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comparison tool-data/bwa_index.loc.sample @ 0:198009598544 draft

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author romaingred
date Wed, 11 Oct 2017 09:57:58 -0400
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649 <div class="file-info">
650 42 lines (40 sloc)
651 <span class="file-info-divider"></span>
652 1.92 KB
653 </div>
654 </div>
655
656
657
658 <div itemprop="text" class="blob-wrapper data type-text">
659 <table class="highlight tab-size js-file-line-container" data-tab-size="8">
660 <tr>
661 <td id="L1" class="blob-num js-line-number" data-line-number="1"></td>
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>
663 </tr>
664 <tr>
665 <td id="L2" class="blob-num js-line-number" data-line-number="2"></td>
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>
667 </tr>
668 <tr>
669 <td id="L3" class="blob-num js-line-number" data-line-number="3"></td>
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>
671 </tr>
672 <tr>
673 <td id="L4" class="blob-num js-line-number" data-line-number="4"></td>
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>
675 </tr>
676 <tr>
677 <td id="L5" class="blob-num js-line-number" data-line-number="5"></td>
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>
679 </tr>
680 <tr>
681 <td id="L6" class="blob-num js-line-number" data-line-number="6"></td>
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>
683 </tr>
684 <tr>
685 <td id="L7" class="blob-num js-line-number" data-line-number="7"></td>
686 <td id="LC7" class="blob-code blob-code-inner js-file-line">#</td>
687 </tr>
688 <tr>
689 <td id="L8" class="blob-num js-line-number" data-line-number="8"></td>
690 <td id="LC8" class="blob-code blob-code-inner js-file-line">#&lt;unique_build_id&gt; &lt;dbkey&gt; &lt;display_name&gt; &lt;file_path&gt;</td>
691 </tr>
692 <tr>
693 <td id="L9" class="blob-num js-line-number" data-line-number="9"></td>
694 <td id="LC9" class="blob-code blob-code-inner js-file-line">#</td>
695 </tr>
696 <tr>
697 <td id="L10" class="blob-num js-line-number" data-line-number="10"></td>
698 <td id="LC10" class="blob-code blob-code-inner js-file-line">#So, for example, if you had phiX indexed stored in </td>
699 </tr>
700 <tr>
701 <td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
702 <td id="LC11" class="blob-code blob-code-inner js-file-line">#/depot/data2/galaxy/phiX/base/, </td>
703 </tr>
704 <tr>
705 <td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
706 <td id="LC12" class="blob-code blob-code-inner js-file-line">#then the bwa_index.loc entry would look like this:</td>
707 </tr>
708 <tr>
709 <td id="L13" class="blob-num js-line-number" data-line-number="13"></td>
710 <td id="LC13" class="blob-code blob-code-inner js-file-line">#</td>
711 </tr>
712 <tr>
713 <td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
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>
715 </tr>
716 <tr>
717 <td id="L15" class="blob-num js-line-number" data-line-number="15"></td>
718 <td id="LC15" class="blob-code blob-code-inner js-file-line">#</td>
719 </tr>
720 <tr>
721 <td id="L16" class="blob-num js-line-number" data-line-number="16"></td>
722 <td id="LC16" class="blob-code blob-code-inner js-file-line">#and your /depot/data2/galaxy/phiX/base/ directory</td>
723 </tr>
724 <tr>
725 <td id="L17" class="blob-num js-line-number" data-line-number="17"></td>
726 <td id="LC17" class="blob-code blob-code-inner js-file-line">#would contain phiX.fa.* files:</td>
727 </tr>
728 <tr>
729 <td id="L18" class="blob-num js-line-number" data-line-number="18"></td>
730 <td id="LC18" class="blob-code blob-code-inner js-file-line">#</td>
731 </tr>
732 <tr>
733 <td id="L19" class="blob-num js-line-number" data-line-number="19"></td>
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>
735 </tr>
736 <tr>
737 <td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
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>
739 </tr>
740 <tr>
741 <td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
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>
743 </tr>
744 <tr>
745 <td id="L22" class="blob-num js-line-number" data-line-number="22"></td>
746 <td id="LC22" class="blob-code blob-code-inner js-file-line">#...etc...</td>
747 </tr>
748 <tr>
749 <td id="L23" class="blob-num js-line-number" data-line-number="23"></td>
750 <td id="LC23" class="blob-code blob-code-inner js-file-line">#</td>
751 </tr>
752 <tr>
753 <td id="L24" class="blob-num js-line-number" data-line-number="24"></td>
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>
755 </tr>
756 <tr>
757 <td id="L25" class="blob-num js-line-number" data-line-number="25"></td>
758 <td id="LC25" class="blob-code blob-code-inner js-file-line">#index set you have stored. The &quot;file&quot; in the path does not actually</td>
759 </tr>
760 <tr>
761 <td id="L26" class="blob-num js-line-number" data-line-number="26"></td>
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>
763 </tr>
764 <tr>
765 <td id="L27" class="blob-num js-line-number" data-line-number="27"></td>
766 <td id="LC27" class="blob-code blob-code-inner js-file-line">#</td>
767 </tr>
768 <tr>
769 <td id="L28" class="blob-num js-line-number" data-line-number="28"></td>
770 <td id="LC28" class="blob-code blob-code-inner js-file-line">#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa</td>
771 </tr>
772 <tr>
773 <td id="L29" class="blob-num js-line-number" data-line-number="29"></td>
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>
775 </tr>
776 <tr>
777 <td id="L30" class="blob-num js-line-number" data-line-number="30"></td>
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>
779 </tr>
780 <tr>
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>
783 </tr>
784 <tr>
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>
787 </tr>
788 <tr>
789 <td id="L33" class="blob-num js-line-number" data-line-number="33"></td>
790 <td id="LC33" class="blob-code blob-code-inner js-file-line">#</td>
791 </tr>
792 <tr>
793 <td id="L34" class="blob-num js-line-number" data-line-number="34"></td>
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>
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>
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>
810 <td id="LC38" class="blob-code blob-code-inner js-file-line">#</td>
811 </tr>
812 <tr>
813 <td id="L39" class="blob-num js-line-number" data-line-number="39"></td>
814 <td id="LC39" class="blob-code blob-code-inner js-file-line">
815 </td>
816 </tr>
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
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