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  • Where do you find the Bash source files of programs in Linux/Mac OSX?

    - by AndrewKS
    I am currently writing some convenience methods for my terminal in my bash_profile and am sure if what I am writing is "the best way". I figure a good way to verify whether what I'm doing is right or not would be to find some source code of more established programs and see how they do it. My question then is, where can I find this code on my Mac? An example is, with Macports installed, where is the source code that opens the port interactive console when I type nothing but "port" in my shell? (I added Linux in the title even though I am on a Mac because I assume the answer would be the same for both) Edit: The answer I am looking for is in terms of which directory relative to the programs will I find their unix scripts.

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  • Is it possible to auto update php.ini via a bash script?

    - by Tada.wav
    I'm trying to write an install script and i need to change the sendmail line in php.ini but I want to do this automatically at the moment I'm doing this manually: sudo nano /etc/php5/apache2/php.ini finding the line containing sendmail_path = then editing it to be sendmail_path = /usr/bin/msmtp -t then saving the file. Is it possible to just auto script this to make the change? Thanks a lot

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  • How to Detect that Current (Bash) Shell is a (Vi/Vim) Subshell?

    - by Jeet
    From inside Vi/Vim, I can type: :shell to drop into a shell. Is there any way to detect that I am in a Vi-spawned subshell? The environmental variable SHLVL is 2, but that does not tell me explicitly that I am in a Vi/Vim-spawned subshell. On OS X, the following variables are also set: MYVIMRC, VIMRUNTIME, VIM. How universal are these? Can I count on these being set in any system, if and only if I am in a Vi/Vim subshell? If not, is there any portable, robust and hopefully efficient way to tell that I am in a Vi/Vim subshell? Thanks.

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  • how do I concatenate a regex in a bash alias?

    - by Rodreegez
    Hello, I can't for the life of me how to create an alias that will switch to a given project directory. I keep all my projects in a folder called Projects i.e. ~/Project/blog ~/Project/whatever I'd like to have an alias along the lines of p whatever that would equate to cd ~/Project/$1 where $1 is whatever is given to p. I have tried various combinations of alias p="cd ~/Projects/\$1" with all the usual suspects for regex escaping but I can't quite get it. Any ideas?

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  • Bash: how to interrupt this script when there's a CTRL-C?

    - by WizardOfOdds
    I wrote a tiny Bash script to find all the Mercurial changesets (starting from the tip) that contains the string passed in argument: #!/bin/bash CNT=$(hg tip | awk '{ print $2 }' | head -c 3) while [ $CNT -gt 0 ] do echo rev $CNT hg log -v -r$CNT | grep $1 let CNT=CNT-1 done If I interrupt it by hitting ctrl-c, more often than not the command currently executed is "hg log" and it's that command that gets interrupted, but then my script continues. I was then thinking of checking the return status of "hg log", but because I'm piping it into grep I'm not too sure as to how to go about it... How should I go about exiting this script when it is interrupted? (btw I don't know if that script is good at all for what I want to do but it does the job and anyway I'm interested in the "interrupted" issue)

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  • How do you convert date taken from a bash script to milliseconds in a Java program?

    - by Matt Pascoe
    I am writing a piece of code in Java that needs to take a time sent from a bash script and parse the time to milliseconds. When I check the millisecond conversion on the date everything is correct except for the month I have sent which is January instead of March. Here is the variable I create in the bash script, which later in the script I pass to the Java program: TIME=`date +%m%d%Y_%H:%M:%S` Here is the Java code which parses the time to milliseconds: String dt = "${scriptstart}"; java.text.SimpleDateFormat scriptStart = new java.text.SimpleDateFormat("MMDDyyyy_HH:mm:ss"); long start = scriptStart.parse(dt).getTime(); The goal of this statement is to find the elapsed time between the start of the script and the current system time. To troubleshoot this I printed out the two: System Time = 1269898069496 (converted = Mon Mar 29 2010 16:27:49 GMT-0500 (Central Daylight Time)) Script Start = 03292010_16:27:45 Script Start in Milli = 1264804065000 (Converted = Fri Jan 29 2010 16:27:45 GMT-0600 (Central Standard Time))

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  • Is there a bash shortcut for traversing similar directory structures?

