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#!/bin/zsh -f # txtgrep: grep only text files command grep -in "$1" `file "${2}"/* | egrep 'script|text' | awk -F: '{print $1}'`;
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#!/bin/zsh -f # sgrep: grep the output of set set | grep -i --binary-files=text "$1"
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#!/bin/zsh -f # prompt_simple_setup # Create a simple minimal prompt (eg: zsh-%), and put the other usual stuff # into the title bar (and if availble) the $PWD and penultimate directory # in the tab. Also enable transient display of a running command (eg vim). # Currently works with iTerm (OSX) and konsole (KDE)...
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#!/bin/zsh -f command ls $* | xargs -n 1 tar -zxvf
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#!/bin/zsh -f # whichre: search for commands using regular expressions command echo $PATH | awk 'BEGIN{ RS = ":" } { print }' | xargs ls | grep "$1";
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#!/bin/zsh -f # # Function to invoke sudo vim with a .vimrc file if it is needed to edit a protected file # # set -x # uncomment to debug version="2.0.1" ############################################################################### function resetter { # re-initialize everything: unset i binplistfile="" o...
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#!/bin/zsh -f # invoke tidy to do in-place cleanup and conversion to xhtml if [[ "$@":e == xml ]];then command tidy -m -xml "$@" else command tidy -m -asxml "$@" fi
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#!/bin/zsh -f # Created by William Scott on 2007-05-03. # Copyright (c) 2007. All rights reserved. version="0.0.2" # set -x # depfinder # Look at the contents of a debian package and find the dependencies. ############################################################################### # Created by on . # ...
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#!/bin/zsh -f # locwd: locate files that match exactly function locwd { locate "*/${@}"; }
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#!/bin/zsh -f # ppath: list the Perl #INC path perl -e 'print map "$_\n", @INC'
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#!/bin/zsh -f # Bug: I can't get this to work for directories with spaces. # cd $_ will work fine for those cases. # Execute cd "$(dirname $_)" if $_ is a file # Execute cd "$_" if $_ is a directory # or, more generally, get the numbered string position in the last line and cd to it (or it's directory) # eg: # l...
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#!/bin/zsh -f # dotgrep: grep through invisible files for arguments command ls -A1 | sed -n '/^\./p' | xargs -n1 grep -iInH "$1";
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#!/bin/zsh -f command osascript -e 'open location "$1"'
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#!/bin/zsh -f # Make an image file transparent, saving a backup. if [[ $(which convert) == *not\ found* ]];then print "Cannot find ImageMagick convert command" return 1 fi foreach imagefile in "$@" cp $imagefile $imagefile.bak convert -transparent white $imagefile /tmp/$imagefile cp /tmp/$image...
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#!/bin/zsh -f # find duplicate files on specified directory tree # Author: Karl Zimmerman osize=0 osum=0 ofile="" newFile () { osum="${1}" osize="${2}" ofile="${3}" } find "${1}" -type f -exec sum {} \; 2>/dev/null | sort | while read sum size file; do [ ${osize} != ${size} ] && newFile ${su...
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#!/bin/zsh -f command ps -auxww | command grep -i "${1}" | command grep -v "[p ]grep"
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#!/bin/zsh # Make a namot output pdb file not suck so much # Requires cns, fix_dna_rna (from cns) and pdbset (from ccp4) to be in the path. # You might need to alias cns_solve to cns or change the script. # I ask to invoke pymol (which I have as a zsh function) at the end to look at this. # Change it to your favorite...
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#!/bin/zsh -f # There is a bug in OS X x-windows that interferes with xdlmapman and xdldataman. # The pop-up frameless window that permits you to select map or data format does # not appear unless you first iconify the major display window. This is always # tedious and sometimes everything freezes. This shell script...
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#!/bin/zsh -f if [[ -z $(which rwcontents) ]];then print "rwcontents, which is part of CCP4, is not in your $PATH" fi command rwcontents XYZIN $1 << eof | grep -v Matched >| /tmp/rwcontents_tmp.html eof command open /tmp/rwcontents_tmp.html command rm -i /tmp/rwcontents_tmp.html
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#!/bin/zsh -f # To avoid possible recursions: alias cns=""; unalias cns # set -x ####################################### # CNS 1.2 obtained from David Gohara # # <http://gohara.wustl.edu/software.html> ####################################### if [[ -d $CNS_SOLVE/mac-intel-darwin/bin && ($(uname) == Darwin ...
