I have a sh file with 1.000.000 of instructions "rm -f", but is not working. This runs on a ubuntu server 16.04
I tried this.
#!/bin/bash
/bin/rm -f /media/pictures2015/pictures/FTP/20150806/5939757.tif
/bin/rm -f /media/pictures2015/pictures/FTP/20150806/5939758.tif
/bin/rm -f /media/pictures2015/pictures/FTP/20150805/5939759.tif
And this
#!/bin/bash
rm -f /media/pictures2015/pictures/FTP/20150806/5939757.tif
rm -f /media/pictures2015/pictures/FTP/20150806/5939758.tif
rm -f /media/pictures2015/pictures/FTP/20150805/5939759.tif
The sh file has all the permissions, but don't wokr. With the "split" command change the sh file of 1.000.000 lines to two sh files of 500.000 lines.
The output dont show any error !!!
Thank You
the error was caused because the list of the images exported from phpmyadmin and at the end of the line I am with the "CR-LF" format, so investigate how to remove it and find the dos2unix program, install it in ubuntu, run and it worked.
The final solution I found on this link cyberciti
Thanks !!!!
Related
have to use a .sh script to unpack and prep some databases. The code is the following:
#
# Downloads and unzips all required data for AlphaFold.
#
# Usage: bash download_all_data.sh /path/to/download/directory
set -e
DOWNLOAD_DIR="$1"
for f in $(ls ${DOWNLOAD_DIR}/*.tar.gz)
do
tar --extract --verbose --file="${DOWNLOAD_DIR}/${f}" /
--directory="${DOWNLOAD_DIR}/mmseqs_dbs"
rm "${f}"
BASENAME="$(basename {f%%.*})"
DB_NAME="${BASENAME}_db"
OLD_PWD=$(pwd)
cd "${DOWNLOAD_DIR}/mmseqs_dbs"
mmseqs tar2exprofiledb "${BASENAME}" "${DB_NAME}"
mmseqs createindex "${DB_NAME}" "${DOWNLOAD_DIR}/tmp/"
cd "${OLD_PWD}"
done
When I run the code, I got that error:
(openfold_venv) watson#watson:~/pedro/openfold$ sudo bash scripts/prep_mmseqs_dbs.sh data/
tar: data//data//colabfold_envdb_202108.tar.gz: Cannot open: No such file or directory
tar: Error is not recoverable: exiting now
I don`t understand why the code repeats my "DOWNLOAD_DIR", the correct should be :
data/colabfold_envdb_202108.tar.gz
and not
data//data//colabfold_envdb_202108.tar.gz
Could anyone help me?
New code:
set -e
DOWNLOAD_DIR="$1"
for f in ${DOWNLOAD_DIR}/*.tar.gz;
do
tar --extract --verbose --file="$f" /
--directory="${DOWNLOAD_DIR}/mmseqs_dbs"
rm "${f}"
BASENAME="$(basename {f%%.*})"
DB_NAME="${BASENAME}_db"
OLD_PWD=$(pwd)
cd "${DOWNLOAD_DIR}/mmseqs_dbs"
mmseqs tar2exprofiledb "${BASENAME}" "${DB_NAME}"
mmseqs createindex "${DB_NAME}" "${DOWNLOAD_DIR}/tmp/"
cd "${OLD_PWD}"
done
To answer your first question: why is it repeating? Because you are repeating it in your code:
for f in ${DOWNLOAD_DIR}/*.tar.gz;
do
tar --extract --verbose --file="${DOWNLOAD_DIR}/$f"
If f is downloads/file.tar.gz then ${DOWNLOAD_DIR}/${f} will resolve to downloads/downloads/file.tar.tgz.
As to your second question: the escape character is the backslash \, not the forward slash. Your multiline command should look like this:
tar --extract --verbose --file="${DOWNLOAD_DIR}/${f}" \
--directory="${DOWNLOAD_DIR}/mmseqs_dbs"
I'm building an RPM with my own code and am running into an issue where the RPM is hanging when I install it with yum if I try to launch something as part of the post-install script. For some background, this is a virtual appliance where we've replaced the shell with a program with minimal configuration options. Previously, I couldn't get the program to load via the post-install options in my spec file; it causes the 'installing' line during a yum install to hang. I put a bandaid on it by having a reboot occur. I need this menu to load after installation, but everything I've tried results in yum hanging on the 'installing' line. My latest attempt; using the trap command, causes the same hang. Does anyone have any other ideas?
