12-15-2007
input text into file
hello everyone,
this is my first time posting here so be nice ;-)
I am a bit new at unix scripting and have basically been hacking other peoples scripts to get them to do what I need. I have now hit a bit of a stop. This problem is very basic but I can't just seem to figure out how to get around it.
And so to the problem. Basically I have an application that can interact with a unix prompt. at any one time it can send one command to the unix and return the output. What I need is to read a few lines of text into a file and for the prompt to return the file name for me. This file will be used at a later point so the file name must be random (pretty random). I was going to use the $$ as the file name. the life of this file will be short but if I use a fixed file name there is a chance it will be used by another process (running the same script at the same time).
so basically what I need help with is generating a script file that will take some text in (one or more lines various lenghts) place them in a file and return the file name.
If anyone could help me that would be great.
Regards
Cannon
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LEARN ABOUT DEBIAN
cd-hit-para
CD-HIT-PARA.PL(1) User Commands CD-HIT-PARA.PL(1)
NAME
cd-hit-para.pl - divide a big clustering job into pieces to run cd-hit or cd-hit-est jobs
SYNOPSIS
cd-hit-para.pl options
DESCRIPTION
This script divide a big clustering job into pieces and submit jobs to remote computers over a network to make it parallel. After
all the jobs finished, the script merge the clustering results as if you just run a single cd-hit or cd-hit-est.
You can also use it to divide big jobs on a single computer if your computer does not have enough RAM (with -L option).
Requirements:
1 When run this script over a network, the directory where you
run the scripts and the input files must be available on all the remote hosts with identical path.
2 If you choose "ssh" to submit jobs, you have to have
passwordless ssh to any remote host, see ssh manual to know how to set up passwordless ssh.
3 I suggest to use queuing system instead of ssh,
I currently support PBS and SGE
4 cd-hit cd-hit-2d cd-hit-est cd-hit-est-2d
cd-hit-div cd-hit-div.pl must be in same directory where this script is in.
Options
-i input filename in fasta format, required
-o output filename, required
--P program, "cd-hit" or "cd-hit-est", default "cd-hit"
--B filename of list of hosts,
requred unless -Q or -L option is supplied
--L number of cpus on local computer, default 0
when you are not running it over a cluster, you can use this option to divide a big clustering jobs into small pieces, I suggest you
just use "--L 1" unless you have enough RAM for each cpu
--S Number of segments to split input DB into, default 64
--Q number of jobs to submit to queue queuing system, default 0
by default, the program use ssh mode to submit remote jobs
--T type of queuing system, "PBS", "SGE" are supported, default PBS
--R restart file, used after a crash of run
-h print this help
More cd-hit/cd-hit-est options can be speicified in command line
Questions, bugs, contact Weizhong Li at liwz@sdsc.edu
cd-hit-para.pl 4.6-2012-04-25 April 2012 CD-HIT-PARA.PL(1)