I'm writing a bash script Test.sh that aims to execute anotherscript (a linux executable file):
#!/bin/bash -l
mp1='/my/path1/'
mp2='/my/path2/anotherscript'
for myfile in $mp1*.txt; do
echo "$myfile"
"$mp2 $myfile -m mymode"
echo "finished file"
done
Notice that anotherscript takes as arguments $myfile and options -m mymode.
But I get the file not found error (says Test.sh: line 8: /my.path2/anotherscript: No such file or directory).
My questions are:
I have followed this question to get my bash script to run the executable file. But I'm afraid I still get the error above.
Am I specifying arguments as they should to execute the file?
I suggest you use
sh -c "$mp2 $myfile -m mymode"
instead of just
"$mp2 $myfile -m mymode"
#!/bin/bash -l
dir=`find /my/path1/ -name "*.txt"`
mp2='/my/path2/anotherscript'
for myfile in "$dir"; do
echo "$myfile"
"$mp2" "$myfile" -m mymode
echo "finished file"
done
Make sure anotherscript has execution right (chmod +x anotherscript).
Related
I am trying to write a processing script and I am stuck at the beginning. It does not seem to be wrong but I cannot simply understand where the error is as it is completing the execution but not giving any output. Any debugging help?
#!/bin/sh
#
# Call with following arguments
# sh test.sh <output_basename> <fastq folder> <output_folder_loc>
#
#
bn=$1
floc=$2
outloc=$3
#Create an output directory
#opdir=$bn"_processed"
mkdir $outloc/$bn"_processed"
echo "output directory for fastq $outloc/$bn"_processed" ..."
fout=$outloc/$bn"_processed"
echo "$fout ..."
echo "performing assembly to create one fastq file for each read mates ..."
zcat $floc/*R1*.fastq.gz > $fout/$bn_R1.fastq
zcat $floc/*R2*.fastq.gz > $fout/$bn_R2.fastq
echo "done"
Run command:
sh test.sh S_13_O1_122 /home/vdas/data/floc/Sample_S_13_O1_122_S12919 /home/vdas/data/OC/RNA-Seq/STAR_run/mut_out
I do not see any wrong in the code and it is also runnning without error but still am not getting any output. Can anyone point me the problem?
First try to change two lines like this:
mkdir -p "$outloc/${bn}_processed"
fout="$outloc/${bn}_processed"
mkdir -p is good when $outloc directory doesn't exist yet.
you could test your arguments (the following may be only in bash, but do work when bash is invoked as /bin/sh)
var=$1
if [ ${#var} -eq 0 ]; then
echo "var is not defined" >&2
exit 1
fi
that will test that the variable has some length, you might want to test other aspects as well, for instance does
ls $floc/*R1*.fastq.gz
produce any output?
#!/bin/sh
#
# Call with following arguments
# sh test.sh <output_basename> <fastq folder> <output_folder_loc>
#
#
bn=$1
floc=$2
outloc=$3
#Create an output directory
#opdir=$bn"_processed"
mkdir $outloc/$bn"_processed"
echo "output directory for fastq $outloc/$bn"_processed" ..."
fout=$outloc/$bn"_processed"
echo "$fout ..."
echo "performing assembly to create one fastq file for each read mates ..."
echo $floc/*R1*.fastq.gz
echo $fout/$bn_R1.fastq
zcat -v $floc/*R1*.fastq.gz > $fout/${bn}_R1.fastq
zcat -v $floc/*R2*.fastq.gz > $fout/${bn}_R2.fastq
echo "done"
`
this may be wath you want,
I am writing a ksh to checkout the code and setup the compilation variables through xenv setup. This is how my script looks at the moment -
#!/usr/bin/ksh
logname=$LOGNAME
homedir="$HOME/${logname}-SVN-Dev/pkgroot"
#Create directory <username>-SVN-Dev to contain copied code.
if [ -z "$logname" ]
then
logname=`/usr/ucb/whoami`
fi
RunCmd "rm -rf $homedir"
RunCmd "mkdir -p $homedir"
## Some code to checkout code
cd $HOME
echo "setenv PKGROOT $homedir">>$HOME/.cshrc
echo "setenv DEVROOT $homedir/src">>$HOME/.cshrc
source $HOME/.cshrc
RunCmd "/xenv/xenv -L -i $homedir/My.env $homedir;"
make -f project.mk createmakefile
The xenv above switches the shell and goes into a new prompt, ia_cross: and my shell exits without executing the "make -f project.mk createmakefile" command.