    - by Steve Weet
    The Korn shell used to have a very useful option to cd for traversing similar directory structures e.g. given the following directorys /home/sweet/dev/projects/trunk/projecta/app/models /home/andy/dev/projects/trunk/projecta/app/models Then if you were in the /home/sweet.... directory then you could change to the equivalent directory in andy's structure by typing cd sweet andy So if ksh saw 2 arguments then it would scan the current directory path for the first value, replace it with the second and cd there. Is anyone aware of similar functionality in bash. EDIT 1 Following on from Michal's excellent answer I have now created the following bash function called scd (For Sideways cd) function scd { cd "${PWD/$1/$2}" } EDIT 2 Thanks to @digitalross I can now reproduce the ksh functionality exactly with the code from below (With the addition of a pwd to tell you where you have changed to) cd () { if [ "x$2" != x ]; then builtin cd ${PWD/$1/$2} pwd else builtin cd "$@" fi }

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  • Better way to make a bash script self-tracing?

    - by Kevin Little
    I have certain critical bash scripts that are invoked by code I don't control, and where I can't see their console output. I want a complete trace of what these scripts did for later analysis. To do this I want to make each script self-tracing. Here is what I am currently doing: #!/bin/bash # if last arg is not '_worker_', relaunch with stdout and stderr # redirected to my log file... if [[ "$BASH_ARGV" != "_worker_" ]]; then $0 "$@" _worker_ >>/some_log_file 2>&1 # add tee if console output wanted exit $? fi # rest of script follows... Is there a better, cleaner way to do this?

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  • How do you convert date taken from a bash script to milliseconds in java program?

    - by Matt Pascoe
    I am writing a piece of code in java that needs to take a time sent from a bash script and parse the time to milliseconds. When I check the millisecond conversion on the date everything is correct except for the month I have sent which is January instead of March. Here is the variable I create in the bash script, which later in the script I pass to the java program: TIME=`date +%m%d%Y_%H:%M:%S` Here is the java code which parses the time to milliseconds: String dt = "${scriptstart}"; java.text.SimpleDateFormat scriptStart = new java.text.SimpleDateFormat("MMDDyyyy_HH:mm:ss"); long start = scriptStart.parse(dt).getTime(); The goal of this statement is to find the elapsed time between the start of the script and the current system time. To troubleshoot this I printed out the two: System Time = 1269898069496 (converted = Mon Mar 29 2010 16:27:49 GMT-0500 (Central Daylight Time)) Script Start = 03292010_16:27:45 Script Start in Milli = 1264804065000 (Converted = Fri Jan 29 2010 16:27:45 GMT-0600 (Central Standard Time))

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  • PHP & bash; Linux; Compile my own function

    - by flienteen
    Hi. I would like to make my own program but I have no idea how.. for example I want to make a typical 'Hello $user' program. So.. +-- hi ¦   +-- hi.sh ¦   +-- hi_to.sh hi.sh #!/bin/bash ~/hi/hi_to.sh $1 hi_to.sh #!/usr/bin/php <?php echo "\nHellO ".$argv[1]."\n"; ?> Run it in terminal: me:~/hi ? ./hi.sh User HellO User and my question is: how to compile all this files into one bash program?

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  • Are compound command's second and subsequent lines not effected by HISTCONTROL in bash?

    - by UniMouS
    When consulting bash's man page, it read this sentence about bash history: The second and subsequent lines of a multi-line compound command are not tested, and are added to the history regardless of the value of HISTCONTROL. But I have tried this: $ HISTCONTROL=ignorespace $ if [ -f /var/log/messages ] > then > echo "/var/log/message exists." > fi $ history | tail -2 18 HISTCONTROL=ignorespace 19 history | tail -2 Note that the if is leaded by a space. Why the second line of this if compound command still not appear in the history?

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  • How do I write a bash script to replace words in files and then rename files?

    - by Jason
    Hi All, I have a folder structure, as shown below: I need to create a bash script that does 4 things: It searches all the files in the generic directory and finds the string 'generic' and makes it into 'something' As above, but changes "GENERIC" to "SOMETHING" As above, but changes "Generic" to "Something" Renames any filename that has "generic" in it with "something" Right now I am doing this process manually by using the search and replace in net beans. I dont know much about bash scripting, but i'm sure this can be done. I'm thinking of something that I would run and it would take "Something" as the input. Where would I start? what functions should I use? overall guidance would be great. thanks. I am using Ubuntu 10.5 desktop edition.

