Mercurial > repos > romaingred > pirna_pipeline
view tool-data/bwa_index.loc.sample @ 0:198009598544 draft
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| author | romaingred |
|---|---|
| date | Wed, 11 Oct 2017 09:57:58 -0400 |
| parents | |
| children | 1f1b6c9b09f1 |
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class="user-mention" rel="author">najoshi</a> <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, …</a> </div> <div class="commit-tease-contributors"> <button type="button" class="btn-link muted-link contributors-toggle" data-facebox="#blob_contributors_box"> <strong>1</strong> contributor </button> </div> <div id="blob_contributors_box" style="display:none"> <h2 class="facebox-header" data-facebox-id="facebox-header">Users who have contributed to this file</h2> <ul class="facebox-user-list" data-facebox-id="facebox-description"> <li class="facebox-user-list-item"> <img alt="@najoshi" height="24" src="https://avatars1.githubusercontent.com/u/607905?v=4&s=48" width="24" /> <a 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class="blob-num js-line-number" data-line-number="2"></td> <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> </tr> <tr> <td id="L3" class="blob-num js-line-number" data-line-number="3"></td> <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> </tr> <tr> <td id="L4" class="blob-num js-line-number" data-line-number="4"></td> <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> </tr> <tr> <td id="L5" class="blob-num js-line-number" data-line-number="5"></td> <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> </tr> <tr> <td id="L6" class="blob-num js-line-number" data-line-number="6"></td> <td id="LC6" class="blob-code blob-code-inner js-file-line">#file has this format (longer white space characters are TAB characters):</td> </tr> <tr> <td id="L7" class="blob-num js-line-number" data-line-number="7"></td> <td id="LC7" class="blob-code blob-code-inner js-file-line">#</td> </tr> <tr> <td id="L8" class="blob-num js-line-number" data-line-number="8"></td> <td id="LC8" class="blob-code blob-code-inner js-file-line">#<unique_build_id> <dbkey> <display_name> <file_path></td> </tr> <tr> <td id="L9" class="blob-num js-line-number" data-line-number="9"></td> <td id="LC9" class="blob-code blob-code-inner js-file-line">#</td> </tr> <tr> <td id="L10" class="blob-num js-line-number" data-line-number="10"></td> <td id="LC10" class="blob-code blob-code-inner js-file-line">#So, for example, if you had phiX indexed stored in </td> </tr> <tr> <td id="L11" class="blob-num js-line-number" data-line-number="11"></td> <td id="LC11" class="blob-code blob-code-inner js-file-line">#/depot/data2/galaxy/phiX/base/, </td> </tr> <tr> <td id="L12" class="blob-num js-line-number" data-line-number="12"></td> <td id="LC12" class="blob-code blob-code-inner js-file-line">#then the bwa_index.loc entry would look like this:</td> </tr> <tr> <td id="L13" class="blob-num js-line-number" data-line-number="13"></td> <td id="LC13" class="blob-code blob-code-inner js-file-line">#</td> </tr> <tr> <td id="L14" class="blob-num js-line-number" data-line-number="14"></td> <td id="LC14" class="blob-code blob-code-inner js-file-line">#phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa</td> </tr> <tr> <td id="L15" class="blob-num js-line-number" data-line-number="15"></td> <td id="LC15" class="blob-code blob-code-inner js-file-line">#</td> </tr> <tr> <td id="L16" class="blob-num js-line-number" data-line-number="16"></td> <td id="LC16" class="blob-code blob-code-inner js-file-line">#and your /depot/data2/galaxy/phiX/base/ directory</td> </tr> <tr> <td id="L17" class="blob-num js-line-number" data-line-number="17"></td> <td id="LC17" class="blob-code blob-code-inner js-file-line">#would contain phiX.fa.