Changes between Initial Version and Version 1 of jazz/CloudBurst

Timestamp:

Mar 18, 2011, 11:31:04 AM (13 years ago)

Author:

jazz

Comment:

--

jazz/CloudBurst

@@ +1 @@
+= CloudBurst =
+
+ * [http://cloudburst-bio.sourceforge.net CloudBurst] 
+
+== Installation and Test Procedure 安裝與測試步驟 ==
+
+ * 使用 [http://sourceforge.net/apps/mediawiki/cloudburst-bio/index.php?title=Sample_Results Sample Results] 的資料集
+{{{
+jazz@hadoop:~$ wget "http://downloads.sourceforge.net/project/cloudburst-bio/cloudburst/CloudBurst-1.0.1/CloudBurst-1.0.1.tgz?use_mirror=nchc"
+jazz@hadoop:~$ tar zxvf CloudBurst-1.0.1.tgz
+jazz@hadoop:~$ cd CloudBurst-1.0.1
+jazz@hadoop:~/CloudBurst-1.0.1$ wget "http://downloads.sourceforge.net/project/cloudburst-bio/cloudburst-data/CloudBurst-sample-data/CloudBurst-small-sample.tgz?use_mirror=nchc"
+jazz@hadoop:~/CloudBurst-1.0.1$ tar zxvf CloudBurst-small-sample.tgz
+jazz@hadoop:~/CloudBurst-1.0.1$ hadoop fs -mkdir cloudburst
+jazz@hadoop:~/CloudBurst-1.0.1$ hadoop fs -put CloudBurst-small-sample/100k.br cloudburst/
+jazz@hadoop:~/CloudBurst-1.0.1$ hadoop fs -put CloudBurst-small-sample/s_suis.br cloudburst/
+jazz@hadoop:~/CloudBurst-1.0.1$ hadoop fs -lsr
+drwxr-xr-x   - jazz supergroup          0 2010-04-30 10:55 /user/jazz/cloudburst
+-rw-r--r--   2 jazz supergroup    4493593 2010-04-30 10:55 /user/jazz/cloudburst/100k.br
+-rw-r--r--   2 jazz supergroup     579773 2010-04-30 10:55 /user/jazz/cloudburst/s_suis.br
+jazz@hadoop:~/CloudBurst-1.0.1$ hadoop jar CloudBurst.jar cloudburst/s_suis.br cloudburst/100k.br results 36 3 0 1 240 48 24 24 128 16 >& cloudburst.err
+jazz@hadoop:~/CloudBurst-1.0.1$ tail -n 1 cloudburst.err
+Total Running time:  102.68
+jazz@hadoop:~/CloudBurst-1.0.1$ hadoop fs -get results .
+jazz@hadoop:~/CloudBurst-1.0.1$ java -jar PrintAlignments.jar results | sort -nk4 > 100k.3.txt
+Printing results
+}}}
+ * 在 hadoop.nchc.org.tw 20 台環境下，執行時間約 1 分 13 秒
+ * 根據官方網站的說明，最後輸出的格式(100k.3.txt)是給 [http://genome.ucsc.edu UCSC Genome Browser] 用的格式。
+
+== Reference ==
+
+ * [http://developer.amazonwebservices.com/connect/entry.jspa?externalID=2272&categoryID=263 Amazon Elastic MapReduce > Sample Data Processing Applications > CloudBurst]