I have written some test script for a new machine, but there's an issue that I don't know if it's julia itself or the way I am writting the script.
The julia program is just
module main_prog
println("Program to heat and test a new machine")
println("Does a lot of diagonalizations")
dim = 10
realiz = 5
for ii in 1:realiz
A = randn(dim,dim)
H = (A + A')/2
eig_problem = eig(H)
end
println("End succesful")
end # module
And my bash script is
#!/bin/bash
for i in `seq 1 2`;
do
mkdir job$i
cp diagg_rmt.jl job$i
cd job$i
/home/user/julia/julia ./diagg_rmt.jl &
cd ..
done
When I runt the script, it gives an strange error:
-bash-4.2$ ERROR: getcwd: no such file or directory (ENOENT)
in uv_error at ./stream.jl:1027
in pwd at ./file.jl:8
in abspath at ./path.jl:108
in _include_dependency at ./loading.jl:127
in include_from_node1 at ./loading.jl:296
in process_options at ./client.jl:280
in _start at ./client.jl:378
I have seen another posts of this happening in Ruby, for example, but no idea
what to do here. I am using CentOS Linux release 7.0.1406 (Core)
Related
New to nextflow, attempted to run a loop in nextflow chunk to remove extension from sequence file names and am running into a syntax error.
params.rename = "sequences/*.fastq.gz"
workflow {
rename_ch = Channel.fromPath(params.rename)
RENAME(rename_ch)
RENAME.out.view()
}
process RENAME {
input:
path read
output:
stdout
script:
"""
for file in $baseDir/sequences/*.fastq.gz;
do
mv -- '$file' '${file%%.fastq.gz}'
done
"""
}
Error:
- cause: Unexpected input: '{' # line 25, column 16.
process RENAME {
^
Tried to use other methods such as basename, but to no avail.
Inside a script block, you just need to escape the Bash dollar-variables and use double quotes so that they can expand. For example:
params.rename = "sequences/*.fastq.gz"
workflow {
RENAME()
}
process RENAME {
debug true
"""
for fastq in ${baseDir}/sequences/*.fastq.gz;
do
echo mv -- "\$fastq" "\${fastq%%.fastq.gz}"
done
"""
}
Results:
$ nextflow run main.nf
N E X T F L O W ~ version 22.04.0
Launching `main.nf` [crazy_brown] DSL2 - revision: 71ada7b0d5
executor > local (1)
[71/4321e6] process > RENAME [100%] 1 of 1 ✔
mv -- /path/to/sequences/A.fastq.gz /path/to/sequences/A
mv -- /path/to/sequences/B.fastq.gz /path/to/sequences/B
mv -- /path/to/sequences/C.fastq.gz /path/to/sequences/C
Also, if you find escaping the Bash variables tedious, you may want to consider using a shell block instead.
I need to extract some variables and functions from a zsh script into a bash script. Is there any way to do this? What I've tried (some are embarrassingly wrong, but covering everything):
. /script/path.zsh (zsh-isms exist, so it fails)
exec zsh
. /script/path.zsh
exec bash
zsh << 'EOF'
. /script/path.zsh
EOF
chsh -s zsh
. /script/path.zsh
chsh -s bash
This thread is the closest I've found. Unfortunately, I have too many items to import for that to be feasible, and neither script is anywhere near a polyglot. However, the functions and variables that I need to import are polyglots.
You can "scrape" the zsh source file for what you need, then execute the code in bash using eval. Here's an example for doing this for a few functions:
File script.zsh:
test1() {
echo "Hello from test1"
}
test2() {
echo $((1 + $1))
}
File script.sh (bash):
# Specify source script and functions
source_filename="script.zsh"
source_functions=" \
test1 \
test2 \
"
# Perform "sourcing"
function_definitions="$(python -B -c "
import re
with open('${source_filename}', mode='r') as file:
content = file.read()
for func in '${source_functions}'.split():
print(re.search(func + r'\(\).*?\n}', content, flags=re.DOTALL).group())
" )"
eval "${function_definitions}"
# Try out test functions
test1 # Hello from test1
n=5
echo "$n + 1 is $(test2 $n)" # 5 + 1 is 6
Run the bash script and it will make use of the functions test1 and test2 defined in the zsh script:
bash script.sh
The above makes use of Python, specifically its re module. It simply looks for character sequences of the form funcname(), and assumes that the function ends at the first }. So it's not very general, but works if you write your functions in this manner.
I have a custom 'runner'-script that I need to use to run all of my terminal commands. Below you can see the general idea in the script.