I have tries putting a pipe between make and xenv but that didn't solve this. Any suggestions would really help?
use below command in your script,
echo "make -f project.mk createmakefile" | /xenv/xenv -c -i $homedir/My.env $homedir;
I have a script called autoinstall:
#!/usr/bin/sh
echo "Installasi membutuhkan free space minimal 2MB, pastikan ada punya cukup space di router anda"
read -p "Anda yakin ingin melanjutkan installasi?(y/n) " -n 1 -r
echo ""
if [[ $REPLY = ^[Yy]$ ]]
then
cd /
cd /tmp/
tar -xvf OpenWrt_Angel_Beats_Edition_v1.3.3.tar -C /
chmod -R 744 /root/crt
chmod 744 /www/wget/wget_download.sh
chmod 744 /usr/bin/gsm
chmod 744 /usr/bin/profile
opkg update && opkg install elinks
cp /etc/rc.local /etc/rc.local.backup
cat > /etc/rc.local << END
#!bin/sh
# /etc/rc.local: Local system initialization script.
#
# Put any local startup commands in here. Also, if you have
# anything that needs to be run at shutdown time you can
# make an /etc/rc.d/rc.local_shutdown script and put those
# commands in there.
sh /www/wget/wget_download.sh > /dev/null 2>&1 &
exit 0
END
killall sh /www/wget/wget_download.sh
sh /www/wget/wget_download.sh > /dev/null 2>&1 &
echo "File backup /etc/rc.local.backup telah dibuat, gunakan file ini untuk mengembalikan konfigurasi rc.local anda yang dulu jika diperlukan"
echo "Installasi selesai. Jangan lupa di akun openvpn yang digunakan (/root/crt/xxx.ovpn) tambahkan baris ini:
script-security 2
up client-connect.sh"
else
echo ""
echo "Installasi dibatalkan"
fi
Every command that I put in the first line always gets the error above (line 1:xxx not found) and I'm sure I've typed in the correct command, even echo gives the error like that, how do I solve this?
There can be two problems here:
The file doesn't exist. Usually, for sh, the path is /bin/sh, so it should be #!/bin/sh
You're editing the file on Windows. Windows uses CR+LF as line ending. Unix (and Linux) uses just LF. So for Linux, the command reads "execute /bin/sh<CR> and sh<CR> doesn't exist.
Solution: When editing the file, make sure you use Unix line endings.
The file might have been edited with an editor that insert a Unicode BOM (Byte Order Mark).
Have a look to the first line contents with:
od -c autoinstall | head -1
or
hd -n 16 autoinstall
If you see unexpected characters before #!/usr/bin/sh, you might try one of the methods described here Using awk to remove the Byte-order mark to remove the BOM.
This question already has answers here:
Why can't I change directories using "cd" in a script?
(33 answers)
Closed 7 years ago.
What I'm trying to do
I've created a shell script that I've added to my $PATH that will download and get everything setup for a new Laravel project. I would like the script to end by changing my terminal directory into the new project folder.
From what I understand right now currently it's only changing the directory of the sub shell where the script is actually running. I can't seem to figure out how to do this. Any help is appreciated. Thank you!
#! /usr/bin/env bash
echo -e '\033[1;30m=========================================='
## check for a directory
if test -z "$1"; then
echo -e ' \033[0;31m✖ Please provide a directory name'
exit
fi
## check if directory already exist
if [ ! -d $1 ]; then
mkdir $1
else
echo -e ' \033[0;31m✖ The '"$1"' directory already exists'
exit
fi
# move to directory
cd $1
## Download Laravel
echo -e ' \033[0;32m+ \033[0mDownloading Laravel...'
curl -s -L https://github.com/laravel/laravel/zipball/master > laravel.zip
## Unzip, move, and clean up Laravel
echo -e ' \033[0;32m+ \033[0mUnzipping and cleaning up files...'
unzip -q laravel.zip
rm laravel.zip
cd *-laravel-*
mv * ..
cd ..
rm -R *-laravel-*
## Make the /storage directory writable
echo -e ' \033[0;32m+ \033[0mMaking /storage directory writable...'
chmod -R o+w storage
## Download and install the Generators
echo -e ' \033[0;32m+ \033[0mInstalling Generators...'
curl -s -L https://raw.github.com/JeffreyWay/Laravel-Generator/master/generate.php > application/tasks/generate.php
## Update the application key
echo -e ' \033[0;32m+ \033[0mUpdating Application Key...'
