Ido Tamir idot
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| #!/usr/bin/env python | |
| def toIllu(c): | |
| """returns the 1.5 value of phred+33 | |
| >>> [toIllu(ord(n)) for n in["!",'"',"#","$","H","I","J"]] | |
| ['B', 'B', 'B', 'C', 'g', 'h', 'h'] | |
| """ | |
| if c < 36: | |
| return "B" | |
| elif c > 73: |
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| #!/usr/bin/env python | |
| # | |
| # Copyright (c) 2007, Hans Meine <hans_meine@gmx.net> | |
| # All rights reserved. | |
| # | |
| # This is licensed according to the new BSD license. | |
| # Please send patches / comments, I would be happy about any feedback. | |
| # | |
| # Redistribution and use in source and binary forms, with or without | |
| # modification, are permitted provided that the following conditions |
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| #similar to brentp http://biostar.stackexchange.com/questions/4885/installation-of-tophat-1-1-4 | |
| * in samtools download mkdir lib include/bam bin | |
| * cp libbam.a lib; *.h include/bam ; samtools bin | |
| tophat: | |
| ./configure --with-bam=/path/to/samtools/samtools-0.1.13 --prefix /path/to/tophat/checkout/tophat/tophat.git | |
| make && make install | |
| will create tophat binaries in tophat.git/bin |
idot
/ igb_bed.xml
Created
April 26, 2011 13:06
Display files from galaxy in IGB (needs copy of synonyms.txt)
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| <display id="igb_bed" version="1.0.0" name="display in "> | |
| <link id="igb_bed" name="IGB"> | |
| <url>http://localhost:7085/UnibrowControl?version=${buildversion}&${position}&loadresidues=false&feature_url_0=${bed_file.url}&sym_name_0=${thenicename}&sym_method_0=${bed_file.url}&sym_bg_0=0xFFFFFF&graph_show_label_0=true&graph_show_axis_0=true&graph_minvis_0=0.0&graph_maxvis_0=100&graph_float_0=false&graph_style_0=Bar&query_url=${bed_file.url}&server_url=galaxy</url> | |
| <param type="data" name="bed_file_for_name" viewable="False"/> | |
| <param type="template" name="thenicename" viewable="False" strip="True"> | |
| #import re | |
| #set nm=$bed_file_for_name.name | |
| ${re.sub('\W',"_",nm)} | |
| </param> | |
| <param type="data" name="bed_file" url="${thenicename}_${DATASET_HASH}.bed" strip_https="True" /> |
idot
/ uglyPopen.scala
Created
May 3, 2010 10:55
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| class InputActor(latch: CountDownLatch, outputStream : OutputStream) extends Actor { | |
| private val log = LoggerFactory getLogger(Popen getClass) | |
| private val writer = new PrintWriter(outputStream) | |
| def act(){ | |
| react{ | |
| case null => { | |
| ControlUtil.closeInsulated(writer) | |
| latch.countDown |
idot
/ importer.sh
Created
August 16, 2009 14:27
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| #!/bin/sh | |
| cd `dirname $0` | |
| python -ES ./importer/importer.py universe_wsgi.ini $@ |
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