I want to run a program from perl by using system command(or any other ways ).
system("samtools");
I think it should pass this to shell but it complains ,Can't exec "samtools" file or directory does not exist , when I run it.I have tried many other different program for example
system("velveth");
and it works properly but not this one (samtools). Is any of you facing this problem before?
I am really puzzled.
You can give the full path to that file location.
example:
system( "/usr/bin/perl -de 1");
Try putting Linux command inside `` characters. Will work as well.
Did you modify $path for samtools in the current shell manually?
Since system starts a new sub-shell to run your command, you have to append search path for samtools yourself if doesn't exist in your .bashrc. Check it by:
perl -e 'system("echo \$PATH")'
and
echo $PATH
to see if there's any difference.
Related
I am writing a program with two inputs prog1 and prog2 which are both files. I save these two variables as program1 and program2 first and then execute these two files in my program using ./"$program1" and ./"program2", but the output is "No such file or directory" when i used ls to check the files are in the same directory as the script. Can anyone tell me how to execute it? thanks!
First, it seems like your brackets are out of place - ./"$program1" is not a valid expression, either loose the brackets or put it like this: "./$program1".
Then to elaborate a bit on David's comment:
There are two ways you can run another script from your script. One is to make them executable like David said.
However, you can also use the 'source' command to read and execute the content of files, even if they are not executable. So the following command would work in any case:
source "./$program1"
Instead of executing it as ./$prog1 execute it as below.
bash $prog1
bash $prog2
where $prog1 and $prog2 are variables which have the path of the bash scripts.
When I try to run a Perl script which is called via Linux script manually it works fine but not executable via CRON.
Linux_scrip.sh conatains Perl_script and the command is,
perl_path/perl Perl_script.pl
I got perl_path using which perl command.
Can anyone suggest why is it not executable via CRON entry.
Most likely suspects:
Current work directory isn't as expected.
Permission issues[1].
Environment variables aren't setup as expected.
Requirement of a terminal can't be met.
See the crontab tag wiki for more pitfalls and some debugging tips.
The first thing you should do is to read the error message.
This isn't likely to be an issue for you own cron job, but I've included it since it's quite a common problem for scripts run from other services.
Most probable cause is current working directory.
Before perl command execution, write a command to change directory.
Something like :
cd perl_path;
perl Perl_script.pl
This is a pretty simple one... I just want to make a perl script executable without the preceding perl command, and instead let the environment deduce the interpreter from the shebang line. Here is my sample script called test:
#!/usr/bin/perl
print "Hey there\n";
I then use chmod 775 test to make the script executable. If I use the command perl test, I get the output Hey there.
However, if I just type test, I get no output. What's the deal? Why isn't my shebang line making the environment realize this is perl? Can someone please help me?
Don't name your script test. This is a built-in command in most shells, so they don't go looking for an external program.
Also, to run a program in your current directory, you should type ./programname. It's generally a bad idea to have . in your $PATH, which would be necessary to execute it without the directory prefix.
To run something from the current directory you need to prefix "./" to tell it "this directory" ie ./testprogram.
If you type just test it will look in standard install directories like /bin. This is why when you run cp or rm it knows where the executable is.
As mentioned by others, naming scripts test is not allowed with most shells.
I am creating a terminal program and cannot find out what the ending is for Linux. I know in windows it is .cmd. Any help would be great.
Thank you.
Yes, you can remove the .sh at the end and it should work, generally using ./cmd will get it to run. this goes for C programs as well. You do not need to give an extension for the object file, You could then add a path to your bash file and then you can execute it as a normal command.
Look here.
https://stackoverflow.com/a/8779980/2720497
You don't need a file extension on Linux, though typically, people use .sh (sh being short for 'shell').
You can run it one of two ways:
bash myscript.sh
or you can make the script itself executable and run it directly:
chmod a+x myscript.sh # make it executable
./myscript.sh # run it
Linux scripts' first line is typically #!/bin/bash which is the path to the specific shell used to run the script with the second method.
i have very simple shell script
#!/bin/bash
cp -rf /var/www/ksite/app2/* /var/www/ksite/app
echo "----"
echo "done"
but seems cp command fails
if i execute
cp -rf /var/www/ksite/app2/* /var/www/ksite/app
from terminal everything work ok. Can someone tell me how to include cp in shell script?
Thanks
We seem to have doubt as to how this script fails. If there is no error message then this is a strange one. I suggest:
On the command line (which works), do a which cp
Whatever the reply, then copy that and use it as the cp in the script (e.g. /bin/cp)
Check the widcard expansion, run your script with bash -x script-name and see if you get what you expect.
echo $? after the copy in the script - if it is zero then it (thinks it) worked.
Do a ls -ld /var/www/ksite/app from your script, maybe someone set a symbolic link?
If it still fails, source the script from the command-line and see if that works . script-name
Double check that the copy did actually fail! (maybe that should be step 1.)
Make sure you really have bash at /bin/bash. I think a batter hash bang is:
#!/usr/bin/env bash
This uses the env command to locate the bash binary and set the environment.
I had similar problem. What helped me:
I used windows and putty to write script, so I had \r\n at the end of lines. Be sure, you have only \n symbol.
I copied files and the only way it worked for me at script was cp <source_dir>/fileName <dest_dir>/fileName whereas at command line cp <source_dir>/fileName <dest_dir> worked well too.
Just covering all the bases .. do the permissions vary between the excutions .. i.e. do you execute one with sudo/root privileges, the other as user (unlikely, but thought I'd ask since we don't know what the exact error is)
Similar issue to Vladmir where the script was created in Windows. I created a new file "my_bash_script.sh" in the linux environment using VIM, then read the contents of my script into the file:
:r file_made_in_windows.sh
Then I saved, closed, then set the file as executable:
chmod 744 my_bash_script.sh
From there, I ran the script:
./my_bash_script.sh
...and it worked. What a weird issue. I was confounded for a moment.