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#!/bin/zsh -f # version="0.5" ## sca2mtz.zsh print "#####################################################################################################" print "" print " This script will process the sca file output from SCALEPACK using CCP4 programs" print " including truncate, uniquify, and (optionally) mtz2va...
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#!/usr/bin/zsh -f #set -x # Things that can be changed: VERSION="6.0.1" PATCHDIR="/Users/${USER}/src/ccp4/${VERSION}-patches" # You shouldn't need to change these, but might want to: URL="ftp://ftp.ccp4.ac.uk/ccp4/${VERSION}/patches/" DOTDIR="/Users/${USER}/.ccp4patches" if [[ ! -d ${PATCHDIR} ]]; then print "C...
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#!/bin/zsh -f if [[ -z $CCP4_BROWSER && $(uname) == Darwin ]];then CCP4_BROWSER='open' fi if [[ -z $CCP4_BROWSER ]];then CCP4_BROWSER=$MOZILLA fi if [[ -z $CCP4_BROWSER ]];then CCP4_BROWSER='mozilla' fi if [[ -z $CCP4_BROWSER ]];then CCP4_BROW...
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#!/bin/zsh -f if [[ -z $CCP4 || ! -d $CCP4 ]];then print "CCP4 is either not present or the enviornment has not been set up" return 1 fi # Make a map to cover the molecule from refmac output refmac_prefix=$1 if [[ $# != 1 ]];then print "Usage: $0 refmac_output_filename_prefix" return 10 fi if [[ ...
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#!/bin/zsh -f #set -x # For 0.6-pre-1 (revision 2170) # This is a zsh shell script or function that augments the coot command line # experience. Just type "coot" followed by the names of your pdb files, map files, # mtz files and so on. If you have the unix program screen, it starts coot in a # screen session, wh...
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#!/bin/zsh -f if [[ -z $CCP4 || ! -d $CCP4 ]];then print "CCP4 is either not present or the enviornment has not been set up" return 1 fi # Make a map to cover the molecule from refmac output refmac_prefix=$1 if [[ $# != 1 ]];then print "Usage: $0 refmac_output_filename_prefix" return 10 fi if [[ ...
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#!/bin/zsh -f # Feb 3rd, 2006 # Use an x-11-based browser when logged in remotely via ssh # Use an OS X-based browser (or not) when using the OS X GUI interface locally. # set -x # Uncomment to debug if [[ -n $SSH_TTY ]];then use_xbrowser='true' if [[ -n $CNS_REMOTE_BROWSER ]];then CNS_BROWS...
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#!/bin/zsh -f # There is a bug in OS X x-windows that interferes with xdlmapman and xdldataman. # The pop-up frameless window that permits you to select map or data format does # not appear unless you first iconify the major display window. This is always # tedious and sometimes everything freezes. This shell script...
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#!/bin/zsh -f if [[ -z $(which rwcontents) ]];then print "rwcontents, which is part of CCP4, is not in your $PATH" fi command rwcontents XYZIN $1 << eof | grep -v Matched >| /tmp/rwcontents_tmp.html eof command open /tmp/rwcontents_tmp.html command rm -i /tmp/rwcontents_tmp.html
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#!/bin/zsh -f # There is a bug in OS X x-windows that interferes with xdlmapman and xdldataman. # The pop-up frameless window that permits you to select map or data format does # not appear unless you first iconify the major display window. This is always # tedious and sometimes everything freezes. This shell script...
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#!/bin/zsh -f # Feb 3rd, 2006 # Use an x-11-based browser when logged in remotely via ssh # Use an OS X-based browser (or not) when using the OS X GUI interface locally. # set -x # Uncomment to debug if [[ -n $SSH_TTY ]];then use_xbrowser='true' if [[ -n $CNS_REMOTE_BROWSER ]];then CNS_BROWSER=( $...
