CloudBurst

• ​CloudBurst

Installation and Test Procedure 安裝與測試步驟

• 使用 ​Sample Results 的資料集

  jazz@hadoop:~$ wget http://nchc.dl.sourceforge.net/project/cloudburst-bio/cloudburst/CloudBurst-1.1.0/CloudBurst-1.1.0.tgz
  jazz@hadoop:~$ tar zxvf CloudBurst-1.1.0.tgz
  jazz@hadoop:~$ cd CloudBurst-1.1.0
  jazz@hadoop:~/CloudBurst-1.1.0$ wget "http://nchc.dl.sourceforge.net/project/cloudburst-bio/cloudburst-data/CloudBurst-sample-data/CloudBurst-small-sample.tgz"
  jazz@hadoop:~/CloudBurst-1.1.0$ tar zxvf CloudBurst-small-sample.tgz
  jazz@hadoop:~/CloudBurst-1.1.0$ hadoop fs -mkdir cloudburst
  jazz@hadoop:~/CloudBurst-1.1.0$ hadoop fs -put CloudBurst-small-sample/100k.br cloudburst/
  jazz@hadoop:~/CloudBurst-1.1.0$ hadoop fs -put CloudBurst-small-sample/s_suis.br cloudburst/
  jazz@hadoop:~/CloudBurst-1.1.0$ 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 /user/$(whoami)/cloudburst/s_suis.br /user/$(whoami)/cloudburst/100k.br results 36 3 0 1 240 48 24 24 128 16 2 >& 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 ​UCSC Genome Browser 用的格式。

Reference

• ​Amazon Elastic MapReduce > Sample Data Processing Applications > CloudBurst