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264 lines
10 KiB
Bash
264 lines
10 KiB
Bash
#!/bin/bash
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## Process *.Rnw files
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## Written May 14, 2010
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## Taha Ahmed
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####################################################
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# For now, MAKE SURE that the argument consists of
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# a complete filename, with extension, and
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# in the directory of the Rnw file
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####################################################
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clear
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echo "---------------------------------------------------------------"
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echo "cheRTeX -- a script for processing R-Sweave-LaTeX-TikZ projects"
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echo "^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^"
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echo "MMX -- taha.ahmed@mkem.uu.se -- CHEPEC doctoral degree project"
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echo "---------------------------------------------------------------"
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## If the file .latexmkrc exists in the current directory,
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## set the flag ltxmkrc=TRUE
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ltxmkrc=false
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echo "--- Looking for .latexmkrc"
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if [ -e .latexmkrc ]; then
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ltxmkrc=true
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echo "+++ LaTeXMK RC file invoked"
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else
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echo "--- This job did not request LaTeXMK RC file"
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fi
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Rfiletype="R"
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TeXfiletype="tex"
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tikzfiles="*.tikz"
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Rnwfiles="*.Rnw"
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auxfiles="*.aux *.bbl *.bcf *.blg *.fdb* *.figlist *.fls *.lof *.log *.lot *.lox *.makefile *.map *.out *.run* *.tdo *.toc *.dep *.dpth"
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if [ $# -eq 1 ]; then
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# Check if the argument contains a filetype
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# Assumes a complete filename was passed
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jobfilename=$1
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jobfiletype=${jobfilename#*.} # File extension
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jobname=${jobfilename%.*} # Filename without extension part
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echo "<cheRTeX> Detected filename: " $jobname
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echo "<cheRTeX> Detected extension:" $jobfiletype
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# Verifying that the file extension is *.Rnw
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if [[ $jobfiletype == "Rnw" || $jobfiletype == "rnw" || $jobfiletype == "RNW" ]]; then
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# File extension is *.Rnw
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echo "<cheRTeX> Detected *.Rnw extension"
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jobfiletype="Rnw"
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else
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# File extension is not *.Rnw
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echo "<cheRTeX> File extension should be *.Rnw"
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echo "<cheRTeX> Terminating..."
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exit 1
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fi
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# Introducing a short delay to enable on-screen reading of previous echo
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/home/taha/chepec/chetex/common/bash/simpledelay.sh 2
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echo "Delay completed"
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## Handle knitr or pgfSweave jobs separately
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## But how should we tell the difference between them?
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## There is no obvious way to tell the difference (apart from reading the *.Rnw file)
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## IN ALL KNITR DIRECTORIES, CREATE A FILE NAMED: .knitme
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# If the file .knitme exists in the current directory,
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# run knitr commands, otherwise run pgfsweave commands
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echo "--- Looking for .knitme"
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if [ -e .knitme ]; then
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# Run knitr commands for this job
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echo "<cheRTeX> -----------------------"
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echo "<cheRTeX> This is a job for knitr"
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echo "<cheRTeX> -----------------------"
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# Knit
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echo "<cheRTeX> Knitting..."
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Rscript -e "library(knitr); library(methods); knit('$jobname.$jobfiletype')"
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# Introduce delay to give time to read Rscript exit status
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echo "<cheRTeX> -----------------------"
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echo "<cheRTeX> Rscript knitr completed"
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echo "<cheRTeX> -----------------------"
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/home/taha/chepec/chetex/common/bash/simpledelay.sh 4
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else
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# Run pgfSweave commands
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echo "<cheRTeX> ---------------------------"
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echo "<cheRTeX> This is a job for pgfSweave"
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echo "<cheRTeX> ---------------------------"
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# Tangle
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echo "<cheRTeX> Tangling..."
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R CMD Stangle $jobname.$jobfiletype
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# Weave
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echo "<cheRTeX> Weaving..."
