I try to use Paradigm and Pathmark but i couldn't do it with source code. it gives a library error . Is there a galaxy tool for using them?
These tools are not wrapped for Galaxy and available in the Main Galaxy Tool Shed (even though the author states that they are Galaxy compatible). The best way to find out how to use these with Galaxy is to contact the tool author and ask how they intended the usage. When contacting, reporting the problems with the source would also likely be of interest to them.
Once the source code is confirmed to be working, a Galaxy wrapped tool could be created. Your problem with the source could be a true bug, a recently introduced incompatibility, and/or some other issue with the way the tools were installed e.g. dependency issues. The author might be willing to wrap these, or you can, or perhaps someone from the community is willing to take on the project, or it may be in progress.
To make a request to have a tool wrapped or to see if anyone has this planned/in-progress, ask the author first, then consider asking on the firstname.lastname@example.org mailing list. This list reaches the wider Galaxy development community. Not all Galaxy developers review Galaxy Biostars posts as these historically have tended to focus on usage, not development, topics - yet there is some cross-over and we may still get more replies here.
Hopefully this helps, Jen, Galaxy team