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2018-06-12工具坑点合集

2018-06-12工具坑点合集

作者: keaidelele | 来源:发表于2018-06-12 21:35 被阅读47次

    第一大坑,signalP
    解压这个包之后,莫名其妙报错

    ./signalp -t euk -f short test/euk10.fsa > euk10.fsa.short_out
    Can't locate FASTA.pm in @INC (you may need to install the FASTA module) (@INC contains: /usr/cbs/bio/src/signalp-4.1/lib /home/huangle/perl5/lib/perl5/5.22.1/x86_64-linux-gnu-thread-multi /home/huangle/perl5/lib/perl5/5.22.1 /home/huangle/perl5/lib/perl5/x86_64-linux-gnu-thread-multi /home/huangle/perl5/lib/perl5 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at ./signalp line 80.
    BEGIN failed--compilation aborted at ./signalp line 80.
    

    原来是不知道signalP的本地包在哪里。
    查了readme里面什么都没有,一打开源码才知道里面有一个customize的部分:

    ###############################################################################
    #               GENERAL SETTINGS: CUSTOMIZE TO YOUR SITE
    ###############################################################################
    
    # full path to the signalp-4.1 directory on your system (mandatory)
    BEGIN {
        $ENV{SIGNALP} = '/usr/cbs/bio/src/signalp-4.1';
    }
    
    # determine where to store temporary files (must be writable to all users)
    my $outputDir = "/var/tmp";
    
    # max number of sequences per run (any number can be handled)
    my $MAX_ALLOWED_ENTRIES=10000;
    
    

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