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#!/bin/zsh # Make a namot output pdb file not suck so much # Requires cns, fix_dna_rna (from cns) and pdbset (from ccp4) to be in the path. # You might need to alias cns_solve to cns or change the script. # I ask to invoke pymol (which I have as a zsh function) at the end to look at this. # Change it to your favorite...
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#!/bin/zsh -f if [[ ! -x $(which composite) ]];then print "You need to install ImageMagick and have it in your $PATH" return 1 fi # overlay two pdf files and produce a composite in which one file is red and the other is blue. if [[ $# == 3 ]];then composite -density 300x300 -compose copyred "$@" ope...
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#!/bin/zsh -f # set -x # This script will automatically download the USF OS X programs and install them in the directory INSTALLUSFDIR=/usr/local/usf # (change this to /usr/local/xtal/usf or whatever suits you) # If you manually download the USF program binaries for OS X and put them in $INSTALLUSFDIR , # this sc...
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#!/bin/zsh -f # set -x # uncomment to de-bug version="0.5" ## mos2fobs.zsh date_time_stamp="$( command date +'%Y-%m-%d-%H%M' )" print "#####################################################################################################" print "" print " This script will process the mtz file output from mos...
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#!/bin/zsh -f # There is a bug in OS X x-windows that interferes with xdlmapman and xdldataman. # The pop-up frameless window that permits you to select map or data format does # not appear unless you first iconify the major display window. This is always # tedious and sometimes everything freezes. This shell script...
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#!/usr/bin/zsh -f #set -x # Things that can be changed: VERSION="6.0.1" PATCHDIR="/Users/${USER}/src/ccp4/${VERSION}-patches" # You shouldn't need to change these, but might want to: URL="ftp://ftp.ccp4.ac.uk/ccp4/${VERSION}/patches/" DOTDIR="/Users/${USER}/.ccp4patches" if [[ ! -d ${PATCHDIR} ]]; then print "C...
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#!/bin/sh # Fix local nucleic acid pdb files to agree with PDB standards perl -pi -e 's/ADE/A /g' $1 perl -pi -e 's/URA/U /g' $1 perl -pi -e 's/URI/U /g' $1 perl -pi -e 's/GUA/G /g' $1 perl -pi -e 's/CYT/C /g' $1 perl -pi -e 's/THY/T /g' $1 perl -pi -e s/\'/\*/g $1 perl -pi -e 's/(\s\s\s)([CNO]\d\s)/\ \...
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#!/bin/zsh -f # # function ono to be run from Terminal or iTerm or xterm on OS X. Returns the # focus to the terminal window after the program is launched. # ono is run as a screen job so that it can be detached (backgrounded) with control-A d # and resumed with screen -r # The background sub-process returns focus ...
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#!/bin/zsh -f # To avoid possible recursions: alias cns=""; unalias cns # set -x ####################################### # CNS 1.2 obtained from David Gohara # # <http://gohara.wustl.edu/software.html> ####################################### if [[ -d $CNS_SOLVE/mac-intel-darwin/bin && ($(uname) == Darwin ...
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#!/bin/zsh -f # version="0.5" ## sca2mtz.zsh print "#####################################################################################################" print "" print " This script will process the sca file output from SCALEPACK using CCP4 programs" print " including truncate, uniquify, and (optionally) mtz2va...
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#!/bin/zsh -f if [[ -z $CCP4 || ! -d $CCP4 ]];then print "CCP4 is either not present or the enviornment has not been set up" return 1 fi # Make a map to cover the molecule from refmac output refmac_prefix=$1 if [[ $# != 1 ]];then print "Usage: $0 refmac_output_filename_prefix" return 10 fi if [[ ...
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#!/bin/zsh -f if [[ -z $(which rwcontents) ]];then print "rwcontents, which is part of CCP4, is not in your $PATH" fi command rwcontents XYZIN $1 << eof | grep -v Matched >| /tmp/rwcontents_tmp.html eof command open /tmp/rwcontents_tmp.html command rm -i /tmp/rwcontents_tmp.html
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#!/bin/zsh -f #set -x # For 0.6-pre-1 (revision 2170) # This is a zsh shell script or function that augments the coot command line # experience. Just type "coot" followed by the names of your pdb files, map files, # mtz files and so on. If you have the unix program screen, it starts coot in a # screen session, wh...
