From ajb at ebi.ac.uk Thu Jul 15 06:20:34 2010 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 15 Jul 2010 11:20:34 +0100 (BST) Subject: [emboss-announce] EMBOSS 6.3.0 released Message-ID: <39962.86.26.12.63.1279189234.squirrel@webmail.ebi.ac.uk> EMBOSS 6.3.0 is now available and can be downloaded from our ftp server: ftp://emboss.open-bio.org/pub/EMBOSS/ The associated (optional) EMBASSY packages are in the same directory. mEMBOSS, the native Microsoft windows port, can be downloaded from the directory: ftp://emboss.open-bio.org/pub/EMBOSS/windows/ This release provides a platform for further application development. Some highlights include: Network access to BioMart, Ensembl and general SQL databases Support for BAM/SAM files Parsing and validation for NCBI taxonomy and OBO files Scaleable graphics options Rabin-Karp multi-pattern search algorithm implemented EDAM ontology identifiers added Full details are in the attached ChangeLog Installation: There are some new optional steps in the installation. For UNIX: To enable PDF graphics support you will need to have installed the libhpdf development files (a.k.a. libharu, source available via libharu.org). To enable MySQL and/or PostgreSQL support their development files will need to have been installed. For example, under Linux RPM systems the packages would typically be called libharu-devel, mysql-devel & postgresql-devel. Such installations need to be performed prior to the EMBOSS configuration step. The configuration will automatically include support for the above if the relevant files are detected. For Windows (mEMBOSS): No action is required. PDF and MySQL support DLLs are included by the installation. Alan -------------- next part -------------- A non-text attachment was scrubbed... Name: ChangeLog Type: application/octet-stream Size: 11537 bytes Desc: not available URL: From ajb at ebi.ac.uk Mon Jul 19 10:07:17 2010 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 19 Jul 2010 15:07:17 +0100 (BST) Subject: [emboss-announce] EMBOSS 6.3.1 available Message-ID: <38438.86.26.12.63.1279548437.squirrel@webmail.ebi.ac.uk> EMBOSS 6.3.1 is now available and can be downloaded from our ftp server: ftp://emboss.open-bio.org/pub/EMBOSS/ The associated (optional) EMBASSY packages are in the same directory. mEMBOSS, the native Microsoft windows port, can be downloaded from the directory: ftp://emboss.open-bio.org/pub/EMBOSS/windows/ This is a maintenance release. It fixes a compilation failure under Linux Ubuntu distributions. The bug causing the failure was in a function not actually used by the EMBOSS main package but was used by two of the EMBASSY packages. It could cause some output file permissions to be set incorrectly on other operating systems or distributions. The remaining minor differences over 6.3.0 are: a) The optional configuration switch for PDF is now called --with-hpdf to bring it into line with the documentation. b) The default restriction isoschizomer data file has been updated. c) svg & pdf are now only reported once under graphics devices. For mEMBOSS, the only changes are 'b)' and 'c)' We apologise for any inconvenience caused. Alan From ajb at ebi.ac.uk Wed Jul 21 05:41:38 2010 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Wed, 21 Jul 2010 10:41:38 +0100 (BST) Subject: [emboss-announce] Patch/Fix 1 for EMBOSS 6.3.1 available Message-ID: <41463.86.26.12.63.1279705298.squirrel@webmail.ebi.ac.uk> This is available as separate drop-in replacement files, or as a patch file, from the ftp://emboss.open-bio.org/pub/EMBOSS/fixes/ directory hierarchy. Instructions are also available there. Problem addressed: In some circumstances the inclusion of PDF support could prevent the inclusion of MySQL support. If you required MySQL support and have already successfully installed it then there is no need to apply this patch. Similarly, the patch is unnecessary if you didn't want MySQL support included. Alan From ajb at ebi.ac.uk Thu Jul 15 10:20:34 2010 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Thu, 15 Jul 2010 11:20:34 +0100 (BST) Subject: [emboss-announce] EMBOSS 6.3.0 released Message-ID: <39962.86.26.12.63.1279189234.squirrel@webmail.ebi.ac.uk> EMBOSS 6.3.0 is now available and can be downloaded from our ftp server: ftp://emboss.open-bio.org/pub/EMBOSS/ The associated (optional) EMBASSY packages are in the same directory. mEMBOSS, the native Microsoft windows port, can be downloaded from the directory: ftp://emboss.open-bio.org/pub/EMBOSS/windows/ This release provides a platform for further application development. Some highlights include: Network access to BioMart, Ensembl and general SQL databases Support for BAM/SAM files Parsing and validation for NCBI taxonomy and OBO files Scaleable graphics options Rabin-Karp multi-pattern search algorithm implemented EDAM ontology identifiers added Full details are in the attached ChangeLog Installation: There are some new optional steps in the installation. For UNIX: To enable PDF graphics support you will need to have installed the libhpdf development files (a.k.a. libharu, source available via libharu.org). To enable MySQL and/or PostgreSQL support their development files will need to have been installed. For example, under Linux RPM systems the packages would typically be called libharu-devel, mysql-devel & postgresql-devel. Such installations need to be performed prior to the EMBOSS configuration step. The configuration will automatically include support for the above if the relevant files are detected. For Windows (mEMBOSS): No action is required. PDF and MySQL support DLLs are included by the installation. Alan -------------- next part -------------- A non-text attachment was scrubbed... Name: ChangeLog Type: application/octet-stream Size: 11537 bytes Desc: not available URL: From ajb at ebi.ac.uk Mon Jul 19 14:07:17 2010 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Mon, 19 Jul 2010 15:07:17 +0100 (BST) Subject: [emboss-announce] EMBOSS 6.3.1 available Message-ID: <38438.86.26.12.63.1279548437.squirrel@webmail.ebi.ac.uk> EMBOSS 6.3.1 is now available and can be downloaded from our ftp server: ftp://emboss.open-bio.org/pub/EMBOSS/ The associated (optional) EMBASSY packages are in the same directory. mEMBOSS, the native Microsoft windows port, can be downloaded from the directory: ftp://emboss.open-bio.org/pub/EMBOSS/windows/ This is a maintenance release. It fixes a compilation failure under Linux Ubuntu distributions. The bug causing the failure was in a function not actually used by the EMBOSS main package but was used by two of the EMBASSY packages. It could cause some output file permissions to be set incorrectly on other operating systems or distributions. The remaining minor differences over 6.3.0 are: a) The optional configuration switch for PDF is now called --with-hpdf to bring it into line with the documentation. b) The default restriction isoschizomer data file has been updated. c) svg & pdf are now only reported once under graphics devices. For mEMBOSS, the only changes are 'b)' and 'c)' We apologise for any inconvenience caused. Alan From ajb at ebi.ac.uk Wed Jul 21 09:41:38 2010 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Wed, 21 Jul 2010 10:41:38 +0100 (BST) Subject: [emboss-announce] Patch/Fix 1 for EMBOSS 6.3.1 available Message-ID: <41463.86.26.12.63.1279705298.squirrel@webmail.ebi.ac.uk> This is available as separate drop-in replacement files, or as a patch file, from the ftp://emboss.open-bio.org/pub/EMBOSS/fixes/ directory hierarchy. Instructions are also available there. Problem addressed: In some circumstances the inclusion of PDF support could prevent the inclusion of MySQL support. If you required MySQL support and have already successfully installed it then there is no need to apply this patch. Similarly, the patch is unnecessary if you didn't want MySQL support included. Alan