In the bash below, if the answer is "y" then goto function remove. If the answer is "n" then goto the id variable line (where the date is inputted). However, I am getting command remove not found, but remove is a function not an command. I must have the syntax incorrect? Thank you .
Hello All,
I have installed Cygwin on Windows XP and working with some Shell scripting work, I have needed to schedule my script using the cornetab and whatever commands such as "cron", "cron-config" are not working in my cygwin shell,
I re-installed the Cygwin but the same problem is with... (2 Replies)
I currently run a script over a vpnc tunnel to back-up my data to a remote server. However for a number of reasons the tunnel often collapses. If I manually restore the tunnel then the whole thing can continue, but I want to add into my script a section whereby while the transfer is taking place,... (8 Replies)
I am trying to create a shell that asks the user to enter their name, and compare it to my own by saying we have the same name or saying my name and that they have a nice name too. Here is my script...
#!/bin/bash-x
echo "Enter your name".
read name
if
then
echo "My name is Adam too"... (1 Reply)
Hi All,
Linux lxs3er06 2.6.9-67.ELsmp #1 SMP Wed Nov 7 13:58:04 EST 2007 i686 i686 i386 GNU/Linux
Issue:
While executing shell scripts in bash shell, following error messages are thrown:
rm:command not found
On doing little investigation, I added '/bin' to $PATH and on doing echo... (9 Replies)
Hi all
I am relatively new to linux (specifically red hat). I have installed Fedora 13 on my machine and started playing with the terminal when i found a very strange behavior when typing a command that is not found:
the terminal does not prompt me back. In other words, i am logged as root (or... (4 Replies)
I downloaded and installed "Cygwin yesterday onto my PC running Windows XP. When I tried to type "vi" in Cygwin's window, I got the following message bash: vi: Command not found
What shud i do inorder to get into vi editor
Thanks (10 Replies)
I created a script that I need to run from time to time, but get this error message. To get it working again I run this command from time to time:
export PATH="$PATH:~/scripts"
I put all my automated scripts in the /scripts directory and would like to run my scripts from any directory... (5 Replies)
Hello everyone,
I am having problems figuring this out.
This script below is supposed to create a list of file names with their "md5sum", in a file "lib-list.txt"
When I run it "sh component-list.sh " I get this:component-list.sh: 4: component-list.sh: function: not found
component-list.sh:... (4 Replies)
Hello Experts,
I have been trying to send a test mail in our linux server with sendmail command.But I am getting command not found error message.
-->when I tried whether sendmail installed or not with the command
rpm -qa sendmail* I got the below,
sendmail-cf-8.14.4-8.el6.noarch... (26 Replies)
In the bash below I am searching the filevirus-scan.log for the Infected files: 0 line (in bold) and each line for OK.
If both of these are true then the function execute is automatically called and processing starts. If both these conditions are not meet then the line in the
file is sent to the... (2 Replies)
Discussion started by: cmccabe
2 Replies
LEARN ABOUT DEBIAN
bio::tools::run::samtools
Bio::Tools::Run::Samtools(3pm) User Contributed Perl Documentation Bio::Tools::Run::Samtools(3pm)NAME
Bio::Tools::Run::Samtools - a run wrapper for the samtools suite *BETA*
SYNOPSIS
# convert a sam to a bam
$samt = Bio::Tools::Run::Samtools( -command => 'view',
-sam_input => 1,
-bam_output => 1 );
$samt->run( -bam => "mysam.sam", -out => "mysam.bam" );
# sort it
$samt = Bio::Tools::Run::Samtools( -command => 'sort' );
$samt->run( -bam => "mysam.bam", -pfx => "mysam.srt" );
# now create an assembly
$assy = Bio::IO::Assembly->new( -file => "mysam.srt.bam",
-refdb => "myref.fas" );
DESCRIPTION
This is a wrapper for running samtools, a suite of large-alignment reading and manipulation programs available at
<http://samtools.sourceforge.net/>.
RUNNING COMMANDS
To run a "samtools" command, construct a run factory, specifying the desired command using the "-command" argument in the factory
constructor, along with options specific to that command (see "OPTIONS"):
$samt = Bio::Tools::Run::Samtools->new( -command => 'view',
-sam_input => 1,
-bam_output => 1);
To execute, use the "run()" method. Input and output files are specified in the arguments of "run()" (see "FILES"):
$samt->run( -bam => "mysam.sam", -out => "mysam.bam" );
OPTIONS
"samtools" is complex, with many subprograms (commands) and command-line options and file specs for each. This module attempts to provide
commands and options comprehensively. You can browse the choices like so:
$samt = Bio::Tools::Run::Samtools->new( -command => 'pileup' );
# all samtools commands
@all_commands = $samt->available_parameters('commands');
@all_commands = $samt->available_commands; # alias
# just for pileup
@pup_params = $samt->available_parameters('params');
@pup_switches = $samt->available_parameters('switches');
@pup_all_options = $samt->available_parameters();
Reasonably mnemonic names have been assigned to the single-letter command line options. These are the names returned by
"available_parameters", and can be used in the factory constructor like typical BioPerl named parameters.
See <http://samtools.sourceforge.net/samtools.shtml> for the gory details.
FILES
When a command requires filenames, these are provided to the "run()" method, not the constructor ("new()"). To see the set of files
required by a command, use "available_parameters('filespec')" or the alias "filespec()":
$samt = Bio::Tools::Run::Samtools->new( -command => 'view' );
@filespec = $samt->filespec;
This example returns the following array:
bam
>out
This indicates that the bam/sam file (bam) and the output file (out) MUST be specified in the "run()" argument list:
$samt->run( -bam => 'mysam.sam', -out => 'mysam.cvt' );
If files are not specified per the filespec, text sent to STDOUT and STDERR is saved and is accessible with "$bwafac-"stdout()> and
"$bwafac-"stderr()>.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
web:
http://redmine.open-bio.org/projects/bioperl/
AUTHOR - Mark A. Jensen
Email maj -at- fortinbras -dot- us
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = new Bio::Tools::Run::Samtools();
Function: Builds a new Bio::Tools::Run::Samtools object
Returns : an instance of Bio::Tools::Run::Samtools
Args :
perl v5.12.3 2011-06-18 Bio::Tools::Run::Samtools(3pm)