From chaudhrynabeelahmed at gmail.com Mon Jul 16 01:56:42 2012 From: chaudhrynabeelahmed at gmail.com (Nabeel Ahmed) Date: Mon, 16 Jul 2012 10:56:42 +0500 Subject: [EMBOSS] Databases Message-ID: I have recently installed EMBOSS-6.4.0 (Ubuntu 11.10). I am unable to make it work directly with live databases (embl, uniprot) , working totally fine with local sequence files. e.g % *plotorf * Plot potential open reading frames in a nucleotide sequence Input nucleotide sequence: *embl:x13776* *Error:* Failed to open filename 'embl'** Used 'showdb' , displayed table with zero rows. Is there any configuration, i am missing?? Thanks Ahmed From david.bauer at bayer.com Mon Jul 16 04:08:09 2012 From: david.bauer at bayer.com (David Bauer) Date: Mon, 16 Jul 2012 08:08:09 +0000 Subject: [EMBOSS] Databases In-Reply-To: References: Message-ID: <801E8305DB9A574FB64B5A2EE8366A6101619969@BY09QA.DE.bayer.cnb> Hi Ahmed, There is a documentation about the setup of databases in EMBOSS at http://emboss.sourceforge.net/docs/themes/Databases.html This is a little bit outdated now because it does not cover all features available in Version 6.4 but it is still a good starting point. If you want to dive deeply into the EMBOSS administration, there is a book written by the EMBOSS team available from Cambridge University Press: http://www.cambridge.org/gb/knowledge/isbn/item5979238/?site_locale=en_GB HTH, David. -----Urspr?ngliche Nachricht----- Von: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] Im Auftrag von Nabeel Ahmed Gesendet: 16 July 2012 07:57 An: emboss at lists.open-bio.org Betreff: [EMBOSS] Databases I have recently installed EMBOSS-6.4.0 (Ubuntu 11.10). I am unable to make it work directly with live databases (embl, uniprot) , working totally fine with local sequence files. e.g % *plotorf * Plot potential open reading frames in a nucleotide sequence Input nucleotide sequence: *embl:x13776* *Error:* Failed to open filename 'embl'** Used 'showdb' , displayed table with zero rows. Is there any configuration, i am missing?? Thanks Ahmed _______________________________________________ EMBOSS mailing list EMBOSS at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss From david.bauer at bayer.com Mon Jul 16 05:28:40 2012 From: david.bauer at bayer.com (David Bauer) Date: Mon, 16 Jul 2012 09:28:40 +0000 Subject: [EMBOSS] Databases, additional info Message-ID: <801E8305DB9A574FB64B5A2EE8366A61016199B3@BY09QA.DE.bayer.cnb> Hi Ahmed, If you do not want to install databases locally, you can get them from some servers, which are preconfigured in EMBOSS 6.4 You can see the lists of configured servers with "showserver". If you need a sequence from embl, then then you can use the SRS server from the EBI. In your case it would be: "plotorf srs:embl:x13776" If you are behind a http proxy you can add the proxy server in .embossrc in your home directory. SET emboss_proxy "your_proxy_server:port" And if it needs authentication (only BASIC is usable) SET emboss_proxy "your_proxy_server:port Basic username:password" David. -----Urspr?ngliche Nachricht----- Von: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] Im Auftrag von Nabeel Ahmed Gesendet: 16 July 2012 07:57 An: emboss at lists.open-bio.org Betreff: [EMBOSS] Databases I have recently installed EMBOSS-6.4.0 (Ubuntu 11.10). I am unable to make it work directly with live databases (embl, uniprot) , working totally fine with local sequence files. e.g % *plotorf * Plot potential open reading frames in a nucleotide sequence Input nucleotide sequence: *embl:x13776* *Error:* Failed to open filename 'embl'** Used 'showdb' , displayed table with zero rows. Is there any configuration, i am missing?? Thanks Ahmed _______________________________________________ EMBOSS mailing list EMBOSS at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss From ricepeterm at yahoo.co.uk Mon Jul 16 