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  • Why does this Bash regex match return an Exit Status of "2"?

    - by PreservedMoose
    I'm writing a Bash script that needs to scan for the existence of non-ASCII characters in filenames. I'm using the POSIX bracket regex syntax to match the non-ASCII characters, but for some reason, when I test for the match in an if/then statement, the test always returns an Exit Status of 2, and never matches my test string. Here's the code in question: FILEREQ_SOURCEFILE="Filename–WithNonAScII-Charàcters-05sec_23.98.mov" REGEX_MATCH_NONASCII="[^[:ascii:]]" if [[ $FILEREQ_SOURCEFILE =~ $REGEX_MATCH_NONASCII ]]; then echo "Exit Status: $?" echo "Matched!" else echo "Exit Status: $?" echo "No Match" fi This code always returns: Exit Status: 2 No Match I've read and re-read the bash-hackers.org explanation of how regex matching works, as well as this previous question on SO regarding matching non-ASCII characters, but for the life of me, I can't get this to work. What am I missing here?

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  • unexpected EOF and end of document

    - by WASasquatch
    I have been fiddling with this code for a few days. Mind you I am a beginner. I just want to get my script to be able to download a remote file, and scan MineCraft plugins. I got the scan plugins to work, but I'm having two other issues. One, I can't get the mc_addplugin to work correctly, and I get a Unexpected EOF and unexpected end of document when running any other command besides mc_scanplugins or mc_start bash: -c: line 0: unexpected EOF while looking for matching `"' bash: -c: line 1: syntax error: unexpected end of file Help would be so much appreciated! Thanks in advance. #!/bin/bash # /etc/init.d/craftbukkit # version 0.9.1 2012-07-06 (YYYY-MM-DD) ### BEGIN INIT INFO # Provides: craftbukkit # Required-Start: $local_fs $remote_fs # Required-Stop: $local_fs $remote_fs # Should-Start: $network # Should-Stop: $network # Default-Start: 2 3 4 5 # Default-Stop: 0 1 6 # Short-Description: Starts craftbukkit server # Description: Starts and controls the craftbukkit server ### END INIT INFO # SETTINGS SERVICE='craftbukkit-1.2.5-R1.0.jar' OPTIONS='nogui' USERNAME='smith' # LIST ALL THE WORLDS IN YOUR CRAFTBUKKIT SERVER FOLDER WORLDS[1]='world' WORLDS[2]='world_nether' WORLDS[3]='world_the_end' WORLDS[4]='flat_world' MCPATH='/var/www/servers/Foundation' PLUGINSPATH='/var/www/servers/Foundation/plugins' TEMPPLUGINS='/var/www/servers/Foundationplugins/temp_plugins' BACKUPPATH='/var/www/servers/Foundation/backup' CPU_COUNT=2 INVOCATION="java -Xmx2024M -Xms2024M -XX:+UseConcMarkSweepGC -XX:+CMSIncrementalPacing -XX:ParallelGCThreads=$CPU_COUNT -XX:+AggressiveOpts -jar $SERVICE $OPTIONS" ME=`whoami` as_user() { if [ $ME == $USERNAME ] ; then bash -c "$1" else su - $USERNAME -c "$1" fi } mc_start() { if pgrep -u $USERNAME -f $SERVICE > /dev/null then echo "$SERVICE is already running!" else echo "Starting $SERVICE..." cd $MCPATH as_user "cd $MCPATH && screen -dmS craftbukkit $INVOCATION" sleep 7 if pgrep -u $USERNAME -f $SERVICE > /dev/null then echo "$SERVICE is now running." else echo "Error! Could not start $SERVICE!" fi fi } mc_saveoff() { if pgrep -u $USERNAME -f $SERVICE > /dev/null then echo "$SERVICE is running... suspending saves" as_user "screen -p 0 -S craftbukkit -X eval 'stuff \"say The server is preforming a backup. Server going to read-only mode. Do not build...