Ido Tamir idot
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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 $@ |
idot
/ gist:4741d705ab2ed1e2c5fd
Created
April 15, 2015 06:01
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| ### Keybase proof | |
| I hereby claim: | |
| * I am idot on github. | |
| * I am idotamir (https://keybase.io/idotamir) on keybase. | |
| * I have a public key whose fingerprint is CAB5 4E68 808E 591E 4F62 E3BE 0271 0975 3DDF F04E | |
| To claim this, I am signing this object: |
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| ## Prepare data to plot in Euler Grid. | |
| ## Quantity or binary table with columns for samples and rows for features | |
| #### FUNCTIONS ####### | |
| ## convert a (table, matrix,) data.frame to either 0/1 or FALSE/TRUE based on whether values exceed threshold. | |
| ## to invert a threshold use: new.table <- table == FALSE |
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