07:05:57 2012 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Mon, 16 Jul 2012 12:05:57 +0100 Subject: [EMBOSS] Databases In-Reply-To: References: Message-ID: <5003F595.9080407@yahoo.co.uk> On 16/07/2012 06:56, Nabeel Ahmed wrote: > I have recently installed EMBOSS-6.4.0 (Ubuntu 11.10). > I am unable to make it work directly with live databases (embl, uniprot) , > working totally fine with local sequence files. > e.g > > % *plotorf * > Plot potential open reading frames in a nucleotide sequence > Input nucleotide sequence: *embl:x13776* > > *Error:* Failed to open filename 'embl'** > > Used 'showdb' , displayed table with zero rows. That is very strange. EMBOSS 6.4.0 includes a set of installed databases which should appear in showdb. One of these is the data resource catalogue (drcat) which in turn defines the embl database for web access. David Bauer has already explained how to get web access working if you have a proxy to go through, but that does not explain the empty showdb output. With drcat defined in a standard installation, and web access, you should already have access to the embl database (it will not appear in the showdb output of a standard installation, but is reachable by a lookup in DRCAT). Could you please try the command embossversion -full which should include the value of Emboss_Standard. In this directory you should have a file emboss.standard that defines drcat, several other databases, and the servers that David Bauer mentioned. My first guess would be that there is some problem with access permissions to that file. regards Peter Rice EMBOSS Team From charles-listes-emboss at plessy.org Thu Jul 19 00:17:53 2012 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Thu, 19 Jul 2012 13:17:53 +0900 Subject: [EMBOSS] About bulky taxonomy and gene ontology data in the EMBOSS package. In-Reply-To: <20120719034212.19009.93047.reportbug@ghostwheel.internal.ucko.debian.net> References: <20120719034212.19009.93047.reportbug@ghostwheel.internal.ucko.debian.net> Message-ID: <20120719041753.GB8741@falafel.plessy.net> Dear EMBOSS developers, today I received the following bug report about the quantity of data shipped in the Debian package for EMBOSS. > emboss-data recently grew from a slim 5 megabytes to a massive 305. > Closer inspection reveals the primary culprits to be large taxonomy > and gene ontology databases: > > 63927095 ./usr/share/EMBOSS/data/TAXONOMY/names.dmp > 58897689 ./usr/share/EMBOSS/index/taxon.xtax > 53221137 ./usr/share/EMBOSS/data/TAXONOMY/nodes.dmp > 28885180 ./usr/share/EMBOSS/index/taxon.xid > 23876286 ./usr/share/EMBOSS/index/taxon.xup > 20110641 ./usr/share/EMBOSS/data/OBO/gene_ontology.1_2.obo > 13816644 ./usr/share/EMBOSS/index/go.xde > 8964472 ./usr/share/EMBOSS/index/taxon.xrnk > 8963308 ./usr/share/EMBOSS/index/taxon.xgc > 6047464 ./usr/share/EMBOSS/index/go.xnm > 5642511 ./usr/share/EMBOSS/index/taxon.xmgc > 2504535 ./usr/share/EMBOSS/index/go.xac > 2220728 ./usr/share/EMBOSS/index/go.xis > 1292180 ./usr/share/EMBOSS/index/go.xid > [...] > 437512 ./usr/share/EMBOSS/index/go.xns http://bugs.debian.org/682042 In Debian, one solution would be to transfer this data in a separate optional package. But before doing so, I would like to ask you if this data really oughts to be distributed with EMBOSS ? After all, for many other databases, there are scripts to download and index the data after installation. Will EMBOSS 6.5 ship the taxonomy and gene ontology databases as well ? Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From ricepeterm at yahoo.co.uk Thu Jul 19 03:07:21 2012 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Thu, 19 Jul 2012 08:07:21 +0100 Subject: [EMBOSS] About bulky taxonomy and gene ontology data in the EMBOSS package. In-Reply-To: <20120719041753.GB8741@falafel.plessy.net> References: <20120719034212.19009.93047.reportbug@ghostwheel.internal.ucko.debian.net> <20120719041753.GB8741@falafel.plessy.net> Message-ID: <5007B229.6060607@yahoo.co.uk> On 19/07/2012 05:17, Charles Plessy wrote: > Dear EMBOSS developers, > > today I received the following bug report about the quantity of data shipped in > the Debian package for EMBOSS. > >> emboss-data recently grew from a slim 5 megabytes to a massive 305. >> Closer inspection reveals the primary culprits to be large taxonomy >> and gene ontology databases: > > In Debian, one solution would be to transfer this data in a separate optional > package. But before doing so, I would like to ask you if this data really > oughts to be distributed with EMBOSS ? After all, for many other databases, > there are scripts to download and index the data after installation. Will > EMBOSS 6.5 ship the taxonomy and gene ontology databases as well ? They are included in the release which appeared on 15th July (announcement in preparation). For developers the data is updated by rsync ... we could provide scripts to upload and index the data at the end of installation though I found in preparing the release that two ontologies had moved in the last year so that is error-prone. Some EMBOSS applications assume these databases are installed, particularly EDAM and the NCBI taxonomy. EDAM is used for all metadata, the taxonomy for organism searches in data retrieval. The Gene Ontology is included in analysis of GO terms in metadata. So if they are in an optional package ... some things will not work if it is not installed. EDAM I would say is essential. regards, Peter Rice EMBOSS Team From ppetrov at mail.student.oulu.fi Thu Jul 19 08:23:33 2012 From: ppetrov at mail.student.oulu.fi (Petar Petrov) Date: Thu, 19 Jul 2012 15:23:33 +0300 Subject: [EMBOSS] EMBOSS 6.5.0 and jemboss In-Reply-To: <5007B229.6060607@yahoo.co.uk> References: <20120719034212.19009.93047.reportbug@ghostwheel.internal.ucko.debian.net> <20120719041753.GB8741@falafel.plessy.net> <5007B229.6060607@yahoo.co.uk> Message-ID: <20120719152333.dy13qdcrwkgkwc0c@webmail.oulu.fi> Hi, Compiling EMBOSS 6.5.0 does not install runJemboss.csh in /usr/bin nor runJemboss.sh in /usr/share/EMBOSS/jemboss (version 6.4.0 had no problems with this). Any hints of what I can do? The system I compile on is Slackware64 13.37 Also, is there a place where all versions of EMBOSS are stored, including the current one? I ask this because my SlackBuild for 6.4.0 (http://slackbuilds.org/repository/13.37/academic/EMBOSS/) points to a broken link (ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.4.0.tar.gz) after 6.5.0 was released. Regards, Petar From ricepeterm at yahoo.co.uk Thu Jul 19 10:08:28 2012 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Thu, 19 Jul 2012 15:08:28 +0100 Subject: [EMBOSS] EMBOSS 6.5.0 and jemboss In-Reply-To: <20120719152333.dy13qdcrwkgkwc0c@webmail.oulu.fi> References: <20120719034212.19009.93047.reportbug@ghostwheel.internal.ucko.debian.net> <20120719041753.GB8741@falafel.plessy.net> <5007B229.6060607@yahoo.co.uk> <20120719152333.dy13qdcrwkgkwc0c@webmail.oulu.fi> Message-ID: <500814DC.8060907@yahoo.co.uk> On 19/07/2012 13:23, Petar Petrov wrote: > Hi, > > Compiling EMBOSS 6.5.0 does not install runJemboss.csh in /usr/bin nor > runJemboss.sh in /usr/share/EMBOSS/jemboss (version 6.4.0 had no > problems with this). > > Any hints of what I can do? The system I compile on is Slackware64 13.37 We'll check on that and get back to you. > Also, is there a place where all versions of EMBOSS are stored, > including the current one? I ask this because my SlackBuild for 6.4.0 > (http://slackbuilds.org/repository/13.37/academic/EMBOSS/) points to a > broken link (ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.4.0.tar.gz) > after 6.5.0 was released. Previous versions always go to the ftp://emboss.open-bio.org/pub/EMBOSS/old/ directory regards, Peter Rice EMBOSS Team