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}
%description
Installs the program.
%prep
%setup -q
%install
rsync -ar /home/makerpm/rpmbuild/BUILD/%{name}-%{version}/ /home/makerpm/rpmbuild/BUILDROOT/%{name}-%{version}-%{release}.x86_64
find $RPM_BUILD_ROOT -not -type d -printf "%%%attr(%%m,root,root) %%p\n" | sed -e "s|$RPM_BUILD_ROOT||g" > %{_tmppath}/%{name}_contents.txt
%clean
rm -rf ${RPM_BUILD_ROOT}
rm -rf %{_tmppath}/*
rm -rf ${RPM_BUILD_DIR}/*
%changelog
* Sun Jan 25 2014 - %{version} - Modified menu with trap ability so the first reboot isn't required.
%post
function finish {
/bin/launcher
}
chmod 755 /bin/launcher
cat /etc/shells | grep "/bin/launcher"
if [ $? -eq 1 ]
then
echo "/bin/bash" >> /etc/shells
fi
chsh -s /bin/launcher root
trap finish EXIT
#List of all files to be extracted
%files -f %{_tmppath}/%{name}_contents.txt
I have a linux bash script, which has a parameter to update the script self. My problem is, that the script can't update itself, while it's used. Well.. Does someone have a solution?
Currently I try to update the script as following:
# Download latest version
wget -q https://github.com/TS3Tools/TS3UpdateScript/archive/master.zip
# Unzip latest version
unzip master.zip TS3UpdateScript-master/* -x TS3UpdateScript-master/configs/ && mv -f TS3UpdateScript-master/* . && rmdir TS3UpdateScript-master/
But I receive the following error by the script:
replace TS3UpdateScript-master/LICENSE_GNU_GPL.txt? [y]es, [n]o, [A]ll, [N]one, [r]ename: A
ateScript-master/configs
caution: excluded filename not matched: TS3UpdateScript-master/configs/
# many arguments
I hope, someone can help me. Thanks in advance!
It seems that your error comes from file name wildcard without quotes. Bash does globbing first and replaces * with lots of filenames and then runs unzip with this parameters. Try master.zip 'TS3UpdateScript-master/*' -x 'TS3UpdateScript-master/configs/' .
Then there will be a problem with running a new version of script instead of old one running. I think it should be done like that:
#!/bin/bash
version=4
if [ "$UPDATED" != "$0" ]; then
cp self_update.new.sh self_update.sh
exec env UPDATED="$0" "$0" "$#"
fi
echo "This script's version is $version"
Thanks for your help and ideas! I've "outsourced" the code to another script, which contains following code:
#!/usr/bin/env bash
sleep 5s
# Download latest version
wget -q https://github.com/TS3Tools/TS3UpdateScript/archive/master.zip
# Unzip latest version
if [[ $(unzip master.zip TS3UpdateScript-master/* -x TS3UpdateScript-master/configs/*) ]]; then
if [ $(cp -Rf TS3UpdateScript-master/* . && rm -rf TS3UpdateScript-master/) ]; then
rm -rf master.zip
exit 1;
fi
else
rm -rf master.zip
exit 0;
fi
Maybe I am missing something here but I have the following small bash script to delete some old files that get created when using flex and yacc its pretty simple but when I run the script it echos the result to the terminal but does not delete the file I'm probably missing something stupid could you guys point me in the right direction.
#!/bin/bash
echo "rm -f y.tab.h"; (just using one file for now)
I tried changing it to
echo rm -f y.tab.h;
but still no luck
I tried executing it with bash delete.sh and sh delete.sh and even using chmod +x on the file and executing it with ./
Remove echo statement
Just use
rm -f y.tab.h
Im having problems trying to empty a folder in my script.
This is working in my command line:
rm -r Folder1/Folder2/*
But if in my script I do this:
DIR="Folder1/Folder2/"
rm -r "$DIR*"
It says "rm: Folder1/Folder2/*: No such file or directory", where is the problem?
Im running the script in the same folder as I tried the command.
Glob expansion doesn't happen inside quotes.
Try:
rm -r -- "$DIR"*
(Just make really sure you don't put a space after the quotes.)
rm -r $DIR*
That should work, without quotes