galaxy-dist commit 081ce300b688: porocessTaxonomynow removes parenthesis fixing various tree drawing issues in metagenomic tools. Major rework of MG tools needed to ensure reproducibility
# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Anton Nekrutenko <anton@bx.psu.edu> # Date 1289402232 18000 # Node ID 081ce300b688968521edd30f25a020d96999cd64 # Parent 0e3fe3e7b21bfd78461869817c6b43db827d77f0 porocessTaxonomynow removes parenthesis fixing various tree drawing issues in metagenomic tools. Major rework of MG tools needed to ensure reproducibility --- a/test/functional/test_sample_tracking.py +++ b/test/functional/test_sample_tracking.py @@ -388,6 +388,7 @@ 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 @@ -432,3 +433,4 @@ class TestFormsAndRequests( TwillTestCas # Manually delete the group from the database refresh( group ) delete( group ) + ''' --- a/static/welcome.html +++ b/static/welcome.html @@ -2,20 +2,211 @@ <!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" /> - <link rel="stylesheet" href="style/base.css" type="text/css" /> +<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() { + $('.current-quickie').cycle({ + fx: 'fade', + pause: 1, + timeout: 1000, + speed: 1000 + }); +}); +</script></head><body> - <div class="document"> - <div class="donemessagelarge"> - <strong>Hello world! 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href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie_15_lastz_frag/flow.html',width:640,height:480,scroll:'no'})"> + <div class="quickie"> + <img src="images/qk/quickie15_small.png" border="0"> + </div> + </a> + </td> + + + + </tr> + </table> +</div> + +<script type="text/javascript"> + // Scroll to last quickie in box + document.getElementById("previous").scrollLeft = 100000000; +</script> + +<br/> +<br/> +<br/> +<hr/> + +<p><a target="_blank" class="reference" href="http://g2.trac.bx.psu.edu/wiki/GalaxyTeam">The Galaxy team</a> is a part of <a target="_blank" class="reference" href="http://www.bx.psu.edu">BX</a> at <a target="_blank" class="reference" href="http://www.psu.edu">Penn State</a>.</p> + +This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, <a target="_blank" class="reference" href="http://www.huck.psu.edu">The Huck Institutes of the Life Sciences</a>, and <a target="_blank" class="reference" href="http://www.ics.psu.edu">The Institute for CyberScience at Penn State</a>. +<p><small>Galaxy build: <b>$Rev 3885:1ab9d6b0ddfc$</b></small></p> +</div> +</div></body></html> --- a/scripts/taxonomy/processTaxonomy.sh +++ b/scripts/taxonomy/processTaxonomy.sh @@ -10,5 +10,9 @@ 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
participants (1)
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