I submitted a ksh script in the background last night before leaving work:
./ping_test &
When I came into work this morning I discovered that it had stopped running when my session timed out.
So, I then tried it again this morning and logged out before letting it time out as one unix site... (4 Replies)
I'm a newbie in scripting attempting to create a script where i can submit a job (in maestro/tivoli) with parameters,in maestro CLI i can do that no problem,i'm thinking about creating a script that will accept input while the script is executing, more like below structure:
exec the script
-... (1 Reply)
Dear All
I am trying to write a script to set the SGE job execution order. I named each job with 'job1', 'job2' and 'job3'. I want my script to do: When 'job1' execution is complete, 'job2' is executed; when both 'job1' and 'job2' are complete, 'job3' is executed.
First, I tried this... (0 Replies)
I was just wondering if it is permissible to qsub from a bash script as follows:
#! /bin/sh
echo "altering .txt in dir $DIR with retokenize.py"
for f in $DIR/txt/*.txt; do
echo $f;
/l2/nlp/i2b2/retokenize.py < $f > ${f//.txt/.tok};
done
echo "altering .tok in dir $DIR with awk... (0 Replies)
hello 2 all
I can't understand how to insert a perl-script into .shml in a right way. <form> should be working but it's not
doing that: <!--#include virtual="/cgi-bin/script.cgi?filename"-->
filename is a name of the file which script is using
the script is used for a score show (the number... (0 Replies)
hi all,
im going to design a web html form so users can input what username and password they want to make the ftp account, once they enter in a username and password they click on the submit button and it submits it to a bash script and then the bash script will run and finish of making the... (3 Replies)
Hi,
I'm trying to edit my working bash script to an SGE script in order to submit it as a job to the cluster.
Currently I have:
#!/bin/bash
# Perform fastqc on files in a specified directory.
for ((j=1; j <=17; j++))
do
directory=/data4/una/batch"$j"/
... (0 Replies)
Hi All,
I'm new in forum.
Many congratulations to everyone for all work.
I'm not an expert in bash script
I've a problem with a sh file.
The sh file run every t minuts and it read data from txt file and then compile form.
Finally, the user, from the web browser click on send.
The script... (0 Replies)
Hi I was hoping some one could help me with a problem I have.
I am trying to collect some information from a web form and save it to a text file.
I found an example on this site that is sort of what I am trying to accomplish, the shell script bellow should echo the input back to the browser... (0 Replies)
Discussion started by: Paul Walker
0 Replies
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)