2010-05-04

• ​CloudBurst 測試步驟
  • 使用 ​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
    

  • 執行時間約 1 mins 13 sec
  • 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。