# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate@bx.psu.edu> # Date 1289402767 18000 # Node ID 2c2a22396a2641a52dc5f200d26a3d947cf11cbd # Parent 081ce300b688968521edd30f25a020d96999cd64 Backed out changeset 081ce300b688 (some files accidentally committed). --- a/test/functional/test_sample_tracking.py +++ b/test/functional/test_sample_tracking.py @@ -388,7 +388,6 @@ class TestFormsAndRequests( TwillTestCas % ( request_two.name, request_two.states.REJECTED ) def test_055_reset_data_for_later_test_runs( self ): """Reseting data to enable later test runs to pass""" - ''' # Logged in as admin_user ################## # Delete request_type permissions @@ -433,4 +432,3 @@ class TestFormsAndRequests( TwillTestCas # Manually delete the group from the database refresh( group ) delete( group ) - ''' --- a/static/welcome.html +++ b/static/welcome.html @@ -2,211 +2,20 @@ <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"><head> -<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -<meta name="generator" content="Docutils 0.3.9: http://docutils.sourceforge.net/" /> -<link rel="stylesheet" href="style/base.css" type="text/css" /> -<style type="text/css"> - - .quickie { - text-align: center; - background: black; - margin: 10px; - } - - .current-quickie { - width: 300px; - background: white; - margin: auto; - } - - .current-quickie img { - padding: 15px; - border: 1px solid #ccc; - margin: auto; - background-color: white; - -moz-border-radius:4px; - -webkit-border-radius:4px; - - } - - .previous { - width: 100%; - overflow: auto; - border: solid #ccc 1px; - -moz-border-radius:4px; - -webkit-border-radius:4px; - - } - .previous .quickie { - padding-top: 10px; - min-height: 90px; - min-width: 150px; - } - #screencasts { - max-width: 50em; - margin-left: auto; - margin-right: auto; - } - -</style> -<script type="text/javascript" src="http://galaxy.psu.edu/welcome_img/jquery.min.js"></script> -<script type="text/javascript" src="http://galaxy.psu.edu/welcome_img/jquery.cycle.all.2.72.js"></script> -<script type="text/javascript"> - -$(document).ready(function() { - $('.current-quickie').cycle({ - fx: 'fade', - pause: 1, - timeout: 1000, - speed: 1000 - }); -}); -</script> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <link rel="stylesheet" href="style/base.css" type="text/css" /></head><body> -<div class="document"> -<h3 align="center">Here is what's happening...</h3> -<div align="center" class="current-quickie"> - <a target="_blank" href="http://usegalaxy.org/cloud"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.001.png" width="300" height="200"></a> - <a target="_blank" href="http://bitbucket.org/galaxy/galaxy-central/wiki/ISMB2010_GalaxyTutorial_3_RunningYourOwn"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.002.png" width="300" height="200"></a> - <a target="_blank" href="http://main.g2.bx.psu.edu/u/aun1/p/ismb2010-demo"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.003.png" width="300" height="200" /></a> - <a target="_blank" href="http://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/Tutorial/DataLibrariesSampleTracking"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.004.png" width="300" height="200" /></a> - <a target="_blank" href="http://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.005.png" width="300" height="200" /></a> -</div> - -<h3 align="center">Live Quickies</h3> - -<div class="previous" id="previous"> - <table border="0" cellpadding="0" cellspacing="0" width="100%"> - <tr> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie1_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie2_Grouping/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie2_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie3_Intervals/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie3_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie4_whatsNew/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie4_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie5_join/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie5_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie6_share/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie6_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie7_sr_beta/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie7_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie8_solid_single_end/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie8_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie9_solid_mate_pair/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie9_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie10_custom_genome/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie10_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie_11_illumina_se/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie11_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie12_illumina_pe/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie12_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie_13_fastq_basic/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie13_small.png" border="0"> - </div> - </a> - </td> - - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie_14_fastq_adv/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie14_small.png" border="0"> - </div> - </a> - </td> - <td> - <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie_15_lastz_frag/flow.html',width:640,height:480,scroll:'no'})"> - <div class="quickie"> - <img src="images/qk/quickie15_small.png" border="0"> - </div> - </a> - </td> - - - - </tr> - </table> -</div> - -<script type="text/javascript"> - // Scroll to last quickie in box - document.getElementById("previous").scrollLeft = 100000000; -</script> - -<br/> -<br/> -<br/> -<hr/> - -<p><a target="_blank" class="reference" href="http://g2.trac.bx.psu.edu/wiki/GalaxyTeam">The Galaxy team</a> is a part of <a target="_blank" class="reference" href="http://www.bx.psu.edu">BX</a> at <a target="_blank" class="reference" href="http://www.psu.edu">Penn State</a>.</p> - -This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, <a target="_blank" class="reference" href="http://www.huck.psu.edu">The Huck Institutes of the Life Sciences</a>, and <a target="_blank" class="reference" href="http://www.ics.psu.edu">The Institute for CyberScience at Penn State</a>. -<p><small>Galaxy build: <b>$Rev 3885:1ab9d6b0ddfc$</b></small></p> -</div> -</div> + <div class="document"> + <div class="donemessagelarge"> + <strong>Hello world! It's running...</strong> + <hr> + To customize this page edit <code>static/welcome.html</code> + </div> + <br/> + <img src="images/noodles.png" alt="WWFSMD?" style="display: block; margin-left: auto; margin-right: auto;" /> + <hr/> + This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>. + </div></body></html> --- a/scripts/taxonomy/processTaxonomy.sh +++ b/scripts/taxonomy/processTaxonomy.sh @@ -10,9 +10,5 @@ cat gi_taxid_nucl.dmp gi_taxid_prot.dmp echo "Sorting gi2tax files..." sort -n -k 1 gi_taxid_all.dmp > gi_taxid_sorted.txt rm gi_taxid_nucl.dmp gi_taxid_prot.dmp gi_taxid_all.dmp -echo "Removing parenthesis from names.dmp" -cat names.dmp | sed s/\(/_/g | sed s/\)/_/g > names.temporary -mv names.dmp names.dmp.orig -mv names.temporary names.dmp