i'm trying to use cross_match and gcphrap with pregap4 with Staden Package 1.7 installed under Windows 98, with no luck. The error messages i'm getting are:
cross_match_svec::init: cross_match is not in user's PATH
phrap_assemble::init: gcphrap is not in user's PATH
Where should i put the exe files of those two programs (i tried windows-bin directory, and serveral others but...), or what file should i modify to add the PATH line? (heh, or maybe which docs should i read again?)
(the first problem with pregap4 i actually encountered with cross_match and phrap assembly modules enabled was tclpip84.dll not present but i installed Activetcl and put the lacking file in /windows-bin/ direcory of Staden Package)
Thanks for your time,
Cross_match and gcphrap are not part of the staden package. Rather they're from Phil Green's lab. The staden package has interfaces to use these programs if they are installed and on your path, but we cannot provide source or binaries for them.
Furthermore, they're hard to get working on windows. I believe they're only available commercially for that system (see phrap.org for source or phrap.com for commercial precompiled windows binaries).
phred/phrap/cross_match are easily compiled under Windows when you have CYGWIN installed.
You then have to move the .exe-files into the windows-bin folder of Staden, together with the cygwin1.dll. We have made good experience with Phil Greens software within Staden.
Then you must take care that your Working Folder (where all your data files live) has no blanks in its full path; i.e., AVOID using \Documents and Settings\myname\..., Rather place your folder somewhere like C:\analysis\project1\clone199-A .