11-06-2014
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:
10 More Discussions You Might Find Interesting
1. UNIX for Dummies Questions & Answers
Hello,
How do I make a command line argument required using getopts?
Thanks. (6 Replies)
Discussion started by: yoi2hot4ya
6 Replies
2. Programming
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... (2 Replies)
Discussion started by: enuenu
2 Replies
3. UNIX for Dummies Questions & Answers
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 (2 Replies)
Discussion started by: skooly5
2 Replies
4. UNIX for Dummies Questions & Answers
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 $1 after every number. I don't want that I just want... (2 Replies)
Discussion started by: skooly5
2 Replies
5. Shell Programming and Scripting
Hi,
I have to store all the command line arguments into an array.
I have the following code.
**********************
#! /bin/sh
set -A arr_no_updates
i=1
while
do
arr_no_updates=$($i)
echo ${arr_no_updates}
i=$(($i+1))
done**************** (1 Reply)
Discussion started by: little_wonder
1 Replies
6. Shell Programming and Scripting
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 (2 Replies)
Discussion started by: gcampton
2 Replies
7. UNIX for Dummies Questions & Answers
In ubuntu man page there is this command. What are values of ARGS I can use? (0 Replies)
Discussion started by: mojoman
0 Replies
8. Shell Programming and Scripting
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 (3 Replies)
Discussion started by: niteesh_!7
3 Replies
9. Emergency UNIX and Linux Support
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 $3
--VInodh (10 Replies)
Discussion started by: vino_hymi
10 Replies
10. Shell Programming and Scripting
Store args passed in array but not the first 2 args.
# bash
declare -a arr=("$@")
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 (2 Replies)
Discussion started by: iaav
2 Replies
LEARN ABOUT CENTOS
yaml::any
YAML::Any(3) User Contributed Perl Documentation YAML::Any(3)
NAME
YAML::Any - Pick a YAML implementation and use it.
SYNOPSIS
use YAML::Any;
$YAML::Indent = 3;
my $yaml = Dump(@objects);
DESCRIPTION
There are several YAML implementations that support the Dump/Load API. This module selects the best one available and uses it.
ORDER
Currently, YAML::Any will choose the first one of these YAML implementations that is installed on your system:
YAML::XS
YAML::Syck
YAML::Old
YAML
YAML::Tiny
OPTIONS
If you specify an option like:
$YAML::Indent = 4;
And YAML::Any is using YAML::XS, it will use the proper variable: $YAML::XS::Indent.
SUBROUTINES
Like all the YAML modules that YAML::Any uses, the following subroutines are exported by default:
Dump
Load
and the following subroutines are exportable by request:
DumpFile
LoadFile
METHODS
YAML::Any provides the following class methods.
YAML::Any->order;
This method returns a list of the current possible implementations that YAML::Any will search for.
YAML::Any->implementation;
This method returns the implementation the YAML::Any will use. This result is obtained by finding the first member of YAML::Any->order
that is either already loaded in %INC or that can be loaded using "require". If no implementation is found, an error will be thrown.
AUTHOR
Ingy doet Net <ingy@cpan.org>
COPYRIGHT
Copyright (c) 2008. Ingy doet Net.
This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
See <http://www.perl.com/perl/misc/Artistic.html>
POD ERRORS
Hey! The above document had some coding errors, which are explained below:
Around line 191:
Non-ASCII character seen before =encoding in 'doet'. Assuming UTF-8
perl v5.16.3 2012-07-13 YAML::Any(3)