#!/usr/bin/env bash
echo "Running '$#'"
# do stuff before running cmd
$#
echo "Done"
# do stuff after running cmd
I can use the script in bash as follows:
$ ./run.sh echo test
Running 'echo test'
test
Done
$
I would like to use it like this:
$ echo test
Running 'echo test'
test
Done
$
Bash has the trap ... DEBUG and PROMPT_COMMAND, which lets me execute something before and after a command, but is there something that would allow me to execute instead of the command?
There is also the command_not_found_handle which would work if I had an empty PATH env variable, but that seems too dirty.
After some digging, I ended up looking at the source code and found that bash does not support custom executors. Below is a patch to add a new handle that works similarly as the command_not_found_handler.
diff --git a/eval.c b/eval.c
index f02d6e40..8d32fafa 100644
--- a/eval.c
+++ b/eval.c
## -52,6 +52,10 ##
extern sigset_t top_level_mask;
#endif
+#ifndef EXEC_HOOK
+# define EXEC_HOOK "command_exec_handle"
+#endif
+
static void send_pwd_to_eterm __P((void));
static sighandler alrm_catcher __P((int));
## -172,7 +176,15 ## reader_loop ()
executing = 1;
stdin_redir = 0;
- execute_command (current_command);
+ SHELL_VAR *hookf = find_function (EXEC_HOOK);
+ if (hookf == 0) {
+ execute_command (current_command);
+ } else {
+ char *command_to_print = make_command_string (current_command);
+ WORD_LIST *og = make_word_list(make_word(command_to_print), (WORD_LIST *)NULL);
+ WORD_LIST *wl = make_word_list(make_word(EXEC_HOOK), og);
+ execute_shell_function (hookf, wl);
+ }
exec_done:
QUIT;
One can then define function command_exec_handle() { eval $1; } which will be executed instead of the original command given in the prompt. The original command is fully in the first parameter. The command_exec_handle can be given in .bashrc and it works as expected.
Notice: this is very dangerous! If you mess up and put a bad command_exec_handler in your .bashrc, you might end up with a shell that does not execute commands. It will be quite hard to fix without booting from a live cd.
It seems you have the same problem listed here. If you want to run some commands if your original command was not found, the Bash 4's command_not_found_handler will certainly fit your needs.
Try to be more specific, maybe with some code snippets that do or do not work, in order to help us to help you...
My current project involves the use of a .go executable written on Fortran 77 in the mid-eighties. My only access to it currently is through ssh to a server using csh. I have written the following script:
set inpdir = $argv[1]
mkdir ${inpdir}"_out"
set j = 1
while ($j <= 5)
set i = 0
while ($i <= 20)
"tms96-fnl.go <./"${inpdir}"/inp"${j}"0"${i}".d> ./"${inpdir}"_out/out"${j}"0"${i}
set i = i + 1
end
set j = j + 1
end
The result is the message:
tms96-fnl.go <./fftf/inp100.d> ./fftf_out/out100 -Command not found
Syntax error
If i were to key the contents of that message (sans the "-Command not found") while in the same working directory as the script it executes as expected.
The problem is the arrangement of quotes. You have:
"tms96-fnl.go <./"${inpdir}"/inp"${j}"0"${i}".d> ./"${inpdir}"_out/out"${j}"0"${i}
Which would interpret a command that looks like tms96-fnl.go <./. I would do:
tms96-fnl.go < ./"${inpdir}"/inp"${j}"0"${i}".d > ./"${inpdir}"_out/out"${j}"0"${i}"
I have a Bash script that builds a string to run as a command
Script:
#! /bin/bash
matchdir="/home/joao/robocup/runner_workdir/matches/testmatch/"
teamAComm="`pwd`/a.sh"
teamBComm="`pwd`/b.sh"
include="`pwd`/server_official.conf"
serverbin='/usr/local/bin/rcssserver'
cd $matchdir
illcommando="$serverbin include='$include' server::team_l_start = '${teamAComm}' server::team_r_start = '${teamBComm}' CSVSaver::save='true' CSVSaver::filename = 'out.csv'"
echo "running: $illcommando"
# $illcommando > server-output.log 2> server-error.log
$illcommando
which does not seem to supply the arguments correctly to the $serverbin.
Script output:
running: /usr/local/bin/rcssserver include='/home/joao/robocup/runner_workdir/server_official.conf' server::team_l_start = '/home/joao/robocup/runner_workdir/a.sh' server::team_r_start = '/home/joao/robocup/runner_workdir/b.sh' CSVSaver::save='true' CSVSaver::filename = 'out.csv'
rcssserver-14.0.1
Copyright (C) 1995, 1996, 1997, 1998, 1999 Electrotechnical Laboratory.
