I have this line
samtools view -h file | awk '$3=="chr$a" || /^#/' | samtools view -S - -b -o output
the dash between the -S and the -b is supposed to indicate to the program that it is from STDIN. I can run it from a perl script on the command line but as soon as I try to move it into a shell script it just creates the file without outputting any data. Any ideas would be greatly appreciated.
In a shell script the $a inside single quotes will not be expanded:
for a in {1..22} do
samtools view -h AD3.sorted.bam | awk '$3=="chr$a" || /^#/' | samtools view -S - -b -o chr$a.bam
done
If you haven't already, have a look at the samtools FAQ. This has examples for doing similar things to what you want to do with your pipeline.
Its been a while since I used samtools, but I would've written your command like this:
samtools view -h file | awk '$3=="chr$a" || /^#/' | samtools view -S -b - > output.bam
Also you mentioned you had moved the command to a shell script. Is the shell script doing anything else? If it still doesn't work, I would post that for us to look at.
Related
Ok, so I have this command that turns off my touchscreen. It works when I execute it in a root shell.
So this works:
sudo su
/usr/bin/echo $(ls /sys/bus/hid/drivers/hid-multitouch | awk NR==1'{print $1}') > /sys/bus/hid/drivers/hid-multitouch/unbind
And then my touchscreen stops working, which is the result that I wanted.
Now I want to make a touchscreen.service file to execute this on every boot. So in the service file I include:
ExecStart=/usr/bin/echo $(ls /sys/bus/hid/drivers/hid-multitouch | awk NR==1'{print $1}') > /sys/bus/hid/drivers/hid-multitouch/unbind
However it isn't working > nor throwing any errors that I've been able to catch.
I do know from earlier fidlings with .service files that I might actually need to use /usr/bin/sh -c, so I have also tried:
ExecStart=/usr/bin/sh -c "/usr/bin/echo $(ls /sys/bus/hid/drivers/hid-multitouch | awk NR==1'{print $1}') > /sys/bus/hid/drivers/hid-multitouch/unbind"
Yet this also doesn't work.. maybe because of the awk NR==1'{print $1}'part? I have also tried replacing it with awk NR==1'\''{print $1}'\''but again it fails to work.
Does anyone have any ideas on how to get the command that is working in my root cli environment to also work as a systemd service?
To start with,
The syntax of the awk command is just wrong. The quotes are incorrectly placed. The part NR == 1 is part of the awk command to indicate the first line record in the file, i.e.
awk NR==1'{print $1}'
# ^^^^^^^ should be within quotes
awk 'NR == 1 { print $1 }'
Your sequence of echo, ls and the command substitution $(..) doesn't look right. You are effectively echo-ing the literal string /sys/bus/hid/drivers/hid-multitouch (if ls finds the file at that path) over to the pipe and awk just writes that to the /sys/bus/hid/drivers/hid-multitouch/unbind file which might not be your desired action. You just needed to do run the command on the file directly as
awk 'NR == 1 { print $1 }' /sys/bus/hid/drivers/hid-multitouch > /sys/bus/hid/drivers/hid-multitouch/unbind
Now that, that the awk command is fixed, you have two options to run the above command as part of systemd, either put your command in a script or run the command directly. For putting it in a script refer to the Unix.SE answer Where do I put scripts executed by systemd units?. As for running the command directly in ExecStart. Aside from using /bin/sh also use the path /bin/awk
So putting it together and using /bin/ over /usr/bin, you can do below. This command uses ".." over awk script and needs escape of $1
ExecStart=/bin/sh -c '/bin/awk "NR == 1 { print \$1 }" /sys/bus/hid/drivers/hid-multitouch > /sys/bus/hid/drivers/hid-multitouch/unbind'
There're multiple perl scripts that is ran from CYGWIN terminal. An example is,
$ perl IdGeneratorTool.pl JSmith -i userInfo.adb -o JSmith.txt
The above is an example. Were based on input parameter JSmith, it reads a db file, generate an ID and output that to a text file.
Now these perl scripts running on the CYGWIN keeps growing and it's added to a text file like shown below,
$ perl IdGeneratorTool.pl JSmith -i userInfo.adb -o JSmith.txt
$ perl IdGeneratorTool.pl PTesk -i userInfo.adb -o PTesk.txt
$ perl IdGeneratorTool.pl CMorris -i userInfo.adb -o CMorris.txt
$ perl IdGeneratorTool.pl JLawrence -i userInfo.adb -o JLawrence.txt
$ perl IdGeneratorTool.pl TCruise -i userInfo.adb -o TCruise.txt
...
