From ajb at ebi.ac.uk  Tue Aug 10 06:17:46 2010
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Tue, 10 Aug 2010 11:17:46 +0100 (BST)
Subject: [emboss-announce] Patch 1-4 available for EMBOSS-6.3.1
Message-ID: <45351.86.26.12.63.1281435466.squirrel@webmail.ebi.ac.uk>

The latest patch for EMBOSS-6.3.1 is available from:

  ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-4.gz

(and the corresponding discrete files in the directory above). The
latest mEMBOSS containing these fixes is available at:

  ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.3.1.2-setup.exe

This fixes:

    Loading of two Ensembl sequences without the need to reload the
    registry.

    Correction the registration of the Ensembl Genomes database.

    Ensembl Genomes identifiers for species without a stable identifier
    should work. If the identifier does not obey a stable identifier
    pattern then it is matched against Exons, Transcripts and
    Translations in exactly that order.

It also corrects a side-effect of the first patch whereby the build
could fail with a libtool error if the host system had the latest
libtool installed.

Note that direct retrieval from the Ensembl server is still a
work in progress. As an example of its use, the following
commands will work using the example definitions in the
emboss.default.template file (no action required for mEMBOSS users).

seqret ensembl:human:ENST00000262160
seqret 'ensemblgenomes:Escherichia coli K12:EBESCT00000004007'
seqret 'ensemblgenomes:Escherichia coli DH10B:EBESCT00000011809'
seqret 'ensemblgenomes:Schizosaccharomyces pombe:SPAC2F7.03c-1'

(Quotes used when space characters are part of the retrieval term)

Alan



From ajb at ebi.ac.uk  Tue Aug 10 10:17:46 2010
From: ajb at ebi.ac.uk (ajb at ebi.ac.uk)
Date: Tue, 10 Aug 2010 11:17:46 +0100 (BST)
Subject: [emboss-announce] Patch 1-4 available for EMBOSS-6.3.1
Message-ID: <45351.86.26.12.63.1281435466.squirrel@webmail.ebi.ac.uk>

The latest patch for EMBOSS-6.3.1 is available from:

  ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-4.gz

(and the corresponding discrete files in the directory above). The
latest mEMBOSS containing these fixes is available at:

  ftp://emboss.open-bio.org/pub/EMBOSS/windows/mEMBOSS-6.3.1.2-setup.exe

This fixes:

    Loading of two Ensembl sequences without the need to reload the
    registry.

    Correction the registration of the Ensembl Genomes database.

    Ensembl Genomes identifiers for species without a stable identifier
    should work. If the identifier does not obey a stable identifier
    pattern then it is matched against Exons, Transcripts and
    Translations in exactly that order.

It also corrects a side-effect of the first patch whereby the build
could fail with a libtool error if the host system had the latest
libtool installed.

Note that direct retrieval from the Ensembl server is still a
work in progress. As an example of its use, the following
commands will work using the example definitions in the
emboss.default.template file (no action required for mEMBOSS users).

seqret ensembl:human:ENST00000262160
seqret 'ensemblgenomes:Escherichia coli K12:EBESCT00000004007'
seqret 'ensemblgenomes:Escherichia coli DH10B:EBESCT00000011809'
seqret 'ensemblgenomes:Schizosaccharomyces pombe:SPAC2F7.03c-1'

(Quotes used when space characters are part of the retrieval term)

Alan