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R CMD pgfsweave --graphics-only $jobname.$jobfiletype
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# Introduce delay to give time to read R CMD exit status
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echo "<cheRTeX> -------------------------"
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echo "<cheRTeX> R CMD pgfsweave completed"
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echo "<cheRTeX> -------------------------"
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/home/taha/chepec/chetex/common/bash/simpledelay.sh 4
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fi
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# Run vc script if vc exists in working directory
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echo "<cheRTeX> Running vc script"
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if [ -f vc ]; then
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./vc
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fi
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# Run pdflatex, bibtex, and company
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if $ltxmkrc; then
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echo "<cheRTeX> Calling LaTeXMK with RC file"
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/home/taha/chepec/chetex/common/bash/simpledelay.sh 2
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latexmk -r .latexmkrc -pdf -bibtex $jobname
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else
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echo "<cheRTeX> Calling LaTeXMK"
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/home/taha/chepec/chetex/common/bash/simpledelay.sh 2
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latexmk -pdf -bibtex $jobname
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fi
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## THIS IS A QUICK-AND-DIRTY FIX FOR SAMPLE-MATRIX
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# If $jobname is sample-matrix, run knitr and markdown
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if [[ $jobname == "sample-matrix" ]]; then
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echo "<cheRTeX> -----------------------------------------------------------"
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echo "<cheRTeX> sample-matrix detected: running knit() and markdownToHTML()"
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echo "<cheRTeX> -----------------------------------------------------------"
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Rscript -e "library(knitr); knit(input='$jobname.Rmd', output='$jobname.md')"
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Rscript -e "library(markdown); markdownToHTML('$jobname.md', '$jobname.html', stylesheet = 'custom.css')"
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fi
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else
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# Either no arguments, or more than one argument
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if [ $# -eq 0 ]; then
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# Zero arguments. Present a menu of choices
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echo "This is cheRTeX POST-PROCESSING" # only one choice for now
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echo "<1> 'pdf-all' -- Process all .tikz files to pdf graphics"
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echo "<2> 'clean-up' -- Remove all auxiliary files"
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echo "<3> 'wipe-dir' -- Remove all non-essential files and subdirectories"
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echo "Any other input exits the program"
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read usrchoice
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## Determine number of .Rnw files in current directory
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#Rnwfileno=$(ls -1 $Rnwfiles | wc -l)
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#echo "No of .Rnw files: $Rnwfileno"
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#
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## Check if number of .Rnw files larger than one
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#if [ $Rnwfileno -gt 1 ]; then
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# # If larger than one, ask for user input
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# # Indicates more than one Rnw file in current directory.
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# # This introduces a naming ambiguity.
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# # Resolve by asking user for current jobname
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# echo "Found $Rnwfileno .Rnw files in current directory"
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# echo "Please specify the jobname"
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# read jobname
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# if [ -z "$jobname" ]; then
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# # string is null
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# echo "Specified jobname cannot be parsed. Terminating..."
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# exit 1
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# fi
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#else
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# # There is exactly one *.Rnw file is current directory
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# # Fetch the jobname from the .Rnw filename by stripping off the file extension
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# Rnwfilename=$(ls -1 $Rnwfiles)
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# jobname=${Rnwfilename%.*}
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#fi
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#
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#echo "Jobname set to: $jobname"
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if [[ $usrchoice == "pdf-all" || $usrchoice == "1" ]]; then
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echo "<1> 'pdf-all' chosen"
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# This for loop ONLY USED to determine number of *.tikz files in directory
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for tikzfiles in "$tikzfiles"; do tikzfilenumber=${#tikzfiles}; done
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echo "cheRTeX detected $tikzfilenumber TikZ files for processing"
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echo "Starting TikZ file processing..."
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/home/taha/chepec/chetex/common/bash/simpledelay.sh 2
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for tikzfilename in $tikzfiles; do
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# Call tikz2pdf
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echo "<Executing> tikz2pdf $tikzfilename"
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tikz2pdf --once $tikzfilename
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done
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echo "Completed TikZ file processing"
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fi
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if [[ $usrchoice == "clean-up" || $usrchoice == "2" ]]; then
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echo "<2> 'clean-up' chosen"
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rm $auxfiles
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# Still, a rather crude way of cleaning up...
