From bernd.lentes at helmholtz-muenchen.de Wed Jan 16 08:00:23 2013 From: bernd.lentes at helmholtz-muenchen.de (Lentes, Bernd) Date: Wed, 16 Jan 2013 14:00:23 +0100 Subject: [EMBOSS] ./configure blaims about missing package although xorg-x11-proto-devel is installed Message-ID: <15785B7E063D464C86DD482FCAE4EBA5017F71493022@XCH11.scidom.de> Hi, i'm new to EMBOSS and trying to install it for one of our developers. We downloaded the current version, unpacked it and started ./configure. It blaims about missing xorg-x11-proto-devel, although it is installed: pc56846:~/EMBOSS-6.2.0 # rpm -q xorg-x11-proto-devel xorg-x11-proto-devel-7.4-1.24.25.42 The exact error is: X11 graphics have been selected but no X11 header files have been found. This error usually happens on Linux/MacOSX distributions where the optional X11 development files have not been installed. On Linux RPM systems this package is usually called something like xorg-x11-proto-devel whereas on Debian/Ubuntu it may be called x-dev. On MacOSX installation DVDs the X11 files can usually be found as an explicitly named optional installation. I tried version 6.2.0 and 6.5.7. Host is a SLES 11 SP1, 64bit. I also tried "./configure --x-includes=/usr/include/X11/", but it didn't suceed. Any ideas ? Bernd -- Bernd Lentes Systemadministration Institut f?r Entwicklungsgenetik Geb?ude 35.34 - Raum 208 HelmholtzZentrum m?nchen bernd.lentes at helmholtz-muenchen.de phone: +49 89 3187 1241 fax: +49 89 3187 2294 http://www.helmholtz-muenchen.de/idg Wenn ich eine Idee habe, sorge ich als Erstes daf?r, da? die Buchhalter nichts erfahren. Sie sind der Totengr?ber jedes Traumes. Sir Richard Branson Helmholtz Zentrum M?nchen Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) Ingolst?dter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum Registergericht: Amtsgericht M?nchen HRB 6466 USt-IdNr: DE 129521671 From stefanielager at gmail.com Thu Jan 24 00:43:18 2013 From: stefanielager at gmail.com (Stefanie Lager) Date: Thu, 24 Jan 2013 07:43:18 +0200 Subject: [EMBOSS] Translate and convert start codon to Methionine Message-ID: Hi, Is there ANY Emboss program that can translate DNA sequence and convert the different possible start codons to methionine correctly? Transeq doesn't seem to be able to do it, getorf is supposed to be able to do it but the -methionine Y option doesn't seem to work? Stefanie Lager From ricepeterm at yahoo.co.uk Thu Jan 24 04:56:40 2013 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Thu, 24 Jan 2013 09:56:40 +0000 Subject: [EMBOSS] Translate and convert start codon to Methionine In-Reply-To: References: Message-ID: <51010558.1000903@yahoo.co.uk> Dear Stefanie, On 24/01/2013 05:43, Stefanie Lager wrote: > Hi, > > Is there ANY Emboss program that can translate DNA sequence and > convert the different possible start codons to methionine correctly? > Transeq doesn't seem to be able to do it, getorf is supposed to be > able to do it but the -methionine Y option doesn't seem to work? You need to set a couple of options in getorf, Note that -methionine is already on by default, you can set it to 'N' or use -nomethionine to turn off the conversion of start codons in getorf. You have to use a genetic code table with alternative starts, for example: -table 1 uses an alternative genetic code with atg, ttg and ctg as starts, or: -table 11 uses more alternative starts for bacteria and chloroplasts You may need to set the '-find' option. Getorf assumes the sequence is a fragment, so all ORFs are already open until a stop codon is reached. -find 1 requires a start codon in the sequence to open an ORF. If the start codon you are looking for is in an already open reading frame this may be the option you need to translate it as methionine. Hope this helps Peter Rice EMBOSS Team From stefanielager at gmail.com Tue Jan 29 05:19:00 2013 From: stefanielager at gmail.com (Stefanie Lager) Date: Tue, 29 Jan 2013 12:19:00 +0200 Subject: [EMBOSS] Wildcard problem Message-ID: Hi, I have a wildcard problem, which I don't know if it's really an EMBOSS problem? I try to run e.g. seqret *.seq:seqname And this works fine on a linux machine in bash with Emboss 6.3.1, but it does not work in linux running tcsh with Emboss 6.5.7.0 "seqret: No match." Has anyone seen any similar problem? Regards, Stefanie Lager From ricepeterm at yahoo.co.uk Tue Jan 29 06:20:08 2013 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Tue, 29 Jan 2013 11:20:08 +0000 Subject: [EMBOSS] Wildcard problem