I am trying to run the following shell script on windows using sh preprocess.sh on cmd
#!/bin/bash
cd ./raw_data
# echo "download pretrained word embeddings: glove.42B.300d.zip"
# wget https://nlp.stanford.edu/data/wordvecs/glove.42B.300d.zip
# echo "unzip glove.42B.300d.zip"
# unzip glove.42B.300d.zip
echo "add vocab size and embedding size to the head of glove.42B.300d.txt"
n=$(sed -n '$=' glove.42B.300d.txt)
sed -i "1i$n 300" glove.42B.300d.txt
cd ..
echo "process raw data"
python process_raw.py
echo "prepare training, valid, testing data"
if [ ! -d "./log" ]; then
mkdir log
fi
python preprocess.py > log/preprocess.log
echo "Finished! preprocess.log is saved in log directory."
However, I am getting the following error
sed.exe: invalid option -- i
Can anybody please suggest a solution?
Related
I wrote a shellscript as follows, to check for a file in a samba share:
date_gen=$(date --date="3 days ago" +"%-Y%m%d")
fileName=${date_gen}"_Combined Reg Report.xlsx"
if [ ! -f smb://nfs/carboard/"${fileName}" -U ]
then
echo "File does not exist in Bash"
else
echo ${fileName}
fi
exit 1
Can someone please help me what is wrong with this, I am always getting "File does not exist in Bash". File is there in the folder.
Thanks,
Art
You should check if it's mounted and then check for the file
if mount | grep -q /nfs/cardboard
then
if [[ ! -f /nfs/cardboard/"${fileName}" ]]
then
...
fi
else
echo "not mounted"
fi
Checking the existence of a file with smbclient:
filename="$(date --date='3 days ago' '+%Y%m%d')_Combined Reg Report.xlsx"
if smbclient -A smbauth.conf '//nfs/carboard' -c "ls \"$filename\"" > /dev/null 2>&1
then
echo the file exists
else
echo the file is not there
fi
where smbauth.conf is a file storing your credentials in the following format:
username=myuser
password=mypassword
domain=MYDOMAIN
I don't know how escaping exactly works with smbclient (it seems like some characters like " are impossible to escape), but in your case, double-quoting is enough.
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,
Anyone able to help me out? I have a shell script I am working on but for the loop below the command after "echo "first file is $firstbd" is not being executed.. the $PROBIN/proutil ?? Not sure why this is...
Basically I have a list of files in a directory (*.list), I grab them and read the first line and pass it as a parameter to the cmdlet then move the .list and the content of the .list to another directory (the .list has a list of files with full path).
for i in $(ls $STAGEDIR/*.list); do
echo "Working with $i"
# grab first .bd file
firstbd=`head -1 $i`
echo "First file is $firstbd"
$PROBIN/proutil $DBENV/$DBNAME -C load $firstbd tenant $TENANT -dumplist $STAGEDIR/$i.list >> $WRKDIR/$i.load.log
#move the list and its content to finished folder
binlist=`cat $i`
for movethis in $binlist; do
echo "Moving file $movethis to $STAGEDIR/finished"
mv $movethis $STAGEDIR/finished/
done
echo "Finished working with list $i"
echo "Moving it to $STAGEDIR/finished"
mv $i $STAGEDIR/finished/
done
The error I was getting is..
./tableload.sh: line 107: /usr4/dlc/bin/proutil /usr4/testdbs/xxxx2 -C load /usr4/dumpdir/xxxxx.bd tenant xxxxx -dumplist /usr4/dumpdir/PUB.xxxxx.list >> /usr4/dumpdir/PUB.xxxx.list.load.log: A file or directory in the path name does not exist... however if I run "/usr4/dlc/bin/proutil"
The fix was to remove ">> $WRKDIR/$i.load.log".. the binary utility wouldn't run when trying to output results to file.. strange..
A couple of really bad practices here
parse the output of ls
not quoting variables
iterating the lines of a file with cat and for
As shelter comments, you don't check that you've created all the directories in the path for your log file.
A rewrite:
for i in "$STAGEDIR"/*.list; do
echo "Working with $i"
# grab first .bd file
firstbd=$(head -1 "$i")
echo "First file is $firstbd"
# ensure the output directory exists
logfile="$WRKDIR/$i.load.log"
mkdir -p "$(dirname "$logfile")"
"$PROBIN"/proutil "$DBENV/$DBNAME" -C load "$firstbd" tenant "$TENANT" -dumplist "$STAGEDIR/$i.list" >> "$logfile"
# move the list and its content to finished folder
while IFS= read -r movethis; do
echo "Moving file $movethis to $STAGEDIR/finished"
mv "$movethis" "$STAGEDIR"/finished/
done < "$i"
echo "Finished working with list $i"
echo "Moving it to $STAGEDIR/finished"
mv "$i" "$STAGEDIR"/finished/
done
I'm trying to create a shell script that I will download the latest Atomic gotroot rules to my server, unpack them, copy them to the correct folder, etc.,
I've been reading shell tutorials and forum posts for most of the day and the syntax escapes me for some of these. I have run all these commands and I know they work if I manually run them.
