So in the terminal, I can run my program with
./letter --stack -b ship -e shot -c --output W < input.txt > output.txt
How do I achieve the same functionality in Eclipse? I've figured out how to do --stack -b ship -e shot -c --output W by going to the arguments tab under Run configuration.
I've looked online and seen a lot of posts about using the Common tab to input and output redirection but I can't get it working. When I check only the input file, it doesn't work and the Debug perspective shows it's stuck somewhere trying to read from a stream. When I check allocate console and input file, then it gets stuck on user input (aka I can manually type stuff) in the console.
So how do I get < input.txt and by extension > output.txt working?
Related
I have tried to submit the script below to HPC
#!/bin/bash
#PBS -N bwa_mem_tumor
#PBS -q batch
#PBS -l walltime=02:00:00
#PBS -l nodes=2:ppn=2
#PBS -j oe
sample=x
ref=absolute/path/GRCh38.p13.genome.fa
fwd=absolutepath/forward_read.fq.gz
rev=absolutepath/reverse_read.fq.gz
module load bio/samtools/1.9
bwa mem $ref $fwd $rev > $sample.tumor.sam && samtools view -S $sample.tumor.sam -b > $sample.tumor.bam && samtools sort $sample.tumor.bam > $sample.tumor.sorted.bam
However as an output I can get only the $sample.tumor.sam and log file says that
Lmod has detected the following error: The following module(s) are unknown:
"bio/samtools/1.9"
Please check the spelling or version number. Also try "module spider ..."
It is also possible your cache file is out-of-date; it may help to try:
$ module --ignore-cache load "bio/samtools/1.9"
Also make sure that all modulefiles written in TCL start with the string
#%Module
However when I input modeles avail it shows that bio/samtools/1.9 is on the list.
Also when i use the option module --ignore-cache load "bio/samtools/1.9"
the result is the same
If i try to continue working with the sam file and input manually the command line
samtools view -b RS0107.tumor.sam > RS0107.tumor.bam
it shows
[W::sam_read1] Parse error at line 200943
[main_samview] truncated file.
What's possibly wrong with the samtools module ir we with the script?
This question is in addition to the question asked here: https://unix.stackexchange.com/questions/163145/how-to-get-whole-command-line-from-a-process. On my system, the following command results in a PID (as expected):
CUDA_VISIBLE_DEVICES=4,5 python3 main.py 1> out.txt 2> err.txt &
Now, the methods in the stack exchange link above provide many solutions. However, when trying these solutions, I only receive the following information:
python3 main.py
Is there a way to return the entire command line "CUDA_VISIBLE_DEVICES=4,5 python3 main.py 1> out.txt 2> err.txt &", not just the portion "python3 main.py"?
No.
Assuming you're on a Linux system, you can find the individual bits, but you can't put it together.
Assume also that the process's PID is in $pid
The CUDA_VISIBLE_DEVICES=4,5 variable gets added to the environment of the python command. You can find it in /proc/$pid/environ but you can't tell which of those variables were specified on the command line: the user could have written
export CUDA_VISIBLE_DEVICES=4,5
python3 main.py 1> out.txt 2> err.txt &
The file redirections are available in /proc/$pid/fd:
/proc/$pid/fd/1 is a symbolic link to out.txt
/proc/$pid/fd/2 is a symbolic link to err.txt
I don't know how to tell if a process is running in the background.
Since you're just interested in the environment: with bash
declare -A environ
while IFS='=' read -r -d '' var value; do
environ["$var"]="$value"
done < /proc/$pid/environ
echo "process has CUDA_VISIBLE_DEVICE value ${environ[CUDA_VISIBLE_DEVICE]}"
I would like to be able to
Display STDERR on the screen
Copy STDOUT and STDERR in files (and if possible in the same file)
For information, I am using Msys to do that.
.
After doing some research on the SO, I have tried to use something like
<my command> > >(tee stdout.log) 2> >(tee stderr.log)
Bu I got the following error:
sh: syntax error near unexpected token `>'
.
Any idea on how to do that?
There might be no direct solution in Msys but the >(tee ... ) solution works fine in *Nix, OSX, and probably Cygwin.
The workaround is to grep all the errors and warnings we want to keep them on the screen.
I have successfully used the following command for a makefile to compile C code:
make 2>&1 | tee make.log | grep -E "(([Ee]rror|warning|make):|In function|undefined)"
I have a simple script (test.sh) that generates STDOUT and STDERR:
#!/bin/bash
echo hello
rm something
exit
Then, to do what you want execute with the following:
./test.sh > stdout.log 2> >(tee stderr.log >&2)
You'll get the STDERR on the screen, and two separated log files with STDERR and STDOUT. I used part of the answer given here
Note that I am assuming you don't have a file called something on the current directory :)
If you want both STDOUT and STDERR to go to the same file, use the -a option on tee:
./test.sh > std.log 2> >(tee -a std.log >&2)
Using supervisord, how do I execute a command before running the program?
For example in the code below, I want a file to be created before starting the program. In the code below I am using tail -f /dev/null to simulate the background process but this could be any running program like '/path/to/application'.
I tried '&&' and this doesn't seem to work. The requirement is that the file has to be created first in order for the application to work.
[supervisord]
nodaemon=true
logfile=~/supervisord.log
[program:app]
command:touch ~a.c && tail -f /dev/null
The problem is that supervisor isn't running a shell to interpret command sections, so "&&" is just one of 5 space separated arguments it is passing to the touch command; if this ran successfully, then there should be some unusual filenames in its working directory now.
You can use a shell as your command and pass it the shell logic you would like:
command=/bin/sh -c "touch ~a.c && tail -f /dev/null"
Usually, this type of shell wrapper should be the interface provided and managed by the app and is what supervisord and others just know how to call with paths and options, i.e.:
command=myappswrapper.sh ~a.c
(where myappswrapper.sh is:)
#!/bin/sh
touch $1 && tail -f /dev/null
Here is a trick.
You use a shell script to do that and beyond that
[program:app]
command:sh /path/to/your/script.sh
It's can your script.sh
touch ~a.c
exec tail -f /dev/null
notice exec
I am searching for swipl the similar feature as perl -e
In particular, I want to run prolog code in this fashion:
swipl --wanted-flag "fact(a). message:-writeln('hello')." -g "message" -t halt
This is possible to do with
swipl -f file -g "message" -t halt
where the prolog clauses are written in file
I am running swipl on the server side that takes user input as prolog clauses, therefore writing a file on the server is not a good idea.
One thing you can do is to use load_files/2 with the option stream, and load from standard input, not from an argument (you can still pass the entry point as an argument, I guess):
Say in a file fromstdin.pl you have:
main :-
load_files(stdin, [stream(user_input)]),
current_prolog_flag(argv, [Goal|_]),
call(Goal),
halt.
main :- halt(1).
and with this you can do:
$ echo 'message :- format("hello~n").' | swipl -q -t main fromstdin.pl -- message
|: hello
The comments by #false to this answer and the question will tell you what this |: is, if you are wondering, but if it annoys you, just do:
$ echo 'message :- format("hello~n").' \
| swipl -q -t main fromstdin.pl -- message \
| cat
hello
instead.
This will let you read any Prolog from standard input and call an arbitrary predicate from it. Whether this is a clever thing to do, I don't know. I would also not be surprised if there is a much easier way to achieve the same.