class="dropdown-item" id="js-new-issue">Open new issue</a></li>
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843 </ul>
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844 </div>
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846
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847 </div>
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848
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849 </div>
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850
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851 <button type="button" data-facebox="#jump-to-line" data-facebox-class="linejump" data-hotkey="l" class="d-none">Jump to Line</button>
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852 <div id="jump-to-line" style="display:none">
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853 <!-- '"` --><!-- </textarea></xmp> --></option></form><form accept-charset="UTF-8" action="" class="js-jump-to-line-form" method="get"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /></div>
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854 <input class="form-control linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" aria-label="Jump to line" autofocus>
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855 <button type="submit" class="btn">Go</button>
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856 </form> </div>
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857
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858 </div>
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859 <div class="modal-backdrop js-touch-events"></div>
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860 </div>
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861
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862 </div>
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900 </button>
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901 You can't perform that action at this time.
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906 <script crossorigin="anonymous" src="https://assets-cdn.github.com/assets/frameworks-db06d5e5cc508b59a3d6d16c22bb523005ca9fc0c513cbb039b32a25204b6be7.js"></script>
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907
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908 <script async="async" crossorigin="anonymous" src="https://assets-cdn.github.com/assets/github-da65661edce7dd1ef92a685ec40dae4e270e94dc323d9b2c7762d98dcff91964.js"></script>
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911
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912
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931
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