2000 - 2009 RoboCup Soccer Simulator Maintenance Group.
Usage: /usr/local/bin/rcssserver [[-[-]]namespace::option=value]
[[-[-]][namespace::]help]
[[-[-]]include=file]
Options:
help
display generic help
include=file
parse the specified configuration file. Configuration files
have the same format as the command line options. The
configuration file specified will be parsed before all
subsequent options.
server::help
display detailed help for the "server" module
player::help
display detailed help for the "player" module
CSVSaver::help
display detailed help for the "CSVSaver" module
CSVSaver Options:
CSVSaver::save=<on|off|true|false|1|0|>
If save is on/true, then the saver will attempt to save the
results to the database. Otherwise it will do nothing.
current value: false
CSVSaver::filename='<STRING>'
The file to save the results to. If this file does not
exist it will be created. If the file does exist, the results
will be appended to the end.
current value: 'out.csv'
if I just paste the command /usr/local/bin/rcssserver include='/home/joao/robocup/runner_workdir/server_official.conf' server::team_l_start = '/home/joao/robocup/runner_workdir/a.sh' server::team_r_start = '/home/joao/robocup/runner_workdir/b.sh' CSVSaver::save='true' CSVSaver::filename = 'out.csv' (in the output after "runnning: ") it works fine.
You can use eval to execute a string:
eval $illcommando
your_command_string="..."
output=$(eval "$your_command_string")
echo "$output"
I usually place commands in parentheses $(commandStr), if that doesn't help I find bash debug mode great, run the script as bash -x script
don't put your commands in variables, just run it
matchdir="/home/joao/robocup/runner_workdir/matches/testmatch/"
PWD=$(pwd)
teamAComm="$PWD/a.sh"
teamBComm="$PWD/b.sh"
include="$PWD/server_official.conf"
serverbin='/usr/local/bin/rcssserver'
cd $matchdir
$serverbin include=$include server::team_l_start = ${teamAComm} server::team_r_start=${teamBComm} CSVSaver::save='true' CSVSaver::filename = 'out.csv'
./me casts raise_dead()
I was looking for something like this, but I also needed to reuse the same string minus two parameters so I ended up with something like:
my_exe ()
{
mysql -sN -e "select $1 from heat.stack where heat.stack.name=\"$2\";"
}
This is something I use to monitor openstack heat stack creation. In this case I expect two conditions, an action 'CREATE' and a status 'COMPLETE' on a stack named "Somestack"
To get those variables I can do something like:
ACTION=$(my_exe action Somestack)
STATUS=$(my_exe status Somestack)
if [[ "$ACTION" == "CREATE" ]] && [[ "$STATUS" == "COMPLETE" ]]
...
Here is my gradle build script that executes strings stored in heredocs:
current_directory=$( realpath "." )
GENERATED=${current_directory}/"GENERATED"
build_gradle=$( realpath build.gradle )
## touch because .gitignore ignores this folder:
touch $GENERATED
COPY_BUILD_FILE=$( cat <<COPY_BUILD_FILE_HEREDOC
cp
$build_gradle
$GENERATED/build.gradle
COPY_BUILD_FILE_HEREDOC
)
$COPY_BUILD_FILE
GRADLE_COMMAND=$( cat <<GRADLE_COMMAND_HEREDOC
gradle run
--build-file
$GENERATED/build.gradle
--gradle-user-home
$GENERATED
--no-daemon
GRADLE_COMMAND_HEREDOC
)
$GRADLE_COMMAND
The lone ")" are kind of ugly. But I have no clue how to fix that asthetic aspect.
To see all commands that are being executed by the script, add the -x flag to your shabang line, and execute the command normally:
#! /bin/bash -x
matchdir="/home/joao/robocup/runner_workdir/matches/testmatch/"
teamAComm="`pwd`/a.sh"
teamBComm="`pwd`/b.sh"
include="`pwd`/server_official.conf"
serverbin='/usr/local/bin/rcssserver'
cd $matchdir
$serverbin include="$include" server::team_l_start="${teamAComm}" server::team_r_start="${teamBComm}" CSVSaver::save='true' CSVSaver::filename='out.csv'
Then if you sometimes want to ignore the debug output, redirect stderr somewhere.
For me echo XYZ_20200824.zip | grep -Eo '[[:digit:]]{4}[[:digit:]]{2}[[:digit:]]{2}'
was working fine but unable to store output of command into variable.
I had same issue I tried eval but didn't got output.
Here is answer for my problem:
cmd=$(echo XYZ_20200824.zip | grep -Eo '[[:digit:]]{4}[[:digit:]]{2}[[:digit:]]{2}')
echo $cmd
My output is now 20200824