[Bio-Linux] Bio-Linux EMBOSS and proxies

[Dan Swan]

Hi All,

just a quick note to say that whilst we were setting up for an MRes
practical we ran into an issue with EMBOSS.  Not sure if this has been
covered before/elsewhere

Seqret was returning errors of 'no route to host' when attempting to
fetch EMBL records.  We eventually traced this to being a proxy issue,
seqret doesn't understand $http_proxy.  If other institutions access
the web via a proxy there are two workarounds:

1) Type this at the command line, or add it into your login scripts:

export EMBOSS_PROXY=yourcache.ac.uk:portnum

(where yourcache.ac.uk is your proxy host and portnum is your proxy
port (eg 8080))

2) In /usr/local/bioinf/EMBOSS/EMBOSS/emboss/emboss.default add a line such as:

SET EMBOSS_PROXY yourcache.ac.uk:portnum

it is important *not* to include a leading "http://" to the proxy address.

Hope this is useful to someone else.

Dan Swan

--
Senior Research Associate, Bioinformatics Support Unit,
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