PBS 是公开源代码的作业管理系统，在此环境下运行，用户不需要指定程序在哪些节点上运行，程序 所需的硬件资源由PBS 管理和分配。 1、PBS 命令 PBS 提供4 条命令用于作业管理。 (1) qsub 命令—用于提交作业脚本 命令格式： qsub [-a date_time] [-c interval] [-C directive_prefix] [-e path] [-I] [-j join] [-k keep] [-l resource_list] [-m mail_options] [-M user_list][-N name] [-o path] [-p priority] [-q destination] [-r c] [-S path_list] [-u user_list][-v variable_list] [-V] [-W additional_attributes] [-z] [script] 参数说明：因为所采用的选项一般放在pbs 脚本中提交，所以具体见PBS 脚本选项。 […]
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for Single CPU Job zyshen@e2lx001:/home/zyshen> cat /disk/rdisk03/test_1cpu.sh #!/bin/csh # # #PBS -l nodes=1:ppn=1 # #******** Script for job submission with single CPU #******** The lines above must be included in any job script #******** ‘nodes’ is number of nodes and ‘ppn’ is number of CPU per node, which are both ‘=1′ in this case. # […] #!/usr/bin/perl -w use strict; use Bio::SeqIO; use Bio::Seq::Quality; use Getopt::Long; die “pass a fasta and a fasta-quality file\n” unless @ARGV; my ($seq_infile,$qual_infile) = (scalar @ARGV == 1) ?($ARGV[0], “$ARGV[0].qual”) : @ARGV; ## Create input objects for both a seq (fasta) and qual file my $in_seq_obj = Bio::SeqIO->new( -file => $seq_infile, -format => ‘fasta’, ); my […] #!/usr/bin/env perl # Convert a fastq to a fasta/qual combo using BioPerl, with some Linux commands use Bio::Perl; use Data::Dumper; use strict; use warnings; use threads; use Thread::Queue; use Getopt::Long; my $settings={}; $|=1; my %numSequences; # static for a subroutine exit(main()); sub main{ die(“Usage: $0 -i inputFastqFile [-n numCpus -q outputQualfile -f outputFastaFile]”) if(@ARGV<1); GetOptions($settings,(‘numCpus=s’,’input=s’,’qualOut=s’,’fastaOut=s’)); […] #! /usr/bin/env python2.7 desc = “”” Split an ACE format assembly file into multiple single ACE files each with a single contig. The resulting ACE contig files are formatted so that they can be read by CodonCode (http://www.codoncode.com). $ ACEAssemblySplitter.py test.ace -s 2 -e 3 – prints the second and third contigs in the test.ace […] a=[‘a’,’b’,’c’,’a’,’d’,’a’] 如何把所有的’a’删除呢？ 我的笨方法： for i in a: if i == ‘a': a[a.index(i)] = ” while ” in a: a.remove(”) 命令： perl -MCPAN -e shell 初次运行CPAN时需要做一些设置，一路回车在最后选一个最近的CPAN镜像站点。例如国内的中国自由软件库： ftp://freesoft.cgi.gov.cn/pub/languages/perl/CPAN 获得帮助 cpan>h 列出CPAN上所有模块的列表 cpan>m 安装模块 perl -MCPAN -e shell cpan> install IO::Wrap cpan> install Net::Server cpan> install MIME::Words 也可以合并成一条命令，如： perl -MCPAN -e ‘install Net::Server’ 退出 cpan>q 如果自动安装失败，可以手动安装跳过测试： cd /root/.cpan/build/Net-Server-0.97/ perl Makefile.PL make install |
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