[EMBOSS] Anybody still using W2H?

mathog mathog at caltech.edu
Thu May 1 23:44:58 UTC 2014


Are any of you still running a W2H server for EMBOSS on linux?  We have 
been for a long while, using the INTRANET=yes setting.  For reasons that 
are not very clear it seems to have stopped working.  EmbossExplorer is 
still working, as are all the other perl based interfaces, it is just 
W2H that has gone south.  Two things that are broken are:

1.  it refuses to upload sequence
2.  it will not run any programs.

A bunch of debug statements dropped into the .pl files turned up that 
the "GET" response, which is supposed to pass data in, is instead coming 
in completely empty.  So for instance, for the 2nd problem, it complains 
that it cannot find ".acd", which should have been "program.acd", but it 
either dropped or never received the program name.

W2H sets up directories for users in /tmp/_W2H_/USERXXXXX owned by 
apache:apache, like it always did.  And it is keeping track of sessions 
properly, so that each user sees their current directory.  If I manually 
drop a file in there then it is visible in the interface, and can be 
selected, but since W2H loses that information when a run is sent with 
"start", that isn't of much use.

perl 5.16.3 (hardly bleeding edge) on a Mageia 3 system.

Anybody seen this problem before?


David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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