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#!/bin/zsh -f ################################################################################# # # # getpdb -- function to download a pdb file and display it in the default # # pdb display program (chosen with GetInfo comm...
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#!/bin/zsh -f if [[ -z $CCP4_BROWSER && $(uname) == Darwin ]];then CCP4_BROWSER='open' fi if [[ -z $CCP4_BROWSER ]];then CCP4_BROWSER=$MOZILLA fi if [[ -z $CCP4_BROWSER ]];then CCP4_BROWSER='mozilla' fi if [[ -z $CCP4_BROWSER ]];then CCP4_BROW...
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#!/bin/zsh -f getargs=("$@") if [[ -x /usr/bin/mdfind ]];then pymolprefix=($( mdfind MacPyMOL | grep MacPyMOL.app | head -n 1 )) else pymolprefix=($( locate MacPyMOL.app | head -n 1 )) fi if [[ -x $pymolprefix/Contents/MacOS/PyMOL ]];then pymolexec=($pymolprefix/Contents/MacOS/PyMOL) elif [[ -x $pymolpre...
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#!/bin/zsh -f # Feb 3rd, 2006 # Use an x-11-based browser when logged in remotely via ssh # Use an OS X-based browser (or not) when using the OS X GUI interface locally. # set -x # Uncomment to debug if [[ -n $SSH_TTY ]];then use_xbrowser='true' if [[ -n $CNS_REMOTE_BROWSER ]];then CNS_BROWS...
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#!/bin/zsh -f if [[ -z $CCP4 || ! -d $CCP4 ]];then print "CCP4 is either not present or the enviornment has not been set up" return 1 fi # Make a map to cover the molecule from refmac output refmac_prefix=$1 if [[ $# != 1 ]];then print "Usage: $0 refmac_output_filename_prefix" return 10 fi if [[ ...
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#!/bin/zsh -f if [[ -z $(which rwcontents) ]];then print "rwcontents, which is part of CCP4, is not in your $PATH" fi command rwcontents XYZIN $1 << eof | grep -v Matched >| /tmp/rwcontents_tmp.html eof command open /tmp/rwcontents_tmp.html command rm -i /tmp/rwcontents_tmp.html
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#!/bin/zsh -f # set -x # uncomment to de-bug version="0.5" ## mos2fobs.zsh date_time_stamp="$( command date +'%Y-%m-%d-%H%M' )" print "#####################################################################################################" print "" print " This script will process the mtz file output from mos...
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#!/bin/zsh -f # Feb 3rd, 2006 # Use an x-11-based browser when logged in remotely via ssh # Use an OS X-based browser (or not) when using the OS X GUI interface locally. # set -x # Uncomment to debug if [[ -n $SSH_TTY ]];then use_xbrowser='true' if [[ -n $CNS_REMOTE_BROWSER ]];then CNS_BROWSER=( $...
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#!/bin/zsh -f getargs=("$@") if [[ -x /usr/bin/mdfind ]];then pymolprefix=($( mdfind MacPyMOL | grep MacPyMOL.app | head -n 1 )) else pymolprefix=($( locate MacPyMOL.app | head -n 1 )) fi if [[ -x $pymolprefix/Contents/MacOS/PyMOL ]];then pymolexec=($pymolprefix/Contents/MacOS/PyMOL) elif [[ -x $pymolpre...
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#!/bin/zsh -f if [[ ! -x $(which composite) ]];then print "You need to install ImageMagick and have it in your $PATH" return 1 fi # overlay two pdf files and produce a composite in which one file is red and the other is blue. if [[ $# == 3 ]];then composite -density 300x300 -compose copyred "$@" ope...
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#!/bin/zsh -f # set -x # This script will automatically download the USF OS X programs and install them in the directory INSTALLUSFDIR=/usr/local/usf # (change this to /usr/local/xtal/usf or whatever suits you) # If you manually download the USF program binaries for OS X and put them in $INSTALLUSFDIR , # this sc...
