Edit - I don't know how to delete posts. The question I asked here ended up not being the question I should have asked as I didn't realise I needed to edit my script to comply with SGE.
Hi,
My script is:
Code:
#!/bin/bash
# Perform fastqc on files in a specified directory.
for ((j=1; j <=17; j++))
do
files=/data4/user/batch"$j"/*.fastq.gz
for i in $files;
do
fastqc -f fastq -o /data4/user/test/fastqc/ $i
done
done
The command I'm running is:
Code:
qsub -o fastqc.log ~/bin/fastqc.sh
The error I'm getting is:
Code:
Badly placed ()'s
I don't understand what's happening.
Thanks!
Una
Moderator's Comments:
Please use CODE tags as required by forum rules!
Last edited by una1992; 10-26-2017 at 11:02 AM..
Reason: I asked the wrong Q.
Hi,
when I execute the below script, I am getting following error "Badly placed ()'s". can anyone please help me fix
----------------------------------------------------------
# Usage: ani -n -a -s -w -d
#
#
# help_ani() To print help
#
help_ani()
{
echo "Usage: $0 -n -a -s -w -d"... (3 Replies)
Hi,
I am doing the following but it complains and says "for:badly formed number"
does anyone know why?
#!/bin/tcsh
foreach(....)
............
set depth=64
set width=23
if ($depth==64) then
echo "if"
set addr_bits=5
else
echo "else"
endif
echo "addr_bits:$addr_bits"
echo... (3 Replies)
how can I delete one line above and below the matching pattern ?
e.g I want to delete the line above and below the line with %CLI- in example below :
$CHECKSUM $1$DGA1043:TSTST01.DBF;1
%CLI-E-OPENIN, error opening $1$DGA1043:TSTST01.DBF
-RMS-E-FLK, file currently locked by another user
... (6 Replies)
I have the following script running every day numerous times a day and it works fine, but very occasionally I get the following error
if: Badly formed number.
Anyone know why?
Here is the script that runs with the follow parms
LCTMDBSE 100000 130000 160000
#!/bin/csh
... (0 Replies)
I have this file:
NPANXX|BILLDATE|DIVCODE|COMID|RAO|LIKECODE|BOSS|SORD|STATECODE|
087001|BP01|H|SWBT| |041|IMR6|IMSR6|AR|
087002|BP03|H|SWBT| |042|IMR6|IMSR6|AR|
087003|BP05|H|SWBT| |043|IMR6|IMSR6|AR|
....
these are the things that i HAve to do:
Insert a new column named “TEST”
All... (14 Replies)
i'm trying to run the following program but i keep getting the message "badly placed ()'s" can u help?
#include "modularity_mat.h"
#include "../sparse_mlpl/sparse_matrix.h"
adj_matrix_arr* allocate_mem_for_matrix_arr (int y) {
/* Create the adj matrix and allocate memory */
... (2 Replies)
The shell error message "Badly placed ()'s" can occur for a surprisingly simple oversight. If the script begins with a shell-invocation comment, but is missing the exclamation-point, it is simply a comment and not an invocation. If you attempt to execute it from a shell other than the shell you... (4 Replies)
The terminal is bash.
Whenever I try to execute csh just by itself it gives Badly Placed ()'s.
Whenever I try to use csh with a script it also gives Badly Placed ()'s.
My script is this, there is nothing wrong with it, since it used by other students in class as well. (I have also asked... (5 Replies)
I dont know why this Linux would give me badly placed () error all the time for this;
#include <stdio.h>
int main()
{
register int num=0 ;
while ((num < 5))
++num;
printf("Pass %d \n", num) ;
return 0 ;
}
can anyone help me please? (11 Replies)
Discussion started by: sizzler786
11 Replies
LEARN ABOUT REDHAT
purity
PURITY(6) Games Manual PURITY(6)NAME
purity - a general purpose purity test
SYNOPSIS
/usr/games/purity [ flags ] [ testname ]
DESCRIPTION
Purity is an interactive purity test program with a simple, user interface and datafile format. For each test, questions are printed to
the your terminal, and you are prompted for an answer to the current question. At a prompt, these are your choices:
y Answer "yes" to the question.
n Answer "no" to the question.
b Backup one question, if you answered it incorrectly, or someone is watching you take the test, and you don't (or do) want to
admit a different answer.
r Redraw the current question.
q Quit the test, and print the current score.
? Print a help screen for the current prompt.
k Kill a section of the test. This skips all the questions of the test until the next subject heading.
a Toggle answer mode between real answers and obfuscated answers. Real answers print "yes" and "no", while obfuscated answers
are "Maybe" and "maybe". Obfuscated answers are preferred if you are shy, and don't want people to be able to read your
answers over your shoulder as you take the test.
d Toggle dERanGe output.
s Print your current score on the test you are taking.
l Toggle score logging.
At the end of the test, your score is printed out. For most purity tests, lower scores denote more "experience" of the test material.
FLAGS
These are the command line flags for the test.
-a Show real answers (i.e. "yes" and "no") instead of obfuscated ones (i.e. "Maybe" and "maybe") as you answer the questions.
-d PrINt THe tESt in DerANgeD pRInT.
-f Take the test in fast mode. Only the questions are printed, and not any other text blocks, like the introdution, subject
headers, and the conclusion.
-l Take the test without having your score logged.
-p Print the test without prompting for answers. This is useful for making hard copies of the tests without having to edit out
the prompts by hand.
-r Decrypt the test using the Rot 13 algorithm. This is done as a form of "protection", such that if you read a rot13 test and
it offends you, it's your own fault.
-z zoom through more prompts in large text blocks. The default is to prompt the user for more when a screenful of text has been
printed without any user input.
DATAFILE FORMAT
The format of the datafiles is a very simple format, intended such that new tests can quickly and easily be converted to run with the test.
There are four types of text in a purity test datafile. Each type is contained in a bracket type of punctuation. The definitions are as
follows:
the styles of text blocks are:
{ plain text block }
[ subject header ]
( test question )
and < conclusion >
Plain text blocks are printed out character for character.
Subject headers are preceded by their subject numbers, starting at 1, and then printed as text blocks.
Questions are preceded by their numbers, and then prompt the user to answer the question, keeping track of the user's current score.
Conclusions first calculate and print the user's score for the test, then print out the conclusion as a text block.
If you wish to include any of the various bracket punctuation in your text, the backslash ("") character will escape the next character.
To print a question with parentheses, you would use the following format:
(have you ever written a purity test (like this one)?)
the output would be this:
1. have you ever written a purity test (like this one)?
and then it would have asked the user for her/his answer.
For a generic datafile, use the "sample" datafile for the test.
FILES
/var/games/purity.scores the score logfile
/usr/share/games/purity/* test data files
AUTHOR
Eric Lechner, lechner@ucscb.ucsc.edu
18 December 1989 PURITY(6)
10-25-2017
