comparison gatk-tools @ 6:a4e5c90cf6cb draft

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author lz_hust
date Sat, 01 Jun 2019 07:03:27 -0400
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719 <div class="width-full d-flex">
720 <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>
721 <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>
722 </div>
723 </div>
724
725 <div class="js-modal-download-mac py-2 px-3 d-none">
726 <h4 class="lh-condensed mb-3">Launching GitHub Desktop<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4>
727 <p class="text-gray">If nothing happens, <a href="https://desktop.github.com/">download GitHub Desktop</a> and try again.</p>
728 <p><button class="btn-link js-get-repo-modal-download-back">Go back</button></p>
729 </div>
730
731 <div class="js-modal-download-windows py-2 px-3 d-none">
732 <h4 class="lh-condensed mb-3">Launching GitHub Desktop<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4>
733 <p class="text-gray">If nothing happens, <a href="https://desktop.github.com/">download GitHub Desktop</a> and try again.</p>
734 <p><button class="btn-link js-get-repo-modal-download-back">Go back</button></p>
735 </div>
736
737 <div class="js-modal-download-xcode py-2 px-3 d-none">
738 <h4 class="lh-condensed mb-3">Launching Xcode<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4>
739 <p class="text-gray">If nothing happens, <a href="https://developer.apple.com/xcode/">download Xcode</a> and try again.</p>
740 <p><button class="btn-link js-get-repo-modal-download-back">Go back</button></p>
741 </div>
742
743 <div class="js-modal-download-visual-studio py-2 px-3 d-none">
744 <h4 class="lh-condensed mb-3">Launching Visual Studio<span class="animated-ellipsis-container"><span class="animated-ellipsis">...</span></span></h4>
745 <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>
746 <p><button class="btn-link js-get-repo-modal-download-back">Go back</button></p>
747 </div>
748
749 </div>
750 </div>
751 </details>
752
753 </div>
754
755
756
757
758 <include-fragment src="/huster16/gatk-tools/tree-commit/8396208ba320ef1f0cd4b6b02607a2d2aae5f760" class="commit-tease commit-loader">
759 <div class="blank loader-loading">
760 <img alt="" class="loader" src="https://github.githubassets.com/images/spinners/octocat-spinner-32-EAF2F5.gif" width="16" height="16" />
761 Fetching latest commit…
762 </div>
763 <div class="loader-error">
764 Cannot retrieve the latest commit at this time.
765 </div>
766 </include-fragment>
767
768
769 <include-fragment class="file-wrap" src="/huster16/gatk-tools/file-list/master">
770 <a class="d-none js-permalink-shortcut" data-hotkey="y" href="/huster16/gatk-tools/tree/8396208ba320ef1f0cd4b6b02607a2d2aae5f760">Permalink</a>
771
772 <table class="files js-navigation-container js-active-navigation-container" data-pjax>
773 <thead>
774 <tr>
775 <th><span class="sr-only">Type</span></th>
776 <th><span class="sr-only">Name</span></th>
777 <th><span class="sr-only">Latest commit message</span></th>
778 <th><span class="sr-only">Commit time</span></th>
779 </tr>
780 </thead>
781
782
783 <tbody>
784 <tr class="warning include-fragment-error">
785 <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>
786 <td class="content" colspan="3">Failed to load latest commit information.</td>
787 </tr>
788
789 <tr class="js-navigation-item">
790 <td class="icon">
791 <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>
792 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
793 </td>
794 <td class="content">
795 <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>
796 </td>
797 <td class="message">
798 <span class="css-truncate css-truncate-target">
799 </span>
800 </td>
801 <td class="age">
802 <span class="css-truncate css-truncate-target"></span>
803 </td>
804 </tr>
805 <tr class="js-navigation-item">
806 <td class="icon">
807 <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>
808 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
809 </td>
810 <td class="content">
811 <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>
812 </td>
813 <td class="message">
814 <span class="css-truncate css-truncate-target">
815 </span>
816 </td>
817 <td class="age">
818 <span class="css-truncate css-truncate-target"></span>
819 </td>
820 </tr>
821 <tr class="js-navigation-item">
822 <td class="icon">
823 <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>
824 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
825 </td>
826 <td class="content">
827 <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>
828 </td>
829 <td class="message">
830 <span class="css-truncate css-truncate-target">
831 </span>
832 </td>
833 <td class="age">
834 <span class="css-truncate css-truncate-target"></span>
835 </td>
836 </tr>
837 <tr class="js-navigation-item">
838 <td class="icon">
839 <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>
840 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
841 </td>
842 <td class="content">
843 <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>
844 </td>
845 <td class="message">
846 <span class="css-truncate css-truncate-target">
847 </span>
848 </td>
849 <td class="age">
850 <span class="css-truncate css-truncate-target"></span>
851 </td>
852 </tr>
853 <tr class="js-navigation-item">
854 <td class="icon">
855 <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>
856 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
857 </td>
858 <td class="content">
859 <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>
860 </td>
861 <td class="message">
862 <span class="css-truncate css-truncate-target">
863 </span>
864 </td>
865 <td class="age">
866 <span class="css-truncate css-truncate-target"></span>
867 </td>
868 </tr>
869 <tr class="js-navigation-item">
870 <td class="icon">
871 <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>
872 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
873 </td>
874 <td class="content">
875 <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>
876 </td>
877 <td class="message">
878 <span class="css-truncate css-truncate-target">
879 </span>
880 </td>
