I am having trouble running a .sh file. The code 'x=${file_name:0:$z-11}' is giving me a bad substitution error. However when I run in BASH it works. Thing is when this goes to production the .sh will not be running in BASH. Is there a way to substring a string not in BASH or a way to invoke... (2 Replies)
Hi all-
I'm trying to search through some .gz log files to verify certain feeds have passed through our app.
I have a small script that I wrote in hopes that I could automate the checking but haven't been able to get the zgrep to work. When I copy it to the command line directly it works... (2 Replies)
Ubuntu 9.10 is my linux distro
Based on forums they say that the problem is with environment .
here is my case:
login as user, then sudo -s
using this command: s3cmd put file s3://bucket >>worked!
now here is the simple script intended for testing:
#! /bin/bash
env >/tmp/cronjob.log... (1 Reply)
Hey guys. Hopefully this is an easy one but having reference similar problems on the web I still can't fix it.
I am doing a recursive find and replace from a script. Of course I could just run the damn thing from the command line but it's bugging me now and want to get it working.
grep -rl... (4 Replies)
I'm reading about debugging aids in bash and have come across the set command. It says in my little book that an addition to typing
set
you can also use them "on the command line when running a script..." and it lists this in a small table:
set -o option Command Line... (5 Replies)
Hi All,
This command works when I type it on but when I run the batch file it doesn't..any ideas why?
attrib.exe * | find /c /v "" >filecount.txt (1 Reply)
I am working with a sh script on a solaris 9 zone (sol 10 host) that grabs information to build the configuration command line. the variables Build64, SSLopt, CONFIGopt, and CC are populated in the script. the script includes
CC=`which gcc`
CONFIGopt=' --prefix=/ --exec-prefix=/usr... (8 Replies)
OSX 10.9
I am building a script that evaluates the difference between 2 files. Here is a command that does not work transparently.
Running this command in Terminal yields great results; however when I put that line in a .sh script, I get the errors shown below. Am I doing something silly?
... (1 Reply)
Oracle Linux 6.
Trying to set up a simple monitoring of memory usage. This command does exactly what I want at the command line:
echo $(date +%Y-%m-%d" "%H:%M:%S) $(grep PageTables /proc/meminfo) >> /home/oracle/meminfo.logBut when I put it in my crontab:
* * * * * echo $(date +%Y-%m-%d"... (2 Replies)
The below command works in the terminal interactively but not as part of a bash script. I though maybe I needed to escape the "$dir" so it isn't interpreted literally, but that's not it. Thank you :).
interactively in terminal
dir=/path/to
new=$(ls "$dir"/*.csv -tr | tail -n 1) && echo... (6 Replies)
Discussion started by: cmccabe
6 Replies
LEARN ABOUT DEBIAN
vcf-isec
VCF-ISEC(1) User Commands VCF-ISEC(1)NAME
vcf-isec - create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files
SYNOPSIS
vcf-isec [OPTIONS] file1.vcf file2.vcf ...
DESCRIPTION
About: Create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files.
Note that lines from all files can be intermixed together on the output, which can yield unexpected results.
OPTIONS -C, --chromosomes <list|file>
Process the given chromosomes (comma-separated list or one chromosome per line in a file).
-c, --complement
Output positions present in the first file but missing from the other files.
-d, --debug
Debugging information
-f, --force
Continue even if the script complains about differing columns.
-o, --one-file-only
Print only entries from the left-most file. Without -o, all unique positions will be printed.
-n, --nfiles [+-=]<int>
Output positions present in this many (=), this many or more (+), or this many or fewer (-) files.
-p, --prefix <path>
If present, multiple files will be created with all possible isec combinations. (Suitable for Venn Diagram analysis.)
-t, --tab <chr:pos:file>
Tab-delimited file with indexes of chromosome and position columns. (1-based indexes)
-w, --win <int>
In repetitive sequences, the same indel can be called at different positions. Consider records this far apart as matching (be it a
SNP or an indel).
-h, -?, --help
This help message.
EXAMPLES
bgzip file.vcf; tabix -p vcf file.vcf.gz bgzip file.tab; tabix -s 1 -b 2 -e 2 file.tab.gz
vcf-isec 0.1.5 July 2011 VCF-ISEC(1)