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Hi, jdilts

You only need interpolation and you got it already with the double quotes.
print BSUB "
...
...
fasta_16S=$path/\${id}/\${id}_bacterial_minreadlen$MIN_READ_LENGTH_16S.fasta\n";
...

perl -ne 'length > 9 && $last && print "$last$_"; $last = $_' ${sample}.fasta > result.fasta

Explanation:

length > 9: only if the length of the line is more than 9 (to accommodate the newline...

Does it have to be perl?
awk 'length($2)>8{print RS $0}' RS=\> ORS= "${sample}.fasta"

Try:
awk -F- '{print $2}'
or
cut -d- -f2

Try the bg mount option!

mount -t cifs is a driver in the Linux kernel(one of two, actually!) which Samba is unnecessary for. I don't know what you configured Samba for either.

Samba's generally used as a server, not...

Enjoy: perlrun - perldoc.perl.org (http://perldoc.perl.org/perlrun.html)

There are few ways actually. I think this is the most elegant:perl -s -n -e 'if($_=~/.*\:.*\:.*$amp/){print "$_";}' -- -amp="$amp" $sam >> $ampsam

One way:
#!/usr/bin/perl
use strict;
use warnings;

my %FINALcontigs = (
'mira_rep_c765:119reads**', 'ctctactggaagactgac',
'mira_rep_c7454:54reads**',...

Take a look at the info on these links:
Perl - Printing duplicates in a hash (http://www.tek-tips.com/viewthread.cfm?qid=1363591)
How do I find and count duplicate values in a perl hash - Stack...

try:
#!/usr/bin/perl

%hash = (
key1 => "jeri",
key2 => "corona",
key3 => "una"
);

print "\nforward sort...\n\n";

foreach $key (sort {length($hash{$a}) cmp length($hash{$b})} keys...

There are transforms like soundex that nullify spelling differences.

Regex that tolerates missing or extra every byte of key gets too loose, fast. You might construct an extended regex where for...

sed -e 's#.*/Home/\(.*\)/plugin_out/.*#\1#g'

NOTE: .* is greedy. It will capture from first "/Home/" to last "/plugin_out/", so the g (global) is useless in this case.

It tries to create the file before running it because that's how redirection works. You can't change what file stdout goes to for a different program once it's already running, but it's easy to do...

I read ( but its the end of the day... and had very strange annoying support...) :
If there is a file callled {TSP_FILEPATH_PLUGIN_DIR} , then remove it with all if exist subdirectories and content...

-f forces the delete without a Y/N question
-r recurses (goes down into) sub-directories.

rm -rf directory_name

remove all of the files including subdirectories in directory_name, then...

I can reproduce the error in Post #1 by converting the script posted to MSDOS text file format, then executing it.
Was the the script created with a Microsoft Windows editor such as Notepad?

If...

Can you change it to:

cat ${TSP_FILEPATH_BARCODE_TXT} | grep "^barcode" | while read BARCODE_LINE
do
etc...
done

(no backtick... to see if they are in cause...)

That's printing the second field in the variable value where the field-separator is a comma.

E.g., if BARCODE_LINE contains "FIELD 1,FIELD 2,FIELD 3,FIELD 4", after this assignment BARCODE_ID...

.* means any character (and that includes space) any number of times.

Your command is removing the longest string ending with /.

E.g.,

$ echo "HI THERE"|sed -e 's_.*/__g'
HI THERE

$ echo...

I would say that the remote server is creating the zip file, with 644 permission, the perl procedure fetches the zip files on local machine.

Since zip file is created on remote server with root...

He means to run the id command, and see what it does. Not a trick question.

What is the output of id ?

What user did you log in as? If you logged in as root, you're root. sudo also runs things as root.

How can it put root permission on a file if you are not root?

I think you still have not learned what my collegue tried to tell you:

It is dead simple:

Do not work or use root account except...