MD5=`date +”%N” | md5`
sed -ie 's/YourSecretKeyGoesHere!/'"$MD5"'/' application/config/application.php
rm application/config/application.phpe
## Create .gitignore and initial git if -git is passed
if [ "$2" == "-git" ]; then
echo -e ' \033[0;32m+ \033[0mInitiating git...'
touch .gitignore
curl -s -L https://raw.github.com/gist/4223565/be9f8e85f74a92c95e615ad1649c8d773e908036/.gitignore > .gitignore
# Create a local git repo
git init --quiet
git add * .gitignore
git commit -m 'Initial commit.' --quiet
fi
echo -e '\033[1;30m=========================================='
echo -e ' \033[0;32m✔ Laravel Setup Complete\033[0m'
## Change parent shell directory to new directory
## Currently it's only changing in the sub shell
filepath=`pwd`
cd "$filepath"
You can technically source your script to run it in your parent shell instead of spawning a subshell to run it. This way whatever changes you make to your current shell (including changing directories) persist.
source /path/to/my/script/script
or
. /path/to/my/script/script
But sourcing has its own dangers, use carefully.
(Peripherally related: how to use scripts to change directories)
Use a shell function to front-end your script
setup () {
# first, call your big script.
# (It could be open-coded here but that might be a bit ugly.)
# then finally...
cd someplace
}
Put the shell function in a shell startup file.
Child processes (including shells) cannot change current directory of parent process. Typical solution is using eval in the parent shell. In shell script echo commands you want to run by parent shell:
echo "cd $filepath"
In parent shell, you can kick the shell script with eval:
eval `sh foo.sh`
Note that all standard output will be executed as shell commands. Messages should output to standard error:
echo "Some messages" >&2
command ... >&2
This can't be done. Use exec to open a new shell in the appropriate directory, replacing the script interpreter.
exec bash
I suppose one possibility would be to make sure that the only output of your script is the path name you want to end up in, and then do:
cd `/path/to/my/script`
There's no way your script can directly affect the environment (including it's current directory) of its parent shell, but this would request that the parent shell itself change directories based on the output of the script...
I am attempting to write a bash script that changes directory and then runs an existing script in the new working directory.
This is what I have so far:
#!/bin/bash
cd /path/to/a/folder
./scriptname
scriptname is an executable file that exists in /path/to/a/folder - and (needless to say), I do have permission to run that script.
However, when I run this mind numbingly simple script (above), I get the response:
scriptname: No such file or directory
What am I missing?! the commands work as expected when entered at the CLI, so I am at a loss to explain the error message. How do I fix this?
Looking at your script makes me think that the script you want to launch a script which is locate in the initial directory. Since you change you directory before executing it won't work.
I suggest the following modified script:
#!/bin/bash
SCRIPT_DIR=$PWD
cd /path/to/a/folder
$SCRIPT_DIR/scriptname
cd /path/to/a/folder
pwd
ls
./scriptname
which'll show you what it thinks it's doing.
I usually have something like this in my useful script directory:
#!/bin/bash
# Provide usage information if not arguments were supplied
if [[ "$#" -le 0 ]]; then
echo "Usage: $0 <executable> [<argument>...]" >&2
exit 1
fi
# Get the executable by removing the last slash and anything before it
X="${1##*/}"
# Get the directory by removing the executable name
D="${1%$X}"
# Check if the directory exists
if [[ -d "$D" ]]; then
# If it does, cd into it
cd "$D"
else
if [[ "$D" ]]; then
# Complain if a directory was specified, but does not exist
echo "Directory '$D' does not exist" >&2
exit 1
fi
fi
# Check if the executable is, well, executable
if [[ -x "$X" ]]; then
# Run the executable in its directory with the supplied arguments
exec ./"$X" "${#:2}"
else
# Complain if the executable is not a valid
echo "Executable '$X' does not exist in '$D'" >&2
exit 1
fi
Usage:
$ cdexec
Usage: /home/archon/bin/cdexec <executable> [<argument>...]
$ cdexec /bin/ls ls
ls
$ cdexec /bin/xxx/ls ls
Directory '/bin/xxx/' does not exist
$ cdexec /ls ls
Executable 'ls' does not exist in '/'
One source of such error messages under those conditions is a broken symlink.
However, you say the script works when run from the command line. I would also check to see whether the directory is a symlink that's doing something other than what you expect.
Does it work if you call it in your script with the full path instead of using cd?
#!/bin/bash
/path/to/a/folder/scriptname
What about when called that way from the command line?