* files:</td> </tr> <tr> <td id="L18" class="blob-num js-line-number" data-line-number="18"></td> <td id="LC18" class="blob-code blob-code-inner js-file-line">#</td> </tr> <tr> <td id="L19" class="blob-num js-line-number" data-line-number="19"></td> <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> </tr> <tr> <td id="L20" class="blob-num js-line-number" data-line-number="20"></td> <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> </tr> <tr> <td id="L21" class="blob-num js-line-number" data-line-number="21"></td> <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> </tr> <tr> <td id="L22" class="blob-num js-line-number" data-line-number="22"></td> <td id="LC22" class="blob-code blob-code-inner js-file-line">#...etc...</td> </tr> <tr> <td id="L23" class="blob-num js-line-number" data-line-number="23"></td> <td id="LC23" class="blob-code blob-code-inner js-file-line">#</td> </tr> <tr> <td id="L24" class="blob-num js-line-number" data-line-number="24"></td> <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> </tr> <tr> <td id="L25" class="blob-num js-line-number" data-line-number="25"></td> <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> </tr> <tr> <td id="L26" class="blob-num js-line-number" data-line-number="26"></td> <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> </tr> <tr> <td id="L27" class="blob-num js-line-number" data-line-number="27"></td> <td id="LC27" class="blob-code blob-code-inner js-file-line">#</td> </tr> <tr> <td id="L28" class="blob-num js-line-number" data-line-number="28"></td> <td id="LC28" class="blob-code blob-code-inner js-file-line">#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa</td> </tr> <tr> <td id="L29" class="blob-num js-line-number" data-line-number="29"></td> <td id="LC29" class="blob-code blob-code-inner js-file-line">#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa</td> </tr> <tr> <td id="L30" class="blob-num js-line-number" data-line-number="30"></td> <td id="LC30" class="blob-code blob-code-inner js-file-line">#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa</td> </tr> <tr> <td id="L31" class="blob-num js-line-number" data-line-number="31"></td> <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> </tr> <tr> <td id="L32" class="blob-num js-line-number" data-line-number="32"></td> <td id="LC32" class="blob-code blob-code-inner js-file-line">#...etc...</td> </tr> <tr> <td id="L33" class="blob-num js-line-number" data-line-number="33"></td> <td id="LC33" class="blob-code blob-code-inner js-file-line">#</td> </tr> <tr> <td id="L34" class="blob-num js-line-number" data-line-number="34"></td> <td id="LC34" class="blob-code blob-code-inner js-file-line">#Note that for backwards compatibility with workflows, the unique ID of</td> </tr> <tr> <td id="L35" class="blob-num js-line-number" data-line-number="35"></td> <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> </tr> <tr> <td id="L36" class="blob-num js-line-number" data-line-number="36"></td> <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> </tr> <tr> <td id="L37" class="blob-num js-line-number" data-line-number="37"></td> <td id="LC37" class="blob-code blob-code-inner js-file-line">#hg19 entry above looks odd. New genomes can be better-looking.</td> </tr> <tr> <td id="L38" class="blob-num js-line-number" data-line-number="38"></td> <td id="LC38" class="blob-code blob-code-inner js-file-line">#</td> </tr> <tr> <td id="L39" class="blob-num js-line-number" data-line-number="39"></td> <td id="LC39" class="blob-code blob-code-inner js-file-line"> </td> </tr> <tr> <td id="L40" class="blob-num js-line-number" data-line-number="40"></td> <td id="LC40" class="blob-code blob-code-inner js-file-line">hg19_chr12 hg19_chr12 hg19_chr12 /data/refs/hg19/chr12.fa</td> </tr> <tr> <td id="L41" class="blob-num js-line-number" data-line-number="41"></td> <td id="LC41" class="blob-code blob-code-inner js-file-line">hg19_chr20 hg19_chr20 hg19_chr20 /data/refs/hg19/chr20.fa</td> </tr> </table> <div class="BlobToolbar position-absolute js-file-line-actions dropdown js-menu-container js-select-menu d-none" aria-hidden="true"> <button class="btn-octicon ml-0 px-2 p-0 bg-white border border-gray-dark rounded-1 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