[EMBOSS] EMBOSS-Explorer Follow-up

Ryan Golhar golharam at umdnj.edu
Mon Sep 11 16:28:30 UTC 2006

So I stepped through the code for tfm and it looks like it initially
looks in /usr/share/EMBOSS/doc/programs/html.  So 'make install' is
putting the html docs in /usr/share/EMBOSS/doc/html/emboss/apps/...  But
why?  Was this an inadvertant change?

> -----Original Message-----
> From: Ryan Golhar [mailto:golharam at umdnj.edu] 
> Sent: Monday, September 11, 2006 11:38 AM
> To: 'emboss at emboss.open-bio.org'
> Subject: EMBOSS-Explorer
> Does anyone know how to get a hold of Luke McCarthy?  The 
> email address I have for him is getting bounced back and he 
> hasn't responded to his sourceforge email.
> Since I'm on the topic...I have two problems with 
> EMBOSS-Explorer and EMBOSS 4.0.0:
> 1.  EMBOSS-Explorer uses the path of 
> /usr/share/EMBOSS/doc/programs/html, however EMBOSS html docs 
> are installed in /usr/share/EMBOSS/doc/html/emboss.  The 
> EMBASSY docs are in /usr/share/EMBOSS/doc/html/embassy.  
> This seems to be completely different than where the text 
> documents are installed, /usr/share/EMBOSS/doc/programs/txt.  
> It looks like EMBOSS v3 was installing the html docs in 
> /usr/share/EMBOSS/doc/programs/html, but that has changed in v4.
> So, either the EMBOSS installation needs to be told to 
> install in /usr/share/EMBOSS/doc/programs/html, or 
> EMBOSS-Explorer needs to be updated to look in 2 different 
> directories, one for EMBOSS and one for EMBASSY.
> As a third option, EMBOSS-Explorer could run 'tfm -html' to 
> get the html doc generated on the fly.  This is probably 
> overkill though.
> 2.  The new programs introduce new datatypes in the ACD files 
> that EMBOSS-Explorer doesn't recognize.  I get an 'unknown 
> data type' message display in my browser for these apps.
> --
> Ryan Golhar  -  golharam at umdnj.edu
> The Informatics Institute of UMDNJ

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