In-Reply-To: References: Message-ID: <5107B068.4030608@yahoo.co.uk> On 29/01/2013 10:19, Stefanie Lager wrote: > Hi, > > I have a wildcard problem, which I don't know if it's really an EMBOSS > problem? I try to run e.g. It is a shell problem .. but it does show up another EMBOSS problem. > seqret *.seq:seqname > > And this works fine on a linux machine in bash with Emboss 6.3.1, but > it does not work in linux running tcsh with Emboss 6.5.7.0 > > "seqret: No match." > > Has anyone seen any similar problem? That would be a shell problem, not an EMBOSS problem. Using tcsh the shell tries to expand *.seq into a list of filenames on the command line. This can give unwanted effects, for example with two files matching *.seq you could get a valid seqret command line where the second file becomes the output file and is overwritten (note that seqret has a valid output file name and does not prompt for an output file in the example below). % ls -l *.seq total 2 -rw-r--r-- 1 pmr None 30 Jan 29 10:45 abc.seq -rw-r--r-- 1 pmr None 26 Jan 29 10:45 xyz.seq % seqret *.seq % ls -l *.seq total 2 -rw-r--r-- 1 pmr None 30 Jan 29 10:45 abc.seq -rw-r--r-- 1 pmr None 30 Jan 29 10:48 xyz.seq The solution should be to put quotes around any wildcards - in filenames or in any other options, because the shell may try to expand them into filenames. However, if you put quotes around the "*.seq" wildcard filename to keep the shell form interpreting it, EMBOSS fails to read the sequence. It should be able to find the identifier 'seqname' in one of the files. This worked in EMBOSS 6.3.1 but seems to have been broken when the query language was rewritten. I will take a look and make a patch for the latest release any other releases affected. regards, Peter Rice EMBOSS Team From sebastien.moretti at unil.ch Thu Jan 31 11:04:11 2013 From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?Moretti_S=E9bastien?=) Date: Thu, 31 Jan 2013 17:04:11 +0100 Subject: [EMBOSS] emma and clustalw2 Message-ID: <510A95FB.3040103@unil.ch> Hi I try to use emma (v 6.5.7.0) with clustalw2 (v 2.1) on Linux x86_64. My environment contains both clustalw and clustalw2, that's why clustalw2 binary is called clustalw2. Accordingly I have changed this line in the emma.acd file (before compilation): external: "clustalw2" instead of external: "clustalw" When I try to run emma, I get this error message: Multiple sequence alignment (ClustalW wrapper) Warning: Cannot find 'clustalw', no ACD external definition found Error: Failed to open filename '00011120B' Problem writing out EMBOSS alignment file Error: File 'msf::00011120B' remove failed, error:2 'No such file or directory' Do you know how to solve this ? Regards -- S?bastien Moretti SIB Vital-IT EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4079/4221 http://www.vital-it.ch/ http://myhits.vital-it.ch/ From uludag at ebi.ac.uk Thu Jan 31 11:37:37 2013 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Thu, 31 Jan 2013 16:37:37 +0000 Subject: [EMBOSS] emma and clustalw2 In-Reply-To: <510A95FB.3040103@unil.ch> References: <510A95FB.3040103@unil.ch> Message-ID: <510A9DD1.4020303@ebi.ac.uk> Hi Sebastien, It looks if I set EMBOSS_CLUSTALW environment variable to point to clustalw2 executable, as in the following example, i don't need to modify the emma.acd file. export EMBOSS_CLUSTALW=~/esbin/clustalw-2.1/bin/clustalw2 Regards, Mahmut > I try to use emma (v 6.5.7.0) with clustalw2 (v 2.1) on Linux x86_64. > My environment contains both clustalw and clustalw2, that's why > clustalw2 binary is called clustalw2. > Accordingly I have changed this line in the emma.acd file (before > compilation): > external: "clustalw2" > instead of > external: "clustalw" > > > When I try to run emma, I get this error message: > > Multiple sequence alignment (ClustalW wrapper) > Warning: Cannot find 'clustalw', no ACD external definition found > Error: Failed to open filename '00011120B' > Problem writing out EMBOSS alignment file > Error: File 'msf::00011120B' remove failed, error:2 'No such file or > directory' From ricepeterm at yahoo.co.uk Thu Jan 31 12:04:20 2013 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Thu, 31 Jan 2013 17:04:20 +0000 Subject: [EMBOSS] emma and clustalw2 In-Reply-To: <510A95FB.3040103@unil.ch> References: <510A95FB.3040103@unil.ch> Message-ID: <510AA414.4040901@yahoo.co.uk> Dear Sebastien, On 31/01/2013 16:04, Moretti S?bastien wrote: > I try to use emma (v 6.5.7.0) with clustalw2 (v 2.1) on Linux x86_64. > My