2018-06-12工具坑點合集

第一大坑，signalP
解壓這個包之後，莫名其妙報錯

./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.

原來是不知道signalP的本地包在哪裡。
查了readme裡面什麼都沒有，一開啟原始碼才知道里面有一個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;