Try Google Transliterate.
google.com/transliterate/
This url will take you to the in-browser version, but the link in the upper right will take you to the downloadable version. I do not know if they support Linux, and I don't know if it what you are looking for. I do not use all of the options it has because I haven't gotten very in-depth into language learning as of yet, but I know that it is nearly identical to Windows IME. I got it because it works the way Windows IME was described to me to work (but would not). It does kanji, hiragana, katakana, and some other options I mentioned before that I have never used.