Mercurial > repos > galaxyp > peptideshaker
changeset 1:7a74818e0eeb draft
Improved some datatype handling
| author | galaxyp |
|---|---|
| date | Thu, 20 Jun 2013 10:53:16 -0400 |
| parents | 0578e296cab4 |
| children | fb591fc7241c |
| files | galaxyp-toolshed-peptideshaker |
| diffstat | 1 files changed, 1488 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxyp-toolshed-peptideshaker Thu Jun 20 10:53:16 2013 -0400 @@ -0,0 +1,1488 @@ +<!DOCTYPE html> +<html lang="en"> +<head> + <meta http-equiv="X-UA-Compatible" content="IE=edge" /> + <meta charset="utf-8"> + <title> + galaxyp / galaxyp-toolshed-peptideshaker — Bitbucket +</title> + <link rel="icon" type="image/png" href="https://d3oaxc4q5k2d6q.cloudfront.net/m/968d9745b7be/img/favicon.png"> + <meta id="bb-canon-url" name="bb-canon-url" content="https://bitbucket.org"> + + +<link rel="stylesheet" href="https://d3oaxc4q5k2d6q.cloudfront.net/m/968d9745b7be/compressed/css/4c9fb96cff70.css" type="text/css" /> +<link rel="stylesheet" href="https://d3oaxc4q5k2d6q.cloudfront.net/m/968d9745b7be/compressed/css/8cc3605411c7.css" type="text/css" /> + + <!--[if lt IE 9]><link rel="stylesheet" href="https://d3oaxc4q5k2d6q.cloudfront.net/m/968d9745b7be/css/aui/aui-ie.css" media="all"><![endif]--> + <!--[if IE 9]><link rel="stylesheet" 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We're also free for small teams! + + </p> + <a class="aui-button aui-button-primary aui-style signup-button" href="/account/signup/">Sign up for free</a> + <span class="close aui-icon aui-icon-small aui-iconfont-close-dialog" title="Dismiss this banner">Close</span> + </div> +</section> + + + + + + <section id="readme"> + + <article class="readme file"> + <p>Tool wrapper for SearchGUI + PeptideShaker. This tool takes any number +of mgf files and performs X! Tandem and OMSSA searches on these via +SearchGUI and merges the results using PeptideShaker.</p> +<p>For Galaxy-P we are installing this tool via CloudBioLinux +(https://github.com/jmchilton/cloudbiolinux/blob/proteomics/cloudbio/custom/bio_proteomics.py). While +this fabric script may not be exactly appropriate for your environment +it may serve as a template for how to install this software. In +particular these tools require CLI wrappers to be placed for +PeptideShaker and SearchGUI that can be installed as demostrated in +these fabric functions.</p> +<p>Note: Also SearchGUI requires a version greater than 1.12.2 which +contained several bugs preventing this from working on the +command-line and via Linux.</p> +<p>Also, PeptideShaker may require xvfb to simulate an X environment if +this is installed on a headless server.</p> +<h1 id="markdown-header-obtaining-tools">Obtaining Tools</h1> +<p>Repositories for all Galaxy-P tools can be found at +https:/bitbucket.org/galaxyp/.</p> +<h1 id="markdown-header-contact">Contact</h1> +<p>Please send suggestions for improvements and bug reports to +jmchilton@gmail.com.</p> +<h1 id="markdown-header-license">License</h1> +<p>All Galaxy-P tools are licensed under the Apache License Version 2.0 +unless otherwise documented.</p> +<h1 id="markdown-header-tool-versioning">Tool Versioning</h1> +<p>Galaxy-P tools will have versions of the form X.Y.Z. Versions +differing only after the second decimal should be completely +compatible with each other. Breaking changes should result in an +increment of the number before and/or after the first decimal. All +tools of version less than 1.0.0 should be considered beta.</p> + </article> + + </section> + + + + <section id="repo-activity"> + <h1> + Recent activity + <a href="/galaxyp/galaxyp-toolshed-peptideshaker/rss" class="icon rss">RSS feed fo galaxyp-toolshed-peptideshaker</a> + </h1> + + + + + + + + + +<div class="newsfeed"> + + + + + + + + + + + + <article class="news-item commit"> + <span class="icon commit"></span> + + + + <a href="/galaxyp"><img alt="galaxyp" src="https://secure.gravatar.com/avatar/655358b258b3fbd64aa5c6f42adade4e?