Hi Perl/UNIX experts,
I have a problem in running a shell script from my perl script (auto.pl).
I run the perl script using
perl auto.pl
from the shell prompt
The shell script picks the files in "input" folder and procesess it.
The shell script blue.sh has this code.
export... (16 Replies)
Hi,
I have an HTML form through which I get some text as input. i need to run a shell script say script.sh inside a perl-cgi script named main_cgi.sh on the form input.
I want to write the contents of the form in a file and then perform some command line operations like grep, cat on the text... (2 Replies)
i want use ssh on the host01 to execute autoexec.sh on the host02 like following :
host01> ssh host02 autoexec.sh
autoexec.sh include nohup command like follwing :
nohup /home/jack/deletedata.sh &
after i execute ssh host02 autoexec.sh one the host01. i can't found deletedata.sh... (1 Reply)
Hi,
I basically have 2 shell scripts.
One is a shell script will get the variable value from the user. The variable is nothing but the IP of the remote system.
Another shell script is a script that does the job of connecting to the remote system using ssh. This uses a expect utility in turn.
... (2 Replies)
Hi All,
I have new for shell scripting.
Problem : I have one scrip at serv1 and path of server is /apps/dev/provimage/scripts and script name:extract_ancillary.bat.
I need to call this script at server2(my working server) and execute at server2 .
Please let me know how to build the... (5 Replies)
I have a shell script (.sh) and I want to pass a parameter value to the awk command but I am getting exception, please assist.
diff=$1$2.diff
id=$2 new=new_$diff
echo "My id is $1"
echo "I want to sync for user account $id"
##awk command I am using is as below
cat $diff | awk... (2 Replies)
Dear Unix gurus,
We have a config shell script file which has 30 variables which needs to be passed to master unix shell script that invokes oracle database sessions. So those 30 variables need to go through the database sessions (They are inputs) via a shell script. one of the variable name... (1 Reply)
Dear Unix gurus,
We have a config shell script file which has 30 variables which needs to be passed to master unix shell script that invokes oracle database sessions. So those 30 variables need to go through the database sessions (They are inputs) via a shell script. one of the variable name... (1 Reply)
Dear Friends,
Please help me on this
my script name is send.csh
In this i have written the statement like this
set args = ( city state country price )
I want to pass this array to another c shell called receiver.csh. and i want to use it in this c shell
or
how to pass to... (2 Replies)
Hi,
I am totally a newbie to any programming languages and I just started an entry level job in an IT company. One of my recent tasks is to create a script that is able to show the log file of linux service (i.e. ntpd service)
lets say, if I run my script ./test.sh, the output should be... (3 Replies)
Discussion started by: xiaogeji
3 Replies
LEARN ABOUT DEBIAN
hhconsensus
HHCONSENSUS(1) User Commands HHCONSENSUS(1)NAME
hhconsensus - calculate the consensus sequence for an A3M/FASTA input file
SYNOPSIS
hhconsensus -i <file> [options]
DESCRIPTION
HHconsensus version 2.0.15 (June 2012) Calculate the consensus sequence for an A3M/FASTA input file. (C) Johannes Soeding, Michael Rem-
mert, Andreas Biegert, Andreas Hauser Remmert M, Biegert A, Hauser A, and Soding J. HHblits: Lightning-fast iterative protein sequence
searching by HMM-HMM alignment. Nat. Methods 9:173-175 (2011).
-i <file>
query alignment (A2M, A3M, or FASTA), or query HMM
Output options:
-s <file>
append consensus sequence in FASTA (default=<infile.seq>)
-o <file>
write alignment with consensus sequence in A3M
-oa3m <file>
same
-oa2m <file>
write alignment with consensus sequence in A2M
-ofas <file>
write alignment with consensus sequence in FASTA
-v <int>
verbose mode: 0:no screen output 1:only warings 2: verbose
Filter input alignment (options can be combined):
-id [0,100] maximum pairwise sequence identity (%) (def=100)
-diff [0,inf[ filter most diverse set of sequences, keeping at least this
many sequences in each block of >50 columns (def=0)
-cov [0,100] minimum coverage with query (%) (def=0)
-qid [0,100] minimum sequence identity with query (%) (def=0)
-qsc [0,100] minimum score per column with query (def=-20.0)
Input alignment format:
-M a2m use A2M/A3M (default): upper case = Match; lower case = Insert; '-' = Delete; '.' = gaps aligned to inserts (may be omitted)
-M first
use FASTA: columns with residue in 1st sequence are match states
-M [0,100]
use FASTA: columns with fewer than X% gaps are match states
Other options:
-addss add predicted secondary structure information from PSIPRED
Example: hhconsensus -i stdin -s stdout
hhconsensus 2.0.15 June 2012 HHCONSENSUS(1)