I know I need to develop some error checking, but I'm just trying to get the commands to run correctly. The main problem at the moment is the syntax of the wget commands, i've got errors about missing semi-colons, divide by zero, unsupported schemes - I've tried various quoting (single and double) and escaping - / " characters in various combinations.
Thanks for any help.
The raw wget command is
wget --user="jim" --password="xxx-yyy-zzz" "http://updates.atomicorp.com/channels/rules/subscription/VERSION"
#!/bin/sh
update_modsec_rules(){
wget=/usr/bin/wget
tar=/bin/tar
apachectl=/usr/bin/apache2ctl
TXT="Script Run Finished"
WORKING_DIR="/var/asl/updates"
TARGET_DIR="/usr/local/apache/conf/modsec_rules/"
EXISTING_FILES="/var/asl/updates/modsec/*"
EXISTING_ARCH="/var/asl/updates/modsec-*"
WGET_OPTS='--user=jim --password=xxx-yyy-zzz'
URL_BASE="http://updates.atomicorp.com/channels/rules/subscription"
# change to working directory and cleanup any downloaded files and extracted rules in modsec/ directory
cd $WORKING_DIR
rm -f $EXISTING_ARCH
rm -f $EXISTING_FILES
rm -f VERSION*
# wget to download VERSION file
$wget ${WGET_OPTS} "${URL_BASE}/VERSION"
# get current MODSEC_VERSION from VERSION file and save as variable
source VERSION
TARGET_DATE=$MODSEC_VERSION
echo $TARGET_DATE
# wget to download current archive
$wget ${WGET_OPTS} "${URL_BASE}/modsec-${TARGET_DATE}.tar.gz"
# extract archive
echo "extracting files . . . "
tar zxvf $WORKING_DIR/modsec-${TARGET_DATE}.tar.gz
echo "copying files . . . "
cp -uv $EXISTING_FILES $TARGET_DIR
echo $TXT
}
update_modsec_rules $# 2>&1 | tee -a /var/asl/modsec_update.log
RESTART_APACHE="/usr/local/cpanel/scripts/restartsrv httpd"
$RESTART_APACHE
Here are some guidelines to use when writing shell scripts.
Always quote variables when you use them. This helps avoid the possibility of misinterpretation. (What if a filename contains a space?)
Don't trust fileglobbing on commands like rm. Use for loops instead. (What if a filename starts with a hyphen?)
Avoid subshells when possible. Your lines with backquotes make me itchy.
Don't exec if you can help it. And especially don't expect any parts of your script after your exec to actually get run.
I should point out that while your shell may be bash, you've specified /bin/sh for execution of this script, so it is NOT a bash script.
Here's a rewrite with some error checking. Add salt to taste.
#!/bin/sh
# Linux
wget=/usr/bin/wget
tar=/bin/tar
apachectl=/usr/sbin/apache2ctl
# FreeBSD
#wget=/usr/local/bin/wget
#tar=/usr/bin/tar
#apachectl=/usr/local/sbin/apachectl
TXT="GOT TO THE END, YEAH"
WORKING_DIR="/var/asl/updates"
TARGET_DIR="/usr/local/apache/conf/modsec_rules/"
EXISTING_FILES_DIR="/var/asl/updates/modsec/"
EXISTING_ARCH="/var/asl/updates/"
URL_BASE="http://updates.atomicorp.com/channels/rules/subscription"
WGET_OPTS='--user="jim" --password="xxx-yyy-zzz"'
if [ ! -x "$wget" ]; then
echo "ERROR: No wget." >&2
exit 1
elif [ ! -x "$apachectl" ]; then
echo "ERROR: No apachectl." >&2
exit 1
elif [ ! -x "$tar" ]; then
echo "ERROR: Not in Kansas anymore, Toto." >&2
exit 1
fi
# change to working directory and cleanup any downloaded files
# and extracted rules in modsec/ directory
if ! cd "$WORKING_DIR"; then
echo "ERROR: can't access working directory ($WORKING_DIR)" >&2
exit 1
fi
# Delete each file in a loop.
for file in "$EXISTING_FILES_DIR"/* "$EXISTING_ARCH_DIR"/modsec-*; do
rm -f "$file"
done
# Move old VERSION out of the way.
mv VERSION VERSION-$$
# wget1 to download VERSION file (replaces WGET1)
if ! $wget $WGET_OPTS $URL_BASE}/VERSION; then
echo "ERROR: can't get VERSION" >&2
mv VERSION-$$ VERSION
exit 1
fi
# get current MODSEC_VERSION from VERSION file and save as variable,
# but DON'T blindly trust and run scripts from an external source.
if grep -q '^MODSEC_VERSION=' VERSION; then
TARGET_DATE="`sed -ne '/^MODSEC_VERSION=/{s/^[^=]*=//p;q;}' VERSION`"
echo "Target date: $TARGET_DATE"
fi
# Download current archive (replaces WGET2)
if ! $wget ${WGET_OPTS} "${URL_BASE}/modsec-$TARGET_DATE.tar.gz"; then
echo "ERROR: can't get archive" >&2
mv VERSION-$$ VERSION # Do this, don't do this, I don't know your needs.
