close Warning: Can't synchronize with repository "(default)" (Unsupported version control system "svn": /usr/lib/python2.7/dist-packages/libsvn/_core.so: failed to map segment from shared object: Cannot allocate memory). Look in the Trac log for more information.

Changes between Version 1 and Version 2 of jazz/11-05-04


Ignore:
Timestamp:
May 4, 2011, 1:26:16 AM (13 years ago)
Author:
jazz
Comment:

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  • jazz/11-05-04

    v1 v2  
    1212~$ tar zxvf velvet_1.1.03.tgz
    1313~$ cd velvet_1.1.03
     14~/velvet_1.1.03$ make
     15~/velvet_1.1.03$ ./velveth output 17 -fasta -short data/test_long.fa
     16~/velvet_1.1.03$ ./velvetg output/ -exp_cov 3 -min_contig_lgth 100
     17}}}
     18 * 使用 gprof 進行 profile 分析
     19{{{
    1420~/velvet_1.1.03$ cat Makefile | sed "s#^CFLAG.*#CFLAGS = -Wall -pg#" >
    1521~/velvet_1.1.03$ mv Makefile.new Makefile
    … …  
    2228152K    gmon.out
    2329}}}
     30 * 使用 [http://code.google.com/p/jrfonseca/wiki/Gprof2Dot gprof2dot] 把 gprof log 轉成 graphviz 的 dot 格式，就可以畫出圖形了。
     31{{{
     32~/velvet_1.1.03$ sudo apt-get install graphviz python
     33~/velvet_1.1.03$ wget http://gprof2dot.jrfonseca.googlecode.com/hg/gprof2dot.py
     34~/velvet_1.1.03$ chmod a+x gprof2dot.py
     35~/velvet_1.1.03$ gprof velveth | ./gprof2dot.py | dot -Tpng -o velveth.png
     36}}}