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In the directory /user/, I have a file header.tex.

In the file /user/dir/main.tex, I use \input{../header.tex}.

When I run pdflatex main.tex from /user/dir, everything works fine. But if I runpdflatex dir/main.tex from /user, I get the File ../header.tex not found error.

Is it possible to define input with respect to the file on which pdflatex is run (here, /user/dir/main.tex), so that pdflatex would work irrespective of the folder from which it is ran?

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    no it is built in to tex that input and default output are relative to the working directory not the directory with the file but you can always write a wrapper script that takes a file path, cds to the file director and then runs pdflatex, or just use \input{header} and arrange that /user is in TEXINPUTS then it will work from anywhere just as article.cls gets input wherever you are as it is in TEXINPUTS – David Carlisle Nov 7 '17 at 23:13
  • @DavidCarlisle Thank you, I wrote an answer based on your comment. – anderstood Nov 8 '17 at 18:20
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This answer is elaborated from David Carlisle's comment, in case it helps someone. Since \input cannot be changed in such a way, there are basically two strategies:

  • Let latex now about the file globally, ideally by adding header.tex to ~/texmf/tex/latex/<username>, or to the variable TEXINPUTS. More details on this answer. In my case, I wanted my files to be self-contained in a single directory (for git), so I went with the second option.

  • Write a script that goes into each directory, run pdflatex and so on. This is the option I used.

First, I generate a list of all tex files and store if in listOfTeX.txt (to be ran from the parent directory):

find . -type f \( -iname "$.tex" \) >> listOfTeX.txt

Then,

while read FILE; do 
    printf "\n ----> $FILE\n"; # prints the file path and name
    DIR=$(dirname "$FILE");    # extracts the directory
    cd $DIR;                   # goes to that directory
    texfot pdflatex $(basename "$FILE") | grep "error";  # run pdflatex
    cd ../;                 # goes back to the parent directory (in my case)
done < listOfTeX.txt

Explanations on the line texfot pdflatex $(basename "$FILE") | grep "error"; : texfot is used to reduce the output of pdflatex, see egreg's answer. Then I use grep "error" to display only the errors. That allows to directly find the problematic files and paths. To be adjusted to your needs of course (same for cd ../).

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