[EMBOSS] ABI to FASTQ with seqret

Peter biopython at maubp.freeserve.co.uk
Mon Apr 26 16:39:40 UTC 2010

On Thu, Apr 22, 2010 at 6:01 PM, Peter Rice <pmr at ebi.ac.uk> wrote:
>> Does this mean there is an updated seqret in a public repository where I
>> can convert an ABI file to FASTQ taking the ABI basecaller's sequence
>> and PHRED scores? I'd be interested to test that... or a patch against
>> EMBOSS 6.2.0.
> It is in the latest CVS code and will appeart in the July release.

Thanks Peter,

I tried to grab this from the anonymous CVS mirror as per the EMBOSS
documentation here:

Unfortunately it failed:

$ cvs -d :pserver:cvs at cvs.open-bio.org:/home/repository/emboss login
Logging in to :pserver:cvs at cvs.open-bio.org:2401/home/repository/emboss
CVS password:
cvs login: authorization failed: server cvs.open-bio.org rejected
access to /home/repository/emboss for user cvs

I know there have been VM problems on this machine (also known as
code.open-bio.org) which have been intermitently been affecting the
anonymous SVN access for other projects like BioPerl.

One short term solution would be to give my OBF username peterc
access to the master Emboss CVS repository on dev.open-bio.org
(joke), or look into an external mirror - for example BioPerl are using
github (and seriously talking about moving from SVN to git). This is
going even more off topic but since ViewCVS broke a while back, I've
found it much harder to browse the Emboss source code :(


Peter C.

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