\"\015'" as_user "screen -p 0 -S craftbukkit -X eval 'stuff \"save-off\"\015'" as_user "screen -p 0 -S craftbukkit -X eval 'stuff \"save-all\"\015'" sync sleep 10 else echo "$SERVICE is not running. Not suspending saves." fi } mc_save() { if pgrep -u $USERNAME -f $SERVICE > /dev/null then echo "$SERVICE is running... Saving worlds..." as_user "screen -p 0 -S craftbukkit -X eval 'stuff \"save-all\"\015'" sync sleep 10 echo "Save complete!" else echo "$SERVICE is not running. Cannot save!" fi } mc_saveon() { if pgrep -u $USERNAME -f $SERVICE > /dev/null then echo "$SERVICE is running... re-enabling saves" as_user "screen -p 0 -S craftbukkit -X eval 'stuff \"save-on\"\015'" as_user "screen -p 0 -S craftbukkit -X eval 'stuff \"say Server backup has completed. Server going to read-write mode. You can now continue building...\"\015'" else echo "$SERVICE is not running. Not resuming saves." fi } mc_stop() { if pgrep -u $USERNAME -f $SERVICE > /dev/null then echo "Stopping $SERVICE" as_user "screen -p 0 -S craftbukkit -X eval 'stuff \"say $SERVERNAME is shutting down in 30 seconds! Please stop what you are doing. Check back later, we'll be back!\"\015'" as_user "screen -p 0 -S craftbukkit -X eval 'stuff \"save-all\"\015'" sleep 30 as_user "screen -p 0 -S craftbukkit -X eval 'stuff \"stop\"\015'" sleep 7 else echo "$SERVICE was not running." fi if pgrep -u $USERNAME -f $SERVICE > /dev/null then echo "Error! $SERVICE could not be stopped." else echo "$SERVICE is stopped." fi } mc_update() { if pgrep -u $USERNAME -f $SERVICE > /dev/null then echo "$SERVICE is running! Will not start update." else MC_SERVER_URL=http://dl.bukkit.org/latest-rb/craftbukkit.jar as_user "cd $MCPATH && wget -q -O $MCPATH/craftbukkit_server.jar.update $MC_SERVER_URL" if [ -f $MCPATH/craftbukkit_server.jar.update ] then if `diff $MCPATH/$SERVICE $MCPATH/craftbukkit_server.jar.update >/dev/null` then echo "You are already running the latest version of $SERVICE. Update anyway? [Y/n]" select yn in "Yes" "No"; do case $yn in Yes ) as_user "mv $MCPATH/$SERVICE $MCPATH/${SERVICE}_old.jar" as_user "mv $MCPATH/craftbukkit_server.jar.update $MCPATH/$SERVICE" echo "$SERVICE updated successfully!"; break;; No ) echo "The update was not installed! Removing temporary files and exiting..." as_user "rm $MCPATH/craftbukkit_server.jar.update" exit;; esac done else as_user "mv $MCPATH/$SERVICE $MCPATH/${SERVICE}_old.jar" as_user "mv $MCPATH/craftbukkit_server.jar.update $MCPATH/$SERVICE" echo "$SERVICE updated successfully!" fi else echo "$SERVICE update could not be downloaded." fi fi } mc_addplugin() { if pgrep -u $USERNAME -f $SERVICE > /dev/null then echo "$SERVICE is running! Please stop the service before adding a plugin." else echo "Paste the URL to the .JAR Plugin..." read JARURL JARNAME=$(basename "$JARURL") if [ -d "$TEMPPLUGINS" ] then as_user "cd $PLUGINSPATH && wget -r -A.jar $JARURL -o temp_plugins/$JARNAME" else as_user "cd $PLUGINSPATH && mkdir $TEMPPLUGINS && wget -r -A.jar $JARURL -o temp_plugins/$JARNAME" fi if [ -f "$TMPDIR/$JARNAME" ] then if [ -f "$PLUGINSPATH/$JARNAME" ] then if `diff $PLUGINSPATH/$JARNAME $TMPDIR/$JARNAME >/dev/null` then echo "You are already running the latest version of $JARNAME." else NOW=`date "+%Y-%m-%d_%Hh%M"` echo "Are you sure you want to overwrite this plugin? [Y/n]" echo "Note: Your old plugin will be moved to the "$TEMPPLUGINS" folder with todays date." select yn in "Yes" "No"; do case $yn in Yes ) as_user "mv $PLUGINSPATH/$JARNAME $TEMPPLUGINS/${JARNAME}_${NOW} && mv $TEMPPLUGINS/$JARNAME $PLUGINSPATH/$JARNAME"; break;; No ) echo "The plugin has not been installed! Removing temporary plugin and exiting..." as_user "rm $TEMPPLUGINS/$JARNAME"; exit;; esac done echo "Would you like to start the $SERVICE now? [Y/n]" select yn in "Yes" "No"; do case $yn in Yes ) mc_start; break;; No ) "$SERVICE not running! To start the service run: /etc/init.d/craftbukkit start"; exit;; esac done fi else echo "Are you sure you want to add this new plugin? [Y/n]" select yn in "Yes" "No"; do case $yn in Yes ) as_user "mv $PLUGINSPATH/$JARNAME $TEMPPLUGINS/${JARNAME}_${NOW} && mv $TEMPPLUGINS/$JARNAME $PLUGINSPATH/$JARNAME"; break;; No ) echo "The plugin has not been installed! Removing temporary plugin and exiting..." as_user "rm $TEMPPLUGINS/$JARNAME"; exit;; esac done echo "Would you like to start the $SERVICE now? [Y/n]?" select yn in "Yes" "No"; do case $yn in Yes ) mc_start; break;; No ) "$SERVICE not running! To start the service run: /etc/init.d/craftbukkit start"; exit;; esac done fi else echo "Failed to download the plugin from the URL you specified!" exit; fi fi } mc_scanplugins() { if [ "$(ls -A $PLUGINSPATH)" ] then shopt -s nullglob PLUGINS=($PLUGINSPATH/*.jar) i=1 for f in "${PLUGINS[@]}" do echo "${i}: $f" PLUGIN[$i]=$f i=$(( $i + 1 )) done echo "Enter the ID of a plugin you want removed, or any other key to cancel." read INPUT if [ ! -z "${INPUT##*[!0-9]*}" ] then if [ -f "${PLUGIN[INPUT]}" ] then echo "Removing plugin..." JAR=$(basename ${PLUGIN[INPUT]}) JARNAME=${JAR%.jar} as_user "rm -f ${PLUGIN[INPUT]}" sleep 2 as_user "cd $PLUGINSPATH && rm -rf ./${JARNAME}" if [ -f "${PLUGINSPATH}/${JARNAME}" ] then echo "Plugin folder could not be removed..." fi echo "Plugin removed." else echo "${PLUGIN[INPUT]}" echo "Invalid plugin! Does not exist! Canceling..." exit; fi else echo "Canceling..." exit; fi else echo "You have no plugins installed." exit; fi } mc_backup() { mc_saveoff for i in "${WORLDS[@]}"; do NOW=`date "+%Y-%m-%d_%Hh%M"` BACKUP_FILE="$BACKUPPATH/${i}_${NOW}.tar" echo "Backing up world: $i..." #as_user "cd $MCPATH && cp -r $i $BACKUPPATH/${i}_`date "+%Y.%m.%d_%H.%M""` as_user "tar -C \"$MCPATH\" -cf \"$BACKUP_FILE\" $i" done echo "Backing up $SERVICE" as_user "tar -C \"$MCPATH\" -rf \"$BACKUP_FILE\" $SERVICE" #as_user "cp \"$MCPATH/$SERVICE\" \"$BACKUPPATH/craftbukkit_server_${NOW}.jar\"" mc_saveon echo "Compressing backup..." as_user "tar -cvzf $BACKUPPATH/server_backup_${NOW}.tar.gz $MCPATH" echo "Backup has completed successfully." } mc_command() { command="$1"; if pgrep -u $USERNAME -f $SERVICE > /dev/null then pre_log_len=`wc -l "$MCPATH/server.log" | awk '{print $1}'` echo "$SERVICE is running... executing command" as_user "screen -p 0 -S craftbukkit -X eval 'stuff \"$command\"\015'" sleep .1 # assumes that the command will run and print to the log file in less than .1 seconds # print output tail -n $[`wc -l "$MCPATH/server.log" | awk '{print $1}'`-$pre_log_len] "$MCPATH/server.log" fi } #Start-Stop here case "$1" in start) mc_start ;; stop) mc_stop ;; restart) mc_stop mc_start ;; save) mc_save ;; update) mc_stop mc_backup mc_update mc_start ;; scanplugins) mc_scanplugins ;; addplugin) mc_addplugin ;; backup) mc_backup ;; status) if pgrep -u $USERNAME -f $SERVICE > /dev/null then echo "$SERVICE is running." else echo "$SERVICE is not running." fi ;; command) if [ $# -gt 1 ]; then shift mc_command "$*" else echo "Must specify server command (try 'help'?)" fi ;; *) echo "Usage: $0 {start|stop|update|backup|status|restart|command \"server command\"}" exit 1 ;; esac exit 0

