Mercurial > repos > romaingred > pirna_pipeline
changeset 3:1f1b6c9b09f1 draft
Uploaded
| author | romaingred |
|---|---|
| date | Thu, 12 Oct 2017 10:23:53 -0400 |
| parents | 02c0b9b2cc02 |
| children | bbe202c54a29 |
| files | tool-data/bwa_index.loc.sample |
| diffstat | 1 files changed, 14 insertions(+), 931 deletions(-) [+] |
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--- a/tool-data/bwa_index.loc.sample Thu Oct 12 10:20:42 2017 -0400 +++ b/tool-data/bwa_index.loc.sample Thu Oct 12 10:23:53 2017 -0400 @@ -1,931 +1,14 @@ - - - - - - -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> - <link rel="dns-prefetch" href="https://assets-cdn.github.com"> - <link rel="dns-prefetch" href="https://avatars0.githubusercontent.com"> - <link rel="dns-prefetch" href="https://avatars1.githubusercontent.com"> - <link rel="dns-prefetch" href="https://avatars2.githubusercontent.com"> - <link rel="dns-prefetch" href="https://avatars3.githubusercontent.com"> - <link rel="dns-prefetch" href="https://github-cloud.s3.amazonaws.com"> - <link rel="dns-prefetch" href="https://user-images.githubusercontent.com/"> - - - - <link crossorigin="anonymous" href="https://assets-cdn.github.com/assets/frameworks-bedfc518345498ab3204d330c1727cde7e733526a09cd7df6867f6a231565091.css" media="all" rel="stylesheet" /> - <link crossorigin="anonymous" href="https://assets-cdn.github.com/assets/github-36dc4044670fb93253d932fbc3a10282233e86290bfaf8285c479925456b3d47.css" media="all" rel="stylesheet" /> - 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</tr> - <tr> - <td id="L2" 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 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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<span class="signed-in-tab-flash">You signed in with another tab or window. <a href="">Reload</a> to refresh your session.</span> - <span class="signed-out-tab-flash">You signed out in another tab or window. <a href="">Reload</a> to refresh your session.</span> - </div> - <div class="facebox" id="facebox" style="display:none;"> - <div class="facebox-popup"> - <div class="facebox-content" role="dialog" aria-labelledby="facebox-header" aria-describedby="facebox-description"> - </div> - <button type="button" class="facebox-close js-facebox-close" aria-label="Close modal"> - <svg aria-hidden="true" class="octicon octicon-x" height="16" version="1.1" viewBox="0 0 12 16" width="12"><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 1.48z"/></svg> - </button> - </div> -</div> - - - </body> -</html> - +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt +#...etc... +# +#Your bwa_index.loc file should include an entry per line for each +#index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: +# +#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa +#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa +#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa +#...etc... \ No newline at end of file