Hi Matthew,
Thanks for that. You are more patient than me (or more optimistic). I
gave up after the first 3 problem points in the script, thinking that
this clearly hadn't bee tested under Windows, and that even if the
configure.pl script was made to run, who knows what other serious or
subtle problems might await me when I actually ran MartService and
MartView.? It sounds like the problems you encountered were actually
quite mild.
Regards,
Roger.
Matthew Hobbs wrote:
Hi,
I run BioMart 0.6 on my laptop under Windows XP.
I agree that there is an issue with paths in the configureBioMart.pl
script. I had to hack it so to disable some of the checks for files
and versions, and hardcode some Windows style paths (see attached diff
file, which might not make it onto the list). Sounds like this is what
you tried too, Roger, and although you say it repeatedly fails for
you, I am fortunate that this patched script works for me. I'm not
much of a Perl programmer, and agree that a better fix is desirable.
Once started, martservice runs as expected except that there is a
small problem with session information occasionally not being cleared
properly (I am using the MySQL session storage option). I haven't
solved this problem, I just clear when necessary all session
information from the MySQL session table with an SQL statement in a
mysql client. This is not too inconvenient since the number of queries
I do per development round is small.
Hope this helps.
Matthew Hobbs
Roger Hull wrote:
I tried this in BioMart 6. I found that the Java programs run fine,
but not the biomart-perl, even with all the pre-requisites installed.
The biomart-perl installation script seems to use Unix conventions
and utilities for files and directories, which failed to run under
Windows XP (even with some Unix-alike utilities installed, and with
Windows support for forward-slash path separators). I found that the
script repeatedly failed even when I tried to patch it each time, and
I gave up. (The script appears to have some support for Windows
conventions, but it didn't look as if this had actually been tested.)
It would be useful for demo though, if someone could fix the script.
Regards,
Roger.
ert