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_team_avatar%2F32%2Fteam_blue.png&s=32" class="avatar avatar32" /></a> + + + <p> + + + <a href="/galaxyp">galaxyp</a> + + pushed 1 commit to + + +<a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a> + + + </p> + <time datetime="2013-06-19T22:19:56+00:00">16 hours ago</time> + + <div class="changeset"> + <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/80ef7cf0d97a14a59b39f2d7eb683531cc02056a" class="changeset-hash">80ef7cf</a> + - + + + improved some datatypes + + + </div> + + + </article> + + + + + + + + + + + + + + + + </article> + + + + + + + <article class="news-item commit"> + <span class="icon commit"></span> + + + + <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&s=32" class="avatar avatar32" /></a> + + + <p> + + + <a href="/jmchilton">John Chilton</a> + + pushed 1 commit to + + +<a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a> + + + </p> + <time datetime="2013-06-07T03:03:07+00:00">2013-06-07</time> + + <div class="changeset"> + <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/113acce8b7eea4ed179411f6704ab5a5d8245da8" class="changeset-hash">113acce</a> + - + + + Ensure unique Experiment/Sample names. Peptideshaker seems to potentially have clean up problem on errors otherwise. + + + </div> + + + </article> + + + + + + + + + + + + + + + + + + + <article class="news-item commit"> + <span class="icon commit"></span> + + + + <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&s=32" class="avatar avatar32" /></a> + + + <p> + + + <a href="/jmchilton">John Chilton</a> + + pushed 1 commit to + + +<a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a> + + + </p> + <time datetime="2013-05-20T15:26:48+00:00">2013-05-20</time> + + <div class="changeset"> + <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/6fa4a7ad242f1ce78db6eaec19099bd1b7f86b2f" class="changeset-hash">6fa4a7a</a> + - + + + Add script to create a target-decoy database for PeptideShaker - seems very picky about the format of the database. + + + </div> + + + </article> + + + + + + + + + + + + + + + + + + + <article class="news-item commit"> + <span class="icon commit"></span> + + + + <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&s=32" class="avatar avatar32" /></a> + + + <p> + + + <a href="/jmchilton">John Chilton</a> + + pushed 2 commits to + + +<a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a> + + + </p> + <time datetime="2013-05-13T18:51:02+00:00">2013-05-13</time> + + <div class="changeset"> + <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/bf3730228118ac8adee5e5fc16f08ad5f9aaaf0e" class="changeset-hash">bf37302</a> + - + + + Add CPS datatype. + + + </div> + + <div class="changeset"> + <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/d63d2ed28d002156d5330d29afbf8afc54adfc3b" class="changeset-hash">d63d2ed</a> + - + + + Improve documentation. + + + </div> + + + </article> + + + + + + + + + + + + + + + + + + + <article class="news-item commit"> + <span class="icon commit"></span> + + + + <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&s=32" class="avatar avatar32" /></a> + + + <p> + + + <a href="/jmchilton">John Chilton</a> + + pushed 1 commit to + + +<a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a> + + + </p> + <time datetime="2013-05-10T21:39:19+00:00">2013-05-10</time> + + <div class="changeset"> + <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/a76da3b08725332a9dc746b3f4e886d047af2e40" class="changeset-hash">a76da3b</a> + - + + + Add license and documentation. + + + </div> + + + </article> + + + + + + + + + + + + + + + + + + + <article class="news-item commit"> + <span class="icon commit"></span> + + + + <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&s=32" class="avatar avatar32" /></a> + + + <p> + + + <a href="/jmchilton">John Chilton</a> + + pushed 1 commit to + + +<a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a> + + + </p> + <time datetime="2013-05-10T21:33:27+00:00">2013-05-10</time> + + <div