Programming :: Shell Scripting For Accepting Input From Different Directories Automatically
Nov 6, 2010
The two shell scripts (t1prog and t2prog) are given below they are working fine. The input for the first program is 't1.det' and for second program is 't1.rnaml'. These two input files are in 'dir1' folder. I am executing the shell like 'sh t1prog > t1out' and 'sh t2prog > t2out' from this directory only. Then I am executing a java program 'java RNA'; for this, t1out and t2out are input files used in the program and I am getting the final output on screen.
The input files 't1.det' and 't1.rnaml' are in different folders with same name and with different values. Each folder specifies one gene sequence input files.
In mfold directory there are 5 directors and each directory contains these input files as shown below
cd mfold
dir1 dir2 dir3 dir4 dir5
cd dir1
t1.det t1.rnaml
[Code].....
for inputs in different directories and executing these and redirecting the final ouput after executing 'java RNA' statement to a file is needed.
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Jul 30, 2011
I'm creating a bash script to do some tasks for me. I would like the script to be run at a set time of everyday. My first question is if it is possible that if one of the commands in the script requires sudo, is there a way to get around it with out making sudo not require a password. Such as, is there a way to include the password in the script? If that is the case, I can always just set the file as read only by sudo. I've been looking for a way to do this, with no success. if I have a command that wants input, how do I give it to the program. For example, if I want to make a zip file that is encrypted, the command would go as:
Code:
zip -r example * -e
now how would I get the script to insert my wanted password.
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Jun 17, 2010
I have a system setup script for my Slackware installations that pulls all packages and source files from another machine and sets everything up to be identical between machines. The script works as expected but make it entirely unattended. How do I make the bash script deal with automatically selecting "Yes" for, for example "Install x(Yes/No): " when prompted by a make file?
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Sep 21, 2010
I am running an application called QuantiSNP [URL]. The binary file is "quantisnp2", called upon in the "run_quantisnp2.sh" supplied by the authors. I am only able to run the application for single file processing (e.g. 1 input file for 1 sample; I can't run the batch file processing because I don't have the necessary BeadStudio report files, which has different formatting for the input files).
The difficulty is that I have 300 samples (300 unique sample IDs) and 3 input files for each sample for a total of 900 runs of this application. I am wondering how would I be able to automate this process as a shell script instead of basically manually changing the sample ID and respective input files every time a run completes? I bolded the single file processing shell script command line options below that need to be changed for each sample/input single file processing run. The command line option "--sampleid" is for the name given to the processed output files corresponding to the sample of interest and there are 3 input files for each sample.
/home2/jason/QuantiSNP/quantisnp/linux64/run_quantisnp2.sh /home2/jason/QuantiSNP/MCR/v79/ --config /home2/jason/QuantiSNP/quantisnp/config/params.dat --levels /home2/jason/QuantiSNP/quantisnp/config/levels-affy.dat --outdir /home2/jason/QuantiSNP/quantisnp_out/ --sampleid sample1 --gender female --input-files /home2/jason/files/sample1_input.txt
Note that each sample has 3 input files, for a total of 3 runs of "quantisnp2" for each sample. e.g.
SAMPLEID INFILE
sample1 /home2/jason/files/sample1_input.txt
sample1 /home2/jason/files/sample1_input2.txt
sample1 /home2/jason/files/sample1_input3.txt
[code]....
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Jun 5, 2011
I am trying to create a shell script similar to ls, but which only lists directories. I have the first half working (no argument version), but trying to make it accept an argument, I am failing. My logic is sound I think, but I'm missing something on the syntax.
Code:
if [ $# -eq 0 ] ; then
d=`pwd`
for i in * ; do
if test -d $d/$i ; then
echo "$i:"
code....
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Jan 12, 2010
in bash scripting...say I want to take the input from a user via a question...I would do this:
Quote:
#!/bin/bash
echo "How large do you want this partition to be in GB (enter only the number)?" read PART_SIZE echo "You want your partition to be $PART_SIZE GB" But I don't want to echo it back to the screen, I want to add it to the content of /etc/fstab. I have been mucking around with sed to find the tmpfs partition in /etc/fstab and add the partition size attribute (this is to use the onboard RAM as a volatile partition)...but am not having any luck...