exit 1
fi
# extract archive
if [ ! -f "$WORKING_DIR/modsec-${TARGET_DATE}.tar.gz" ]; then
echo "ERROR: I'm confused, where's my archive?" >&2
mv VERSION-$$ VERSION # Do this, don't do this, I don't know your needs.
exit 1
fi
tar zxvf "$WORKING_DIR/modsec-${TARGET_DATE}.tar.gz"
for file in "$EXISTING_FILES_DIR"/*; do
cp "$file" "$TARGET_DIR/"
done
# So far so good, so let's restart apache.
if $apachectl configtest; then
if $apachectl restart; then
# Success!
rm -f VERSION-$$
echo "$TXT"
else
echo "ERROR: PANIC! Apache didn't restart. Notify the authorities!" >&2
exit 3
fi
else
echo "ERROR: Apache configs are broken. We're still running, but you'd better fix this ASAP." >&2
exit 2
fi
Note that while I've rewritten this to be more sensible, there is certainly still a lot of room for improvement.
You have two options:
1- changing this to
WGET1=' --user="jim" --password="xxx-yyy-zzz" "http://updates.atomicorp.com/channels/rules/subscription/VERSION"'
then run
wget $WGET1 same to WGET2
Or
2- encapsulating $WGET1 with backquotes ``.
e.g.:
`$WGET`
This applies to any command your executing out of a variable.
Suggested changes:
#!/bin/sh
TXT="GOT TO THE END, YEAH"
WORKING_DIR="/var/asl/updates"
TARGET_DIR="/usr/local/apache/conf/modsec_rules/"
EXISTING_FILES="/var/asl/updates/modsec/*"
EXISTING_ARCH="/var/asl/updates/modsec-*"
WGET1='wget --user="jim" --password="xxx-yyy-zzz" "http://updates.atomicorp.com/channels/rules/subscription/VERSION"'
WGET2='wget --user="jim" --password="xxx-yyy-zzz" "http://updates.atomicorp.com/channels/rules/subscription/modsec-$TARGET_DATE.tar.gz"'
## change to working directory and cleanup any downloaded files and extracted rules in modsec/ directory
cd $WORKING_DIR
rm -f $EXISTING_ARCH
rm -f $EXISTING_FILES
## wget1 to download VERSION file
`$WGET1`
## get current MODSEC_VERSION from VERSION file and save as variable
source VERSION
TARGET_DATE=`echo $MODSEC_VERSION`
## WGET2 command to download current archive
`$WGET2`
## extract archive
tar zxvf $WORKING_DIR/modsec-$TARGET_DATE.tar.gz
cp $EXISTING_FILES $TARGET_DIR
## restart server
exec '/usr/local/cpanel/scripts/restartsrv_httpd' $*;
Pro Tip: If you need string substitution, using ${VAR} is much better to eliminate ambiguity, e.g.:
tar zxvf $WORKING_DIR/modsec-${TARGET_DATE}.tar.gz
#!/bin/bash
# See if registry is set to expire updates
filename=hostnames
> test.log
PARAMETER=Updates
FILE=/etc/.properties
CODE=sudo if [ ! -f $FILE] && grep $PARAMETER $FILE; then echo "File found, parameter not found."
#CODE=grep $PARAMETER $FILE || sudo tee -a /etc/.properties <<< $PARAMETER
while read -r -a line
do
hostname=${line//\"}
echo $hostname":" >> test.log
#ssh -n -t -t $hostname "$CODE" >> test.log
echo $CODE;
done < "$filename"
exit
I want to set "Updates 30" in /etc/.properties on about 50 servers if:
The file exists (not all servers have the software installed)
The parameter "Updates" is not already set in the file (e.g. in case of multiple runs)
I am a little puzzled so far how, because I am not sure if this can be done in 1 line of bash code. The rest of the script works fine.
Ok, here's what i think would be a solution for you. Like explained in this article http://www.unix.com/shell-programming-scripting/181221-bash-script-execute-command-remote-servers-using-ssh.html
invoke the script which contains the commands that you want to be executed at the remote server
Code script 1:
while read -r -a line
do
ssh ${line} "bash -s" < script2
done < "$filename"
To replace a line in a text file, you can use sed (http://www.cyberciti.biz/faq/unix-linux-replace-string-words-in-many-files/)
Code script 2:
PARAMETER=Updates
FILE=/etc/.properties
NEWPARAMETER=Updates ###(What you want to write there)
if [ ! -f $FILE] && grep $PARAMETER $FILE; then exit
sed -i 's/$PARAMETER/$NEWPARAMETER/g' $FILE
So, I'm not certain this covers all your use case, I hope this helps you out if there is anything feel free to ask!