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fi
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if [[ $usrchoice == "wipe-dir" || $usrchoice == "3" ]]; then
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echo "<3> 'wipe-dir' chosen"
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## Remove all but non-essential files
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# get the name of the current directory
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currdirname=${PWD##*/}
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# get a timestamp
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timestamp=$(date +%s)
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# create a unique tmp-dir name
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tmpdirname="${timestamp}-${currdirname}"
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# make a directory in chepec/tmp with the name of the current dir
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mkdir /home/taha/chepec/tmp/$tmpdirname
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# Copy the contents of the current directory to the tmp/$currdirname directory
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cp * -R /home/taha/chepec/tmp/$tmpdirname
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# Empty the current directory of all contents
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rm * -R # note: hidden files and subdir unaffected
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# Return the stuff we want to keep after wipe-dir
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# (we are of course assuming that the following 4 file(type)s always exist)
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# (if in fact they do not exist, use conditional statements instead (see below)
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cp /home/taha/chepec/tmp/$tmpdirname/*.Rnw .
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cp /home/taha/chepec/tmp/$tmpdirname/vc .
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cp /home/taha/chepec/tmp/$tmpdirname/vc.tex .
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cp /home/taha/chepec/tmp/$tmpdirname/vc-git.awk .
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## Return stuff that may not always exist (check first...)
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## The use of conditionals is mainly to avoid annoying "file does not exist" messages...
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# Return *.Rproj file (removal is unnecessary and makes RStudio less useful)
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Rprojfiles=`ls -1 /home/taha/chepec/tmp/$tmpdirname/*.Rproj 2>/dev/null | wc -l`
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if [ $Rprojfiles != 0 ]; then
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cp /home/taha/chepec/tmp/$tmpdirname/*.Rproj .
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fi
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# Return *.rda files (considering peak-data files, which "cost" a lot to create)
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rdafiles=`ls -1 /home/taha/chepec/tmp/$tmpdirname/*.rda 2>/dev/null | wc -l`
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if [ $rdafiles != 0 ]; then
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cp /home/taha/chepec/tmp/$tmpdirname/*.rda .
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fi
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# Return *.Rmd files (R markdown source files)
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Rmdfiles=`ls -1 /home/taha/chepec/tmp/$tmpdirname/*.Rmd 2>/dev/null | wc -l`
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if [ $Rmdfiles != 0 ]; then
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cp /home/taha/chepec/tmp/$tmpdirname/*.Rmd .
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fi
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# Return *.css files (css files) [for sample-matrix]
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cssfiles=`ls -1 /home/taha/chepec/tmp/$tmpdirname/*.css 2>/dev/null | wc -l`
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if [ $cssfiles != 0 ]; then
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cp /home/taha/chepec/tmp/$tmpdirname/*.css .
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fi
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# Return .knitme file [empty file used to indicate knitr jobs]
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knitmefile=`ls -1 /home/taha/chepec/tmp/$tmpdirname/.knitme 2>/dev/null | wc -l`
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if [ $knitmefile != 0 ]; then
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cp /home/taha/chepec/tmp/$tmpdirname/.knitme .
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fi
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fi
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echo "Terminating..."
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exit 1
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fi
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## Here is the wild land of more than one *.Rnw file in current directory
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echo "<cheRTeX> This script can be run with one argument is process mode,"
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echo "<cheRTeX> or with zero arguments in post-processing mode."
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echo "<cheRTeX> Terminating..."
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exit 1
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fi
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echo "------------------------------------"
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echo "=== sample-matrix.sh completed ==="
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echo "=== $(date) ==="
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echo "------------------------------------"
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/home/taha/chepec/chetex/common/bash/simpledelay.sh 10
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exit 1
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