Edit $args within a command Post: 302924137

Sponsored Content

Top Forums UNIX for Dummies Questions & Answers Edit $args within a command Post 302924137 by gandolf989 on Thursday 6th of November 2014 12:47:25 PM

11-06-2014

Registered User

You may want to write a Perl wrapper with the YAML library. Perl and YAML are really good at reading configuration files. You would then have a configuration file with all of the parameters that you need to make the bowtie2 call, you can parse all of the inputs and more simply change the inputs to what you need and make it work. It would probably be easier to read and understand then the approach you are taking. etc..etc..

Here is the install page for YAML. I am using Perl and YAML to build a software installer. The customer will only need to provide the response file to make it work. Which is much easier than handling each parameter separately. And I can directly reference any parameter as $yaml_hash->{field_name}.

YAML - search.cpan.org

This User Gave Thanks to gandolf989 For This Post:

gandolf989

View Public Profile for gandolf989

Find all posts by gandolf989

10 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

required command line args

Hello, How do I make a command line argument required using getopts? Thanks.

2. Programming

Command line args

My program usage takes the form for example; $ theApp 2 "one or more words" i.e. 3 command line arguments; application name, an integer, some text My code includes the following 4 lines: int anInteger; char words; sscanf(argv, "%d", &anInteger); sscanf(argv, "%s", &message); Based...

3. UNIX for Dummies Questions & Answers

command line args

I am trying to print command line arguments one per second. I have this while do echo "6" shift echo "5" shift echo "4" shift echo "3" shift echo "2" shift echo "1" shift done

4. UNIX for Dummies Questions & Answers

command line args 2

I have this while loop and at the end I am trying to get it to tell me the last argument I entered. And with it like this all I get is the sentence with no value for $1. Now I tried moving done after the sentence and it printed the value of $1 after every number. I don't want that I just want...

5. Shell Programming and Scripting

How to retrieve command line args one by on.

Hi, I have to store all the command line arguments into an array. I have the following code. ********************** #! /bin/sh set -A arr_no_updates i=1 while do arr_no_updates=$($i) echo ${arr_no_updates} i=$(($i+1)) done****************

6. Shell Programming and Scripting

How to send a function all command line args?

I have this code, I thought it would automatically know the args sent to script when called from shell. But it seems to not see any... main script: . args . errors . opt . clean dbfile="" opfile="" # calls function in script below chkarg #check commands

7. UNIX for Dummies Questions & Answers

UFW show args command

In ubuntu man page there is this command. What are values of ARGS I can use?

8. Shell Programming and Scripting

command line args in unix

Hi, i have a perl script named test.pl. It is executed as cat *.log|test.pl i need the complete command line args. I tried using basename $0 but im getting test.pl only but not cat *.log... Can anyone help me on this. Thanks in advance

9. Emergency UNIX and Linux Support

Cut | command line args

Hi, Can you please hint me how to achieve the below? Input: $./script.sh start 1 2 Internally inside the script i want to set a single variable with $2 and $3 value? Output: CMD=$1 ARGS=$2 $3 --VInodh

10. Shell Programming and Scripting

Store args passed in array but not the first 2 args

Store args passed in array but not the first 2 args. # bash declare -a arr=("$@") s=$(IFS=, eval 'echo "${arr}"') echo "$s" output: sh array.sh 1 2 3 4 5 6 1,2,3,4,5,6 Desired output: sh array.sh 1 2 3 4 5 6 3,4,5,6

LEARN ABOUT DEBIAN

bowtie2-inspect

BOWTIE2-INSPECT(1)						   User Commands						BOWTIE2-INSPECT(1)

NAME

       bowtie2-inspect - extracts information from a bowtie2 index

SYNOPSIS

       bowtie2-inspect [options]* <bt2_base>

DESCRIPTION

       Bowtie 2 version 2.0.0-beta6 by Ben Langmead (blangmea@jhsph.edu)

       <bt2_base>
	      bt2 filename minus trailing .1.bt2/.2.bt2

	      By  default,  prints  FASTA records of the indexed nucleotide sequences to standard out.	With -n, just prints names.  With -s, just
	      prints a summary of the index parameters and sequences.  With -e, preserves colors if applicable.

OPTIONS

       -a/--across <int>
	      Number of characters across in FASTA output (default: 60)

       -n/--names
	      Print reference sequence names only

       -s/--summary
	      Print summary incl. ref names, lengths, index properties

       -e/--bt2-ref
	      Reconstruct reference from .bt2 (slow, preserves colors)

       -v/--verbose
	      Verbose output (for debugging)

       -h/--help
	      print detailed description of tool and its options

       --help print this usage message

       64-bit Built on lxcsid Fri Jun  1 20:13:13 UTC 2012 Compiler: gcc version 4.7.0 (Debian 4.7.0-8) Options: -O3  -m64  -msse2  -funroll-loops
       -g3 Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

bowtie2-inspect version 2.0.0-beta6				     June 2012							BOWTIE2-INSPECT(1)