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I'm writing a paper using org-mode, using the LaTeX export function to generate the .tex file I need to submit to the journal.

How can I run an external shell command every time I to the C-c C-e l l for LaTeX export? I need to apply a patch to the generated .tex file.

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You might do this by using Org's publishing functions, and setting up one for your project. Take a look in particular at the setting publishing-function, which allows you to specify an arbitrary elisp function by which an org file within a given project is exported.

The publishing function might do a standard export to latex then run a shell command on the resulting file like this:

(defun publish-latex-and-patch (plist filename pub-dir)
  "Export a latex file then patch it by reversing lines"
  (let ((outfile
         (org-publish-org-to 'latex filename ".tex" plist pub-dir)))
    (shell-command (format "tac %s > %s-patched.tex"
                           outfile
                           (file-name-sans-extension outfile)))))

And you would then export your file by doing C-c C-e P f ("publish this file"). Obviously replace tac with your patching command, and exercise hygiene (e.g. escaping) if passing untrusted input to the shell.

There are also many org-export hooks, but they are more designed to modify specify elements within the parse tree during the export process.

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