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  • Allow user to SUDO a script without password.

    - by John Isaacks
    I have a php script with this: <?php #echo exec('whoami'); $output = shell_exec('bash /usr/local/svn/bash_repo/make-live'); echo "$output"; ?> The make-live script contains this: #!/bin/bash cd /var/www-cake sudo svn checkout file:///usr/local/svn/bash_repo/repo/ echo "Head revision has been pushed to live server" So the PHP user who is www-data needs to have nopasswd for that script. I am told I need to add: www-data ALL=NOPASSWD: /usr/local/svn/bash_repo/make-live To sudoers to allow this. First I run sudo visudo but I have no experience with vi so I try to open it in gedit with export EDITOR=gedit && sudo -E visudo which then just opens a sudoers.tmp file which is empty. I add the line and save it. But it doesn't do save. So I just try sudo visudo and I add the line right beneath this part: # User privilege specification root ALL=(ALL) ALL www-data ALL=NOPASSWD: /usr/local/svn/bash_repo/make-live I closed out sudoers and reopened to verify that it has saved. I even restart apache. I run the php file and it still doesn't work. What am I missing?

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  • How do I source a shell script for Node Version Manager?

    - by Matthew Patrick Cashatt
    Hi and thanks for looking! I am new to Linux/Ubuntu, but I have set up an Ubuntu box on which to run Node.js. I have had moderate success, but now I need to be able to easily upgrade my version of Node. Many folks recommend using Node Version Manager. I followed the directions, but when I try to do something like this: nvm ls I get a messaging stating that No command NVM found I have gone back to check the steps I followed to install NVM, but there is one part that is tricky for may and I think to be the culprit: sourcing the file for bash. From the instructions: To activate nvm, you need to source it from your bash shell . ~/nvm/nvm.sh I always add this line to my ~/.bashrc or ~/.profile file to have it automatically sources upon login. Often I also put in a line to use a specific version of node. So which file should I add this to? I am guessing profile since it's ubuntu?? Also, where in the file do I add this line? After I have added this line, do I need to reboot or anything? Any help would be deeply appreciated--especially if you can show me an example profile file with . ~/nvm/nvm.sh integrated so that I can see usage. Thanks, Matt

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  • Autojump in 12.04 doesn't work

    - by hnasarat
    https://launchpad.net/ubuntu/+source/autojump I installed with apt-get, checked out the man page and added . /usr/share/autojump/autojump.sh to my .bashrc, like it says. When I cd around the filesystem, nothing gets added to ~/.local/share/autojump. I then tried adding . /usr/share/autojump/autojump.bash, but that didn't work either. autojump -a ~/Dropbox properly creates a file ~/.local/share/autojump/autojump.txt, but running j Drop < TAB > doesn't autocomplete to j ~/Dropbox/ as it should. However, j < TAB > does autocomplete to j ~/Dropbox. I know my bash-completion is working since it works for git, dd, and others. I know there's a newer version in the repositories set for Quantal. Perhaps that would work? I don't know how to install that version though. I've used autojump with mac homebrew (and it installed without any issue), so I know there is missing functionality. In general I'm really annoyed that I can't get this working...I've spent hours on it! Needless to say, help would be very appreciated.

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  • BASH statements execute alone but return "no such file" in for loop.