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#!/bin/sh # Fix local nucleic acid pdb files to agree with PDB standards perl -pi -e 's/ADE/A /g' $1 perl -pi -e 's/URA/U /g' $1 perl -pi -e 's/URI/U /g' $1 perl -pi -e 's/GUA/G /g' $1 perl -pi -e 's/CYT/C /g' $1 perl -pi -e 's/THY/T /g' $1 perl -pi -e s/\'/\*/g $1 perl -pi -e 's/(\s\s\s)([CNO]\d\s)/\ \...
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#!/bin/zsh -f # # function ono to be run from Terminal or iTerm or xterm on OS X. Returns the # focus to the terminal window after the program is launched. # ono is run as a screen job so that it can be detached (backgrounded) with control-A d # and resumed with screen -r # The background sub-process returns focus ...
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#!/bin/zsh -f ################################################################################# # # # getpdb -- function to download a pdb file and display it in the default # # pdb display program (chosen with GetInfo comm...
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#!/bin/zsh -f # Force 'sudo zsh' to start root as a loging shell to # avoid problems with environment clashes: function sudo { if [[ $# == 1 && $1 = "zsh" ]]; then command sudo /bin/zsh -l else command sudo "$@" fi }
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#!/bin/zsh -f command man -M /usr/share/man "$@";
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#!/bin/zsh -f # bbown: recursively change file type to BBEdit text command find "$@" -type f -exec SetFile -c "R*ch" -t TEXT {} \; ;
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#!/bin/zsh -f # Function man # Requires the zsh function run-help and /usr/bin/info or /sw/bin/info # as well as the command man. I had to fix up a few things in run-help # so be sure to autoload my corrected version that handles multiple # $HELPDIR entries and also gives usable error codes. These features # are req...
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#!/bin/zsh -f command ls -AFlgh "$@" | less
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#!/bin/zsh -f command ls -AFlgh "$@" | less
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#!/bin/zsh -f # Function man # Requires the zsh function run-help and /usr/bin/info or /sw/bin/info # as well as the command man. I had to fix up a few things in run-help # so be sure to autoload my corrected version that handles multiple # $HELPDIR entries and also gives usable error codes. These features # are req...
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#!/bin/zsh -f # Force 'sudo zsh' to start root as a loging shell to # avoid problems with environment clashes: function sudo { if [[ $# == 1 && $1 = "zsh" ]]; then command sudo /bin/zsh -l else command sudo "$@" fi }
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#!/bin/zsh -f # ldot: list <dot>files if [ -n "$1" ]; then command ls -AFlhd "$1"/\.[^\.]*; else command ls -AFlhd \.[^\.]*; fi
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#!/bin/zsh -f function turnOffMailboxRule { echo "starting at `date`" osascript <<-EOF1 --tell application "Finder" -- activate -- activate "Mail" tell application "Mail" activate activate rules set enabled of rule "makemailbox" to false -- end tell end tell EOF1 print "turned off makemailbox rule at `date`" } ...
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#!/bin/zsh -f command man -M /usr/share/man "$@";
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#!/bin/zsh -f command ls -AFlh "$1" | sort -ib -k 1.1,1.2r -k 9i # old version: #command ls -lh ${*} | egrep "^d"; ls -lh $* 2>&-| egrep -v "^d|total "
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#!/bin/zsh -f # bbown: recursively change file type to BBEdit text command find "$@" -type f -exec SetFile -c "R*ch" -t TEXT {} \; ;
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#!/bin/zsh -f command ls -AFlh "$1" | sort -ib -k 1.1,1.2r -k 9i # old version: #command ls -lh ${*} | egrep "^d"; ls -lh $* 2>&-| egrep -v "^d|total "
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#!/bin/zsh -f function turnOffMailboxRule { echo "starting at `date`" osascript <<-EOF1 --tell application "Finder" -- activate -- activate "Mail" tell application "Mail" activate activate rules set enabled of rule "makemailbox" to false -- end tell end tell EOF1 print "turned off makemailbox rule at `date`" } ...
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#!/bin/zsh -f # ldot: list <dot>files if [ -n "$1" ]; then command ls -AFlhd "$1"/\.[^\.]*; else command ls -AFlhd \.[^\.]*; fi
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#!/bin/zsh -f # shell script name: nyquist.zsh # Use iTunes interace to play selected tracks in Decibel, a shareware # audiophile music player application that properly adjusts the sampling # frequency automatically. The main utility of this hack is it allows one # to use Apple's iPod/iPad/iPhone Remote.app to ini...