The portion of /etc/fstab that uses /dev/shm for the tmpfs partition is:
tmpfs /dev/shm tmpfs defaults 0 0
So, if a user says "24" GB to the answer (from above), how do I get it to automatically add that value to the tmpfs partition line in /etc/fstab? So it would look like:
tmpfs /dev/shm tmpfs size=24g,defaults 0 0
I understand that I would also have to come up with a way to put "size=XXg", which I could do with a copied over generic file before this action...then the script would have to find "XX" and replace it with the user's figure...
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Jun 19, 2009
I made a little rsync script for log transfer.
Code:
SERVERS=(SERVER1 SERVER2 SERVER3)
SERVER1_SERV=(web ftp mail)
SERVER2_SERV=(web transcoding)
SERVER3_SERV=(web ftp mail)
for SERVER in ${SERVERS[@]}
do
echo "Starting tranfer for server $SERVER"
for SERVICE in ${$SERVER_$SERVICE[@]}
do
something_to_be_done
fi
done
But when I run it I get ${$SERVER_$SERVICE[@]}: bad substitution
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Sep 5, 2010
How do I create a user account in a shell script? I know this may sound n00bish to you, but I know it's more than just mkdir-ing the home directory and subdirectories.
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Dec 2, 2010
I need to part a string into separate integers ....like "0x0-0xffffffff,0x20000" into 3 integers 0x0 and 0xfffffff and 0x20000.... i can't use any other high-level languages ..
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Mar 15, 2011
I got two cgi shell scripting files. Is it possible when i am in file 1, to call a function from file 2?
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Mar 8, 2010
I want to compare the following two tab-delimited .txt files (both were subsets of the original files) by comparing Columns 3 and 4 simultaneously. It is easy to compare C3 because both C3s are just numbers. But how to compare C4s?Basically, in File1, "G,G" = G in File2, "C,C" = C in File2, "A,A" = A in File2, "T,T"= T in File2.In File2, A/T in Column4 just equals "A,T" or "T,A" in Column4 of File1. C/T in Column4 just equals "C,T" or "T,C" in Column4 of File1, and etc.
File1:
C1C2 C3C4
ih509rs12345467244750"G,G"
ih499rs6049687244911"C,C"
ih508- 7244977"A,A"
[code]....
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Feb 3, 2010
How do i make my strings case-insensitive while comparing them with an if statement?
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Mar 11, 2011
I have a QNX machine with a slinger webserver running on it. With a cgi script i'm trying to do the QNX cksum call and compare it's output value with a fixed output. When i execute the script at the command line it works perfect, but when execute this script by by the webserver in my browser it doesn't work. Here's my code:
#!/bin/sh
FILE="/home/checkfile"
ORIGCHECK="1712885500"
[code].....
Could it be possible that i'm not allowed to do the cksum call in combination with the slinger webserver?
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Jul 3, 2011
so I wrote a simple script to scrape whatsmyip.org for my public IP address and then email it to me if it has changed. I set this up as a cron job ever 30mins.the problem is, it works for about 18 hours and then will have an issue where it says "line 33: [: too many arguments" Which line 33 happens to be my if statement. Now like I said it works fine for about 18 hours, i run the script with 2>&1 to a .out file so i can see what its doing...this is the output of the .out file, the "xxx" does actually show the ip.."PHP Code:
xxx.xxx.xxx.xxx
already in file
xxx.xxx.xxx.xxx
[code]....
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Apr 5, 2011
I am trying to modify a script for research purposes and am having difficulty here as I have little prior experience with C-shell scripting.
The script looks as follows (it includes tcl commands like runFEP that you can ignore)
#!/bin/bash
for ((old=1, new=2; old<=4; old++,new++))
a1=${old}%50
a2=${new}%50
do
cat > input${new}.conf <<EOF
${a1}
code....
My question: I keep getting a syntax error when defining my two variables a1 and a2. I essentially need these variables to be
a1 = value of variable old divided by 50
a2 = value of variable new divided by 50
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Jun 24, 2011
I'm writing a script and I have doubts on how to assign values to an already established variable. The value for the vatriable would be coming from a file with three columns. I'm using the awk command for this. Am I doing it correctly? which of the following two ways is the better one or if both are wrong which one should I use?
#!/bin/nsh
inputfile=$1
rolename=$2
[code]....