From chaudhrynabeelahmed at gmail.com Mon Jul 16 05:56:42 2012 From: chaudhrynabeelahmed at gmail.com (Nabeel Ahmed) Date: Mon, 16 Jul 2012 10:56:42 +0500 Subject: [EMBOSS] Databases Message-ID: I have recently installed EMBOSS-6.4.0 (Ubuntu 11.10). I am unable to make it work directly with live databases (embl, uniprot) , working totally fine with local sequence files. e.g % *plotorf * Plot potential open reading frames in a nucleotide sequence Input nucleotide sequence: *embl:x13776* *Error:* Failed to open filename 'embl'** Used 'showdb' , displayed table with zero rows. Is there any configuration, i am missing?? Thanks Ahmed From david.bauer at bayer.com Mon Jul 16 08:08:09 2012 From: david.bauer at bayer.com (David Bauer) Date: Mon, 16 Jul 2012 08:08:09 +0000 Subject: [EMBOSS] Databases In-Reply-To: References: Message-ID: <801E8305DB9A574FB64B5A2EE8366A6101619969@BY09QA.DE.bayer.cnb> Hi Ahmed, There is a documentation about the setup of databases in EMBOSS at http://emboss.sourceforge.net/docs/themes/Databases.html This is a little bit outdated now because it does not cover all features available in Version 6.4 but it is still a good starting point. If you want to dive deeply into the EMBOSS administration, there is a book written by the EMBOSS team available from Cambridge University Press: http://www.cambridge.org/gb/knowledge/isbn/item5979238/?site_locale=en_GB HTH, David. -----Urspr?ngliche Nachricht----- Von: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] Im Auftrag von Nabeel Ahmed Gesendet: 16 July 2012 07:57 An: emboss at lists.open-bio.org Betreff: [EMBOSS] Databases I have recently installed EMBOSS-6.4.0 (Ubuntu 11.10). I am unable to make it work directly with live databases (embl, uniprot) , working totally fine with local sequence files. e.g % *plotorf * Plot potential open reading frames in a nucleotide sequence Input nucleotide sequence: *embl:x13776* *Error:* Failed to open filename 'embl'** Used 'showdb' , displayed table with zero rows. Is there any configuration, i am missing?? Thanks Ahmed _______________________________________________ EMBOSS mailing list EMBOSS at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss From david.bauer at bayer.com Mon Jul 16 09:28:40 2012 From: david.bauer at bayer.com (David Bauer) Date: Mon, 16 Jul 2012 09:28:40 +0000 Subject: [EMBOSS] Databases, additional info Message-ID: <801E8305DB9A574FB64B5A2EE8366A61016199B3@BY09QA.DE.bayer.cnb> Hi Ahmed, If you do not want to install databases locally, you can get them from some servers, which are preconfigured in EMBOSS 6.4 You can see the lists of configured servers with "showserver". If you need a sequence from embl, then then you can use the SRS server from the EBI. In your case it would be: "plotorf srs:embl:x13776" If you are behind a http proxy you can add the proxy server in .embossrc in your home directory. SET emboss_proxy "your_proxy_server:port" And if it needs authentication (only BASIC is usable) SET emboss_proxy "your_proxy_server:port Basic username:password" David. -----Urspr?ngliche Nachricht----- Von: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] Im Auftrag von Nabeel Ahmed Gesendet: 16 July 2012 07:57 An: emboss at lists.open-bio.org Betreff: [EMBOSS] Databases I have recently installed EMBOSS-6.4.0 (Ubuntu 11.10). I am unable to make it work directly with live databases (embl, uniprot) , working totally fine with local sequence files. e.g % *plotorf * Plot potential open reading frames in a nucleotide sequence Input nucleotide sequence: *embl:x13776* *Error:* Failed to open filename 'embl'** Used 'showdb' , displayed table with zero rows. Is there any configuration, i am missing?? Thanks Ahmed _______________________________________________ EMBOSS mailing list EMBOSS at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss From ricepeterm at yahoo.co.uk Mon Jul 16 