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What I want to do is take textbox input on a website, use java or javascript to convert it to LaTeX code then output a formatted PDF document to the user. I am wondering if this is possible and where I can find the information on setting up an interface with PDFLaTeX from my website.

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Yes it's possible. You may find any info on pdflatex with man pdflatex. Please read the shell-escape section carefully. Furthermore you may consider to install a TeX Distribution like http://www.tug.org/texlive/.

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