[Molecular-evolution] Other: Re - GCG non-support

Steve Thompson via mol-evol%40net.bio.net (by stevet from bio.fsu.edu)
Mon Nov 3 15:56:23 EST 2008


Hi Peter -

I'm picking back up on an old thread from summer 2007 re. the Acclerys GCG 
'retirement.'  Since that time several developments, only a few positive 
in my opinion, have clarified the situation.

One - my online petition at www.petitiononline.com was very successful 
(http://bio.fsu.edu/~stevet/Accelrys_petition.pdf) in gathering 
signatures, almost 200 in a month, and in fostering international 
exposure, as the BioInform article from April 2008 attests 
(http://bio.fsu.edu/~stevet/BioInformGCG.pdf).  But Accelrys remains 
committed to not releasing any GCG code, due to exhorbiant and without 
profit legal expense.  So be it and understood - we tried.

Two - Accelryrs did distirbute the 'perpetual' licenses to all valid 
license holders that were entitled to it, as I announced in this forum 
April 2008, and they worked great, even across multiple nodes in a 
cluster.  Thany you Accelrys.  However . . .

Three - We (FSU) upgraded our Linux cluster that supports GCG and many 
other bioinformatics tools to CentOS version 5.  Unfortunately, almost 
half of the GCG package now fails due to unresolvable library conflicts 
(as I warned would happen - unfortunately sooner than I had hoped).  Our 
systems operations folk initially thought they could fix this but the 
solution has remained ellusive.  The affected programs are all the oldest 
'legacy' programs in the package, although some longtime GCG pragrams like 
Pearson's FastA package remain viable.

Four - SeqLab continues to operate just fine, but without access to many 
of the analytic tools of the package, its usefullness is quite impacted, 
though I still think it's one of the best multiple sequence alignment 
editors around.  This is where you come back in Peter.  It may seem odd to 
ask, but the need is actually larger now that so much of the package no 
longer works in an Enterprise (or CentOS) Linux version 5 environment. 
I'm sure that I am not alone in this situation.  So here goes - I've asked 
it many time before, and I've begun to do the work myself starting with 
PlotCon, but has anybody built SeqLab extension configuration files to 
launch EMBOSS programs?

                              Cheers - Steve
                                                 Steven M. Thompson
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