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#!/bin/zsh -f /Library/iTunes/etc/nyquist.zsh & return 0
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#!/bin/zsh -f # shell script name: nyquist.zsh # Use iTunes interace to play selected tracks in Decibel, a shareware # audiophile music player application that properly adjusts the sampling # frequency automatically. The main utility of this hack is it allows one # to use Apple's iPod/iPad/iPhone Remote.app to ini...
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#!/bin/zsh -f true return 0
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#!/bin/zsh -f # shell script name: nyquist.zsh # Use iTunes interace to play selected tracks in Decibel, a shareware # audiophile music player application that properly adjusts the sampling # frequency automatically. The main utility of this hack is it allows one # to use Apple's iPod/iPad/iPhone Remote.app to ini...
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#!/bin/zsh -f /Library/iTunes/etc/nyquist.zsh & return 0
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#!/bin/zsh -f true return 0
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#!/bin/zsh -f true return 0
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#!/bin/zsh -f # shell script name: nyquist.zsh # Use iTunes inteface to play selected tracks in Audirvana, an open-source # audiophile music player application that properly adjusts the sampling # frequency automatically. The main utility of this hack is it allows one # to use Apple's iPod/iPad/iPhone Remote.app t...
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#!/bin/zsh -f # shell script name: nyquist.zsh # Use iTunes inteface to play selected tracks in Audirvana, an open-source # audiophile music player application that properly adjusts the sampling # frequency automatically. The main utility of this hack is it allows one # to use Apple's iPod/iPad/iPhone Remote.app t...
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#!/bin/zsh -f # shell script name: nyquist.zsh # Use iTunes interace to play selected tracks in Decibel, a shareware # audiophile music player application that properly adjusts the sampling # frequency automatically. The main utility of this hack is it allows one # to use Apple's iPod/iPad/iPhone Remote.app to ini...
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#!/bin/zsh -f # shell script name: nyquist.zsh # Use iTunes inteface to play selected tracks in Audirvana, an open-source # audiophile music player application that properly adjusts the sampling # frequency automatically. The main utility of this hack is it allows one # to use Apple's iPod/iPad/iPhone Remote.app t...
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#!/bin/zsh -f true return 0
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#!/bin/zsh -f # shell script name: nyquist.zsh # Use iTunes inteface to play selected tracks in Audirvana, an open-source # audiophile music player application that properly adjusts the sampling # frequency automatically. The main utility of this hack is it allows one # to use Apple's iPod/iPad/iPhone Remote.app t...
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################################################# ################################################# # # # $ZDOT/zshrc.d/aliases.main.zsh # # # #####################...
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############################################################################## #################### Define $ZDOT_USER ###################### ############################################################################## if [[ $(uname) == Darwin ]];then ZDOT_USER="$HOME/Library/init/zsh" ...
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################################################################## ################################################################## # # # $ZDOT/zshrc.d/environment.keybindings.zshall.zsh # #...
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################################################# ################################################# # # # 001_path_env # # ...
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################################################# ################################################# # # # $ZDOT/zshrc.d/functions.distributed.zsh # # # ...
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# Disable this file by renaming it to macports_env.disabled # Change the absolute path if you have installed in a non-standard location. if [[ -d /opt/local/sbin ]];then PATH=/opt/local/sbin:${PATH} export PATH fi if [[ -d /opt/local/bin ]];then PATH=/opt/local/bin:${PATH} export PATH fi
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################################################################### ################################################################### #### Login Message ###### ################################################################### ###############################################...
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################################################################## ################################################################## # # # $ZDOT/zshrc.d/environment.keybindings.emacs.zsh # # ...
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# File environment.variables.additional.zsh # Add system-specific environment and path variables to this file ################################################################### #### First stuff for all sessions (even non-interactive) ###### ###################################################################...
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################################################# ################################################# # # # environment.x11.oldsetup.zsh # # # ################################################# ...
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################################################# ################################################# # # # $ZDOT/zshrc.d/environment.options.zsh # # # #############...
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################################################# ################################################# # # # $ZDOT/zshrc.d/aliases.additional.zsh # # # ####################...
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