running: samtools view -h /results/analysis/output/Home/user_LIS-27-06mar2013-40p12rpt-swp_4-12.2_207/AIB13-NA17281_rawlib.bam | perl -ne '{ @line = split( /\s+/ ); = 0; while( runplugin/runlevel ""[5] =~ /(\d+)M/g ) { = + -j } if( >= 80 || /results/analysis/output/Home/user_LIS-27-06mar2013-40p12rpt-swp_4-12.2_207/AIB13-NA17281_oldrawlib.bam =~ /^\@/ ) { print /results/analysis/output/Home/user_LIS-27-06mar2013-40p12rpt-swp_4-12.2_207/AIB13-NA17281_oldrawlib.bam } }' | java -Xmx12G -jar /opt/picard/picard-tools-current/SortSam.jar I=/dev/stdin O=/results/analysis/output/Home/user_LIS-27-06mar2013-40p12rpt-swp_4-12.2_207/AIB13-NA17281_rawlib.bam VERBOSITY=WARNING QUIET=TRUE SO=coordinate
String found where operator expected at -e line 1, near "runlevel """
(Do you need to predeclare runlevel?)
Bareword found where operator expected at -e line 1, near "06mar2013"
(Missing operator before mar2013?)
Bareword found where operator expected at -e line 1, near "40p12rpt"
(Missing operator before p12rpt?)
Bareword found where operator expected at -e line 1, near "06mar2013"
(Missing operator before mar2013?)
Bareword found where operator expected at -e line 1, near "40p12rpt"
(Missing operator before p12rpt?)
syntax error at -e line 1, near "; ="
syntax error at -e line 1, near "runlevel """
syntax error at -e line 1, near "( >="
syntax error at -e line 1, near "} }"
Execution of -e aborted due to compilation errors.
#!/usr/bin/perl
open (DATA, file.txt);
@array = <DATA>;
close (DATA);
open (DATA, ">$file.txt");
for (@array) {
s/text/replace text/;
push(@contents,$_);
}
seek(DATA, 0, 0);
print DATA (@contents);
close(DATA);
could someone please explain how this works. i've been... (3 Replies)
i am having a weird error on mac os x running some shell scripts. i am a complete newbie at this and this question concerns 2 scripts. one of which a friend of mine wrote (videochecker.sh) a couple weeks ago and it's been running fine on another machine.
then last week i wrote capture.sh and it... (2 Replies)
so in unix this command works works and shows me a list of directories
find . -name \*.xls -exec dirname {} \; | sort -u | > list.txt
but when i try running a perl script to run this command
my $query = 'find . -name \*.xls -exec dirname {} \; | sort -u | > list.txt';... (2 Replies)
Hello.
I would like to ask your help regarding the cp command. We are using a cp command to create a back-up copy of our file but to no avail. It's just not working. We already checked the file and directory permissions and all seems correct.
We have a script (ftp.script) which calls on... (1 Reply)
The following command works perfectly in Terminal, but not in Applescript. (Returns "unknown token" error for square brackets.)
(new to site. sorry.)
I have an Applescript that is designed to find and remove any square-bracketed text, including the square brackets.
I ran the following code from... (1 Reply)
Hi everyone
I have a problem with my script
If I try directly this command
/usr/bin/nice -n 19 mysqldump -u root --password="******" wiki_schneider -c | nice -n 19 gzip -9 > /point_de_montage/$(date '+%Y%m%d')-wiki-db.sql.gz
It works
But if I simply add this command in a script and... (8 Replies)
In the below perl executes if one file is processed perfect. However, when multiple files are processed in batch which is preferred I get the below error that I can not seem to fix it as the '' necessary for the command to execute, but seem to only work for one -arg option. Thank you :).
... (2 Replies)
I have a file with two line, one is header, the other actual value:
TYPCD|ETID2|ETID|LEG ID|PTYP|PTYP SUB|TRD STATUS|CXL REASON|CACT|CACTNM|ENCD|ENC
D NM|TRDR|ASDT|TRDT|MTDT|STDT|LS|SECID|SECID TYP|SECNM|PAR|STCC|MARKET PRICE|DIS
MARKET PRICE|MARKET PRICE CURRENCY|SRC OF SETTLEMENT... (2 Replies)
I wish to replace "\\n" with a single white space.
The below does the job on command-line:
$ echo '/fin/app/scripts\\n/fin/app/01/sql' | sed -e 's#\\\\n# #g';
/fin/app/scripts /fin/app/01/sql
However, when i have the same code to a shell script it is not able to get me the same output:... (8 Replies)