881 <td class="age">
882 <span class="css-truncate css-truncate-target"></span>
883 </td>
884 </tr>
885 <tr class="js-navigation-item">
886 <td class="icon">
887 <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>
888 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
889 </td>
890 <td class="content">
891 <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>
892 </td>
893 <td class="message">
894 <span class="css-truncate css-truncate-target">
895 </span>
896 </td>
897 <td class="age">
898 <span class="css-truncate css-truncate-target"></span>
899 </td>
900 </tr>
901 <tr class="js-navigation-item">
902 <td class="icon">
903 <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>
904 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
905 </td>
906 <td class="content">
907 <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>
908 </td>
909 <td class="message">
910 <span class="css-truncate css-truncate-target">
911 </span>
912 </td>
913 <td class="age">
914 <span class="css-truncate css-truncate-target"></span>
915 </td>
916 </tr>
917 <tr class="js-navigation-item">
918 <td class="icon">
919 <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>
920 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
921 </td>
922 <td class="content">
923 <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>
924 </td>
925 <td class="message">
926 <span class="css-truncate css-truncate-target">
927 </span>
928 </td>
929 <td class="age">
930 <span class="css-truncate css-truncate-target"></span>
931 </td>
932 </tr>
933 <tr class="js-navigation-item">
934 <td class="icon">
935 <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>
936 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
937 </td>
938 <td class="content">
939 <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>
940 </td>
941 <td class="message">
942 <span class="css-truncate css-truncate-target">
943 </span>
944 </td>
945 <td class="age">
946 <span class="css-truncate css-truncate-target"></span>
947 </td>
948 </tr>
949 <tr class="js-navigation-item">
950 <td class="icon">
951 <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>
952 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
953 </td>
954 <td class="content">
955 <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>
956 </td>
957 <td class="message">
958 <span class="css-truncate css-truncate-target">
959 </span>
960 </td>
961 <td class="age">
962 <span class="css-truncate css-truncate-target"></span>
963 </td>
964 </tr>
965 <tr class="js-navigation-item">
966 <td class="icon">
967 <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>
968 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
969 </td>
970 <td class="content">
971 <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>
972 </td>
973 <td class="message">
974 <span class="css-truncate css-truncate-target">
975 </span>
976 </td>
977 <td class="age">
978 <span class="css-truncate css-truncate-target"></span>
979 </td>
980 </tr>
981 <tr class="js-navigation-item">
982 <td class="icon">
983 <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>
984 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
985 </td>
986 <td class="content">
987 <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>
988 </td>
989 <td class="message">
990 <span class="css-truncate css-truncate-target">
991 </span>
992 </td>
993 <td class="age">
994 <span class="css-truncate css-truncate-target"></span>
995 </td>
996 </tr>
997 <tr class="js-navigation-item">
998 <td class="icon">
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1000 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
1001 </td>
1002 <td class="content">
1003 <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>
1004 </td>
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1016 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
1017 </td>
1018 <td class="content">
1019 <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>
1020 </td>
1021 <td class="message">
1022 <span class="css-truncate css-truncate-target">
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1032 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
1033 </td>
1034 <td class="content">
1035 <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>
1036 </td>
1037 <td class="message">
1038 <span class="css-truncate css-truncate-target">
1039 </span>
1040 </td>
1041 <td class="age">
1042 <span class="css-truncate css-truncate-target"></span>
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1047 <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>
1048 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
1049 </td>
1050 <td class="content">
1051 <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>
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1064 <img width="16" height="16" class="spinner" alt="" src="https://github.githubassets.com/images/spinners/octocat-spinner-32.gif" />
1065 </td>
1066 <td class="content">
1067 <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>
1068 </td>
1069 <td class="message">
1070 <span class="css-truncate css-truncate-target">
1071 </span>
1072 </td>
1073 <td class="age">
1074 <span class="css-truncate css-truncate-target"></span>
1075 </td>
1076 </tr>
1077 </tbody>
1078 </table>
1079
1080 </include-fragment>
1081
1082
1083
1084 <div id="readme" class="Box Box--condensed instapaper_body js-code-block-container">
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1088 README
1089 </h3>
1090 </div>
1091 <div class="Box-body">
1092 <div class="plain"><pre style="white-space: pre-wrap">Installation note:
1093 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>)
1094 to be able to use this tool. Once the license is obtained, the GATK Jar file must then be downloaded and moved
1095 to /mnt/galaxy/tools/GATK/x.x-x on the server. Substitute the appropriate version number in the file path.
1096 Be sure to download the correct version of the Jar file for the toolshed version installed.
1097 </pre></div>
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1166 </div>
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