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Mar 21, 2011
Examples:
Code:
$ ./test.sh -a -c 2
operator is -gt
remcount is
^ value missing!
Code:
$ ./test.sh -b -c 2
operator is -lt
remcount is
^ value missing!
Yet when "-c" is the first argument, its value is present:
Code:
$ ./test.sh -c 2 -b
operator is -lt
remcount is 2
What could I do to ensure the value of "-c" is picked up regardless of the argument order?
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Sep 6, 2010
I have two files, uploads.txt and downloads.txt. I would like to combine the columns of these files based on the ip address. How can I best do this?
Uploads.txt Code: 192.168.0.147 1565369
192.168.0.13 1664855
192.168.0.6 1332868 Downloads.txt Code: 192.168.0.147 9838820
[code]...
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Jul 22, 2011
I have written the following script in my linux server to add users for LDAP database.But i can't able to run this.
The script is as following
#!/bin/bash
echo "Mention the username which you want to convert LDIF format"
read username
if ["$username" -e "/ldiffile/passwd"]; then
echo "Username already exists"
else
cat /etc/passwd | grep -i "$username" >> /ldiffile/passwd
fi
The output which i got :
. ldapadd.sh
Mention the username which you want to convert LDIF format
yal2361
-bash: [yal2361: command not found
please let me know where need to change and what
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Nov 8, 2010
I want to find maximum length file in a given directory. It should search recursivley. I want this to be done using ls and simple looping constructs.
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Jan 21, 2011
I recently started shell programming and my task now is to do a menu display.Currently i am stuck whereby user will input both title and author and it will delete it.
Do i have to use sed command?
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Jan 7, 2010
I have a directory that has about 5,000+ folders in it and I'd like to run a script that outputs any directory that contains a subdirectory.
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Jul 11, 2011
I have one directory with 3 level sub-directories, and about houndard files under those directories. I need a shell script to rename all patern mateched directories and files.
For example: the patern is AA in the directory or file name.
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Jun 9, 2011
I'm building a Linux From Scratch system and partially automating it. I will likely want to do it again, and I would like to try to almost completely automate it.
My current approach is a script that takes an input file and sequentially runs each line in a new instance of bash. If one fails, it gives me the number of the step that failed so that I can use the "--step" option to resume after I fixed the issue.
This has some problems:
A varible created on one line will not be accessible on the next line. This is because each line is run in a separate shell (the reason for this is so that the commands in the input file and the script's internal variables can't interfere). You can't switch users or use chroot, again because each line is run in a separate shell.
What would be nice is to be able to start a bash process in the background and send commands to its stdin. I guess that a named pipe would work, but the named pipe will be gone after a chroot. Is there a way to do it without relying on the filesystem? Also, how do I know if the command failed?
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Mar 10, 2011
How do i take a single line of input from the user in a shell script?
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May 21, 2009
Is there a way to export a variable to parent shell in shell scripting ?
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Feb 28, 2010
What options should I use when I'm using the sort command to sort the top 5 CPU processes (ps -eo user,pid,ppid,%cpu,%mem,fname | sort ??? | head -5) showing max to min usage?
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May 29, 2011
I want a script to get executedutomatically whenever I login.Code is simple:Quote:dateYEs! it prints the date on the screen.I read somewhere that there is login.sh shell script which get executed automatically whenever one opens console.But how to insert the above code into it.?Also, we can put our command in $HOME/.bashrc and it will get executed everytime I start the interactive shell.
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Oct 14, 2010
I would like to develop a shell script that would automatically run a backup program and then shutdown the computers, but I do not know the first thing about script development or even writing scripting.
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Mar 18, 2010
I am facing a problem in Windows due to a virus called Newfolder.exe which creats files with the same name as it's parent directory and an extension .exe and this happens for every directory in the entire hierarchy in the infected pen drive. The antivirus detects them, but is sucking slow. So I thought this is a good opportunity to use the concepts of the all mighty shell script to remove those as they follow the same pattern. Say my complete path is
Code:
/home/pkd/fol1/
The virus would have created an file with complete paths
Quote:
/home/pkd/fol1.exe
If fol1 has two more directories fol11 and fol12 Then there would be two more .exe(virus created) in the following path
Quote:
/home/pkd/fol11/fol11.exe
/home/pkd/fol12/fol12.exe
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