class="changeset"> + <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/29ee7c62dfdc24848cc1111500d544c700ca9008" class="changeset-hash">29ee7c6</a> + - + + + Add sample loc file for toolshed. + + + </div> + + + </article> + + + + + + + + + + + + + + + + + + + <article class="news-item commit"> + <span class="icon commit"></span> + + + + <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&s=32" class="avatar avatar32" /></a> + + + <p> + + + <a href="/jmchilton">John Chilton</a> + + pushed 1 commit to + + +<a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a> + + + </p> + <time datetime="2013-04-12T18:58:24+00:00">2013-04-12</time> + + <div class="changeset"> + <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/8384b7acd805161da0b61203688c61ed0b11b72b" class="changeset-hash">8384b7a</a> + - + + + Fix modification handling. + + + </div> + + + </article> + + + + + + + + + + + + + + + + + + + <article class="news-item commit"> + <span class="icon commit"></span> + + + + <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&s=32" class="avatar avatar32" /></a> + + + <p> + + + <a href="/jmchilton">John Chilton</a> + + pushed 1 commit to + + +<a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a> + + + </p> + <time datetime="2013-04-11T18:38:44+00:00">2013-04-11</time> + + <div class="changeset"> + <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/735b677030185833e6dee7a38e37a0b8ef49a2fb" class="changeset-hash">735b677</a> + - + + + PeptideShaker modifications need to be all lower case. + + + </div> + + + </article> + + + + + + + + + + + + + + + + + + + <article class="news-item commit"> + <span class="icon commit"></span> + + + + <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&s=32" class="avatar avatar32" /></a> + + + <p> + + + <a href="/jmchilton">John Chilton</a> + + pushed 2 commits to + + +<a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a> + + + </p> + <time datetime="2013-04-08T19:54:06+00:00">2013-04-08</time> + + <div class="changeset"> + <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/1f4e30851033eb83986c2d793ba894604f9fe1b0" class="changeset-hash">1f4e308</a> + - + + + Implement modifications for peptide_shaker wrapper. + + + </div> + + <div class="changeset"> + <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/90c86636c57d28ba6f369e0e0d1aa097c46f5d4b" class="changeset-hash">90c8663</a> + - + + + Initial work on building modification list for searchGUI. + + + </div> + + + </article> + + + + + + + + + + + + + + + + + + + <article class="news-item commit"> + <span class="icon commit"></span> + + + + <a href="/jmchilton"><img alt="John Chilton" src="https://secure.gravatar.com/avatar/86cbb595c758989c14ae715c44588998?d=https%3A%2F%2Fd3oaxc4q5k2d6q.cloudfront.net%2Fm%2F968d9745b7be%2Fimg%2Fdefault_avatar%2F32%2Fuser_blue.png&s=32" class="avatar avatar32" /></a> + + + <p> + + + <a href="/jmchilton">John Chilton</a> + + pushed 1 commit to + + +<a href="/galaxyp/galaxyp-toolshed-peptideshaker" title="galaxyp/galaxyp-toolshed-peptideshaker">galaxyp/galaxyp-toolshed-peptideshaker</a> + + + </p> + <time datetime="2013-03-19T19:23:06+00:00">2013-03-19</time> + + <div class="changeset"> + <a href="/galaxyp/galaxyp-toolshed-peptideshaker/commits/21b540795f0663a4633a53c78d733746a463167d" class="changeset-hash">21b5407</a> + - + + + Fix label on protein report. + + + </div> + + + </article> + + + + + + + </article> + + + + + +</div> + + + + + + + </section> + </div> + + <div class="column"> + + + + + <section id="repo-stats"> + +<div class="clone-url"> + <div class="aui-buttons"> + <a href="https://bitbucket.org/galaxyp/galaxyp-toolshed-peptideshaker" + class="aui-button aui-style aui-dropdown2-trigger" aria-haspopup="true" + aria-owns="clone-url-dropdown-overview"> + <span class="dropdown-text">HTTPS</span> + </a> + <div id="clone-url-dropdown-overview" class="aui-dropdown2 aui-style-default"> + <ul class="aui-list-truncate"> + <li> + <a 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