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
A C T G stevet from bio.fsu.edu
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