    - by reve_etrange
    Another one I can't find an answer for, and it feels like I've gone mad. I have a BASH script using a for loop to run a complex command (many protein sequence alignments) on a lot of files (~5000). The loop produces statements that will execute when given alone (i.e. copy-pasted from the error message to the command prompt), but which return "no such file or directory" inside the loop. Script below; there are actually several more arguments but this includes some representative ones and the file arguments. #!/bin/bash # Pass directory with targets as FASTA sequences as argument. # Arguments to psiblast # Common db=local/db/nr/nr outfile="/mnt/scratch/psi-blast" e=0.001 threads=8 itnum=5 pssm="/mnt/scratch/psi-blast/pssm." pssm_txt="/mnt/scratch/psi-blast/pssm." pseudo=0 pwa_inclusion=0.002 for i in ${1}/* do filename=$(basename $i) "local/ncbi-blast-2.2.23+/bin/psiblast\ -query ${i}\ -db $db\ -out ${outfile}/${filename}.out\ -evalue $e\ -num_threads $threads\ -num_iterations $itnum\ -out_pssm ${pssm}$filename\ -out_ascii_pssm ${pssm_txt}${filename}.txt\ -pseudocount $pseudo\ -inclusion_ethresh $pwa_inclusion" done Running this scripts gives "<scriptname> line <last line before 'done'>: <attempted command> : No such file or directory. If I then paste the attempted command onto the prompt it will run. Each of these commands takes a couple of minutes to run.

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  • How do I delete folders in bash after successful copy (Mac OSX)?

    - by cohortq
    Hello! I recently created my first bash script, and I am having problems perfecting it's operation. I am trying to copy certain folders from one local drive, to a network drive. I am having the problem of deleting folders once they are copied over, well and also really verifying that they were copied over). Is there a better way to try to delete folders after rsync is done copying? I was trying to exclude the live tv buffer folder, but really, I can blow it away without consequence if need be. Any help would be great! thanks! #!/bin/bash network="CBS" useracct="tvcapture" thedate=$(date "+%m%d%Y") folderToBeMoved="/users/$useracct/Documents" newfoldername="/Volumes/Media/TV/$network/$thedate" ECHO "Network is $network" ECHO "date is $thedate" ECHO "source is $folderToBeMoved" ECHO "dest is $newfoldername" mkdir $newfoldername rsync -av $folderToBeMoved/"EyeTV Archive"/*.eyetv $newfoldername --exclude="Live TV Buffer.eyetv" # this fails when there is more than one *.eyetv folder if [ -d $newfoldername/*.eyetv ]; then #this deletes the contents of the directories find $folderToBeMoved/"EyeTV Archive"/*.eyetv \( ! -path $folderToBeMoved/"EyeTV Archive"/"Live TV Buffer.eyetv" \) -delete #remove empty directory find $folderToBeMoved/"EyeTV Archive"/*.eyetv -type d -exec rmdir {} \; fi

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  • How To Run A Shell Script Again And Again Having X Interval Of Time?

    - by Muhammad Hassan
    I have a shell script in my Ubuntu Server 14.04 LTS at ./ShellScript.sh. I setup /etc/rc.local to run the shell script after boot but before login using below code. Run this: sudo nano /etc/rc.local then add following and save. #!/bin/sh -e # # rc.local # # This script is executed at the end of each multiuser runlevel. # Make sure that the script will "exit 0" on success or any other # value on error. # # In order to enable or disable this script just change the execution # bits. # # By default this script does nothing. #!/bin/bash ./ShellScript.sh exit 0 Now I want to run/execute this shell script again and again having 15min of time interval between every run after boot but before login. So Can I do it? Update 1:) When I run crontab -e then I got the following. Now What to do? no crontab for root - using an empty one Select an editor. To change later, run 'select-editor'. 1. /bin/ed 2. /bin/nano <---- easiest 3. /usr/bin/vim.basic 4. /usr/bin/vim.tiny Choose 1-4 [2]: After selecting 2, I got crontab: "/usr/bin/sensible-editor" exited with status 2 UPDATE 2:) Update ShellScript.sh like below... #!/bin/bash # Testing ShellScript... while true do echo "ShellScript Start Running..." ********************************** All My Shell Script Codes/Script/Commands ********************************** echo "ShellScript End Running..." exit 0 sleep 900 done Then Run this: sudo nano /etc/rc.local then add following and save. #!/bin/sh -e # # rc.local # # This script is executed at the end of each multiuser runlevel. # Make sure that the script will "exit 0" on success or any other # value on error. # # In order to enable or disable this script just change the execution # bits. # # By default this script does nothing. sh ./ShellScript.sh & exit 0

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  • First 10 programs in a new scripting languge

    - by pro_metedor
    When a peron is learning a new scripting language like: bash python perl pike What kind of simple (yet practical) problem solutions to get through to make say that a person is comprehend with this scripting language enough to approach some complex yet still practical problems encountered in everyday job. In other words, which problems would you give that person to solve to make sure that he/she is familiar with the scripting language.

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