11:05:57 2012 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Mon, 16 Jul 2012 12:05:57 +0100 Subject: [EMBOSS] Databases In-Reply-To: References: Message-ID: <5003F595.9080407@yahoo.co.uk> On 16/07/2012 06:56, Nabeel Ahmed wrote: > I have recently installed EMBOSS-6.4.0 (Ubuntu 11.10). > I am unable to make it work directly with live databases (embl, uniprot) , > working totally fine with local sequence files. > e.g > > % *plotorf * > Plot potential open reading frames in a nucleotide sequence > Input nucleotide sequence: *embl:x13776* > > *Error:* Failed to open filename 'embl'** > > Used 'showdb' , displayed table with zero rows. That is very strange. EMBOSS 6.4.0 includes a set of installed databases which should appear in showdb. One of these is the data resource catalogue (drcat) which in turn defines the embl database for web access. David Bauer has already explained how to get web access working if you have a proxy to go through, but that does not explain the empty showdb output. With drcat defined in a standard installation, and web access, you should already have access to the embl database (it will not appear in the showdb output of a standard installation, but is reachable by a lookup in DRCAT). Could you please try the command embossversion -full which should include the value of Emboss_Standard. In this directory you should have a file emboss.standard that defines drcat, several other databases, and the servers that David Bauer mentioned. My first guess would be that there is some problem with access permissions to that file. regards Peter Rice EMBOSS Team From charles-listes-emboss at plessy.org Thu Jul 19 04:17:53 2012 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Thu, 19 Jul 2012 13:17:53 +0900 Subject: [EMBOSS] About bulky taxonomy and gene ontology data in the EMBOSS package. In-Reply-To: <20120719034212.19009.93047.reportbug@ghostwheel.internal.ucko.debian.net> References: <20120719034212.19009.93047.reportbug@ghostwheel.internal.ucko.debian.net> Message-ID: <20120719041753.GB8741@falafel.plessy.net> Dear EMBOSS developers, today I received the following bug report about the quantity of data shipped in the Debian package for EMBOSS. > emboss-data recently grew from a slim 5 megabytes to a massive 305. > Closer inspection reveals the primary culprits to be large taxonomy > and gene ontology databases: > > 63927095 ./usr/share/EMBOSS/data/TAXONOMY/names.dmp > 58897689 ./usr/share/EMBOSS/index/taxon.xtax > 53221137 ./usr/share/EMBOSS/data/TAXONOMY/nodes.dmp > 28885180 ./usr/share/EMBOSS/index/taxon.xid > 23876286 ./usr/share/EMBOSS/index/taxon.xup > 20110641 ./usr/share/EMBOSS/data/OBO/gene_ontology.1_2.obo > 13816644 ./usr/share/EMBOSS/index/go.xde > 8964472 ./usr/share/EMBOSS/index/taxon.xrnk > 8963308 ./usr/share/EMBOSS/index/taxon.xgc > 6047464 ./usr/share/EMBOSS/index/go.xnm > 5642511 ./usr/share/EMBOSS/index/taxon.xmgc > 2504535 ./usr/share/EMBOSS/index/go.xac > 2220728 ./usr/share/EMBOSS/index/go.xis > 1292180 ./usr/share/EMBOSS/index/go.xid > [...] > 437512 ./usr/share/EMBOSS/index/go.xns http://bugs.debian.org/682042 In Debian, one solution would be to transfer this data in a separate optional package. But before doing so, I would like to ask you if this data really oughts to be distributed with EMBOSS ? After all, for many other databases, there are scripts to download and index the data after installation. Will EMBOSS 6.5 ship the taxonomy and gene ontology databases as well ? Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From ricepeterm at yahoo.co.uk Thu Jul 19 07:07:21 2012 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Thu, 19 Jul 2012 08:07:21 +0100 Subject: [EMBOSS] About bulky taxonomy and gene ontology data in the EMBOSS package. In-Reply-To: <20120719041753.GB8741@falafel.plessy.net> References: <20120719034212.19009.93047.reportbug@ghostwheel.internal.ucko.debian.net> <20120719041753.GB8741@falafel.plessy.net> Message-ID: <5007B229.6060607@yahoo.co.uk> On 19/07/2012 05:17, Charles Plessy wrote: > Dear EMBOSS developers, > > today I received the following bug report about the quantity of data shipped in > the Debian package for EMBOSS. > >> emboss-data recently grew from a slim 5 megabytes to a massive 305. >> Closer inspection reveals the primary culprits to be large taxonomy >> and gene ontology databases: > > In Debian, one solution would be to transfer this data in a separate optional > package. But before doing so, I would like to ask you if this data really > oughts to be distributed with EMBOSS ? After all, for many other databases, > there are scripts to download and index the data after installation. Will > EMBOSS 6.5 ship the taxonomy and gene ontology databases as well ? They are included in the release which appeared on 15th July (announcement in preparation). For developers the data is updated by rsync ... we could provide scripts to upload and index the data at the end of installation though I found in preparing the release that two ontologies had moved in the last year so that is error-prone. Some EMBOSS applications assume these databases are installed, particularly EDAM and the NCBI taxonomy. EDAM is used for all metadata, the taxonomy for organism searches in data retrieval. The Gene Ontology is included in analysis of GO terms in metadata. So if they are in an optional package ... some things will not work if it is not installed. EDAM I would say is essential. regards, Peter Rice EMBOSS Team From ppetrov at mail.student.oulu.fi Thu Jul 19 12:23:33 2012 From: ppetrov at mail.student.oulu.fi (Petar Petrov) Date: Thu, 19 Jul 2012 15:23:33 +0300 Subject: [EMBOSS] EMBOSS 6.5.0 and jemboss In-Reply-To: <5007B229.6060607@yahoo.co.uk> References: <20120719034212.19009.93047.reportbug@ghostwheel.internal.ucko.debian.net> <20120719041753.GB8741@falafel.plessy.net> <5007B229.6060607@yahoo.co.uk> Message-ID: <20120719152333.dy13qdcrwkgkwc0c@webmail.oulu.fi> Hi, Compiling EMBOSS 6.5.0 does not install runJemboss.csh in /usr/bin nor runJemboss.sh in /usr/share/EMBOSS/jemboss (version 6.4.0 had no problems with this). Any hints of what I can do? The system I compile on is Slackware64 13.37 Also, is there a place where all versions of EMBOSS are stored, including the current one? I ask this because my SlackBuild for 6.4.0 (http://slackbuilds.org/repository/13.37/academic/EMBOSS/) points to a broken link (ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.4.0.tar.gz) after 6.5.0 was released. Regards, Petar From ricepeterm at yahoo.co.uk Thu Jul 19 14:08:28 2012 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Thu, 19 Jul 2012 15:08:28 +0100 Subject: [EMBOSS] EMBOSS 6.5.0 and jemboss In-Reply-To: <20120719152333.dy13qdcrwkgkwc0c@webmail.oulu.fi> References: <20120719034212.19009.93047.reportbug@ghostwheel.internal.ucko.debian.net> <20120719041753.GB8741@falafel.plessy.net> <5007B229.6060607@yahoo.co.uk> <20120719152333.dy13qdcrwkgkwc0c@webmail.oulu.fi> Message-ID: <500814DC.8060907@yahoo.co.uk> On 19/07/2012 13:23, Petar Petrov wrote: > Hi, > > Compiling EMBOSS 6.5.0 does not install runJemboss.csh in /usr/bin nor > runJemboss.sh in /usr/share/EMBOSS/jemboss (version 6.4.0 had no > problems with this). > > Any hints of what I can do? The system I compile on is Slackware64 13.37 We'll check on that and get back to you. > Also, is there a place where all versions of EMBOSS are stored, > including the current one? I ask this because my SlackBuild for 6.4.0 > (http://slackbuilds.org/repository/13.37/academic/EMBOSS/) points to a > broken link (ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.4.0.tar.gz) > after 6.5.0 was released. Previous versions always go to the ftp://emboss.open-bio.org/pub/EMBOSS/old/ directory regards, Peter Rice EMBOSS Team