....
......
.......
.........
And the list keeps growing.
I would like to know whether there's a way to execute all these perl scripts which are in a text file in one go.
I'm new to perl and doesn't have much idea as to what are the options.
An ideal scenario might be, a tool where i can open this text file and click a execute button and then it executes all the scripts and output multiple *.txt files into the same directory.
Or maybe a simple perl script that can do it.
Put them into a file makeall (or whatever you want to call it.
Put as a first line #!/bin/bash into the file
In cygwin enter chmod +x makeall
in cygwin enter ./makeall
With this you've created a bash script which'll do all your calls of the perl script.
Another option would to just put all the user information into a csv file and read that one in order to call your script.
WAIT! Even easier!
Put into the makeall script this:
#!/bin/bash
for user in \
JSmith \
PTesk \
CMorris \
JLawrence \
TCruise \
; do
perl IdGeneratorTool.pl "$user" -i userInfo.adb -o "$user".txt
done
Now you just need to add any additional user the same way I did for your examples.
Without seeing the source for IdGeneratorTool.pl it's hard to give any specific advice; but it is generally not hard to turn something like
do_stuff($ARGV[0], $opt_i, $opt_o);
into
while (<>) {
chomp;
$user, $adb, $outputfile = split('\t');
do_stuff($user, $adb, $outputfile);
}
to read the input from a tab-delimited file instead of from command-line arguments.
You can create text file with list of users (one per line) for example user_list.txt
JSmith
PTesk
CMorris
JLawrence
TCruise
Then create bash script process_list.sh with following content in same directory
#!/bin/bash
for user in `cat user_list.txt`
do
perl IdGeneratorTool.pl $user -i userInfo.adb -o ${user}.txt
done
Now make bash script executable chmod +x process_list.sh and it is ready for execution.
Once you need to add new user edit user_list.txt to add one more line into the file.
Polar Bear
I'm trying to run the following command to process the output via Swift 2.0 but I'm having trouble doing so.
netstat -w1 -I en | awk '{ print $3 }'
The command runs as expected when ran manually from the terminal.
I tried the method of calling /bin/sh -c with the full command as an argument but that doesn't output anything. (Similar to https://stackoverflow.com/a/29549342/2110967).
I also tried to pass the data over stdout/stdin from the netstat to the awk but didn't have much luck.
I also tried placing the code into a .sh file and running from there but again the output was never returned.
I'm using here document of sh to run some commands. now I want to parse the output of those commands using awk. However, everytime I execute it, I get the output of the command append with something like this "% No such child process"
This is how my script looks like.
#!/bin/sh
com = "sudo -u username /path/of/file -l"
$com <<EOF | awk '{print $0}'
Commands.
.
.
.
EOF
How am I going to use heredoc and pipeline without appending that unwanted string?
Thanks
Your variable assignment is wrong in a couple of ways. First, you aren't actually assigning a variable; you're trying to run a command named com whose arguments are = and a string "sudo ...". Spaces must not be used on either side of the =:
com="sudo ..."
Second, command lines should not be stored in a variable; the shell's parser can only make that work they way you intend for very simple commands. Type the command out in full, or use a shell function.
com () {
sudo -u username /path/to/file -l
}
com <<EOF | awk '{print $0}'
...
EOF
There's no problem, check :
$ cat <<EOF | awk '{print $1}'
a b c
1 2 3
EOF
a
1
I have a perl script which runs successfully from the root cron on my redhat server.
However, I have added a command to the perl script to execute an ldapsearch and when running the perl script from the command line it works perfectly, yet running from cron, the ldapseach command does not work.
I've the the full path to the ldapsearch executable and I have tried using both system and exec before the ldapsearch command, but no good.
The line in the perl code does the ldap search for container room, greps the specific line in the results, then parses the data and cuts the 1st two characters of the results. The code is:
$userRoom = `exec /usr/local/bin/ldapsearch -h myldap.domain.com '(cn=$user)' room | /bin/grep -i room | /bin/grep -iv internal | /bin/cut -d'=' -f2 | /bin/cut -c 1-2`;
I'm assuming it's an evironment or permissions thing. I just can't find the right answer.
Any suggestions greatly appreciated.