environment contains both clustalw and clustalw2, that's why > clustalw2 binary is called clustalw2. > Accordingly I have changed this line in the emma.acd file (before > compilation): > external: "clustalw2" > instead of > external: "clustalw" The name is fixed within emma source code in a call to ajAcdGetPathC, so changing it in the ACD file will not work. You can define EMBOSS_CLUSTALW to point to clustalw2 in your emboss.default file (for all users), in your personal ~/.embossrc file (only for yourself), or as an environment variable for the current session. > When I try to run emma, I get this error message: > > Multiple sequence alignment (ClustalW wrapper) > Warning: Cannot find 'clustalw', no ACD external definition found This is because emma is looking for "clustalw" explicitly in the path or defined as above. The ACD parser has found an application called "clustalw2" so it completed successfully. However, when emma asks for the path to "clustalw" it is surprised to find that the ACD parser does not know the answer. Hope that helps, Peter Rice EMBOSS Team From bernd.lentes at helmholtz-muenchen.de Wed Jan 16 13:00:23 2013 From: bernd.lentes at helmholtz-muenchen.de (Lentes, Bernd) Date: Wed, 16 Jan 2013 14:00:23 +0100 Subject: [EMBOSS] ./configure blaims about missing package although xorg-x11-proto-devel is installed Message-ID: <15785B7E063D464C86DD482FCAE4EBA5017F71493022@XCH11.scidom.de> Hi, i'm new to EMBOSS and trying to install it for one of our developers. We downloaded the current version, unpacked it and started ./configure. It blaims about missing xorg-x11-proto-devel, although it is installed: pc56846:~/EMBOSS-6.2.0 # rpm -q xorg-x11-proto-devel xorg-x11-proto-devel-7.4-1.24.25.42 The exact error is: X11 graphics have been selected but no X11 header files have been found. This error usually happens on Linux/MacOSX distributions where the optional X11 development files have not been installed. On Linux RPM systems this package is usually called something like xorg-x11-proto-devel whereas on Debian/Ubuntu it may be called x-dev. On MacOSX installation DVDs the X11 files can usually be found as an explicitly named optional installation. I tried version 6.2.0 and 6.5.7. Host is a SLES 11 SP1, 64bit. I also tried "./configure --x-includes=/usr/include/X11/", but it didn't suceed. Any ideas ? Bernd -- Bernd Lentes Systemadministration Institut f?r Entwicklungsgenetik Geb?ude 35.34 - Raum 208 HelmholtzZentrum m?nchen bernd.lentes at helmholtz-muenchen.de phone: +49 89 3187 1241 fax: +49 89 3187 2294 http://www.helmholtz-muenchen.de/idg Wenn ich eine Idee habe, sorge ich als Erstes daf?r, da? die Buchhalter nichts erfahren. Sie sind der Totengr?ber jedes Traumes. Sir Richard Branson Helmholtz Zentrum M?nchen Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) Ingolst?dter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum Registergericht: Amtsgericht M?nchen HRB 6466 USt-IdNr: DE 129521671 From stefanielager at gmail.com Thu Jan 24 05:43:18 2013 From: stefanielager at gmail.com (Stefanie Lager) Date: Thu, 24 Jan 2013 07:43:18 +0200 Subject: [EMBOSS] Translate and convert start codon to Methionine Message-ID: Hi, Is there ANY Emboss program that can translate DNA sequence and convert the different possible start codons to methionine correctly? Transeq doesn't seem to be able to do it, getorf is supposed to be able to do it but the -methionine Y option doesn't seem to work? Stefanie Lager From ricepeterm at yahoo.co.uk Thu Jan 24 09:56:40 2013 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Thu, 24 Jan 2013 09:56:40 +0000 Subject: [EMBOSS] Translate and convert start codon to Methionine In-Reply-To: References: Message-ID: <51010558.1000903@yahoo.co.uk> Dear Stefanie, On 24/01/2013 05:43, Stefanie Lager wrote: > Hi, > > Is there ANY Emboss program that can translate DNA sequence and > convert the different possible start codons to methionine correctly? > Transeq doesn't seem to be able to do it, getorf is supposed to be > able to do it but the -methionine Y option doesn't seem to work? You need to set a couple of options in getorf, Note that -methionine is already on by default, you can set it to 'N' or use -nomethionine to turn off the conversion of start codons in getorf. You have to use a genetic code table with alternative starts, for example: -table 1 uses an alternative genetic code with atg, ttg and ctg as starts, or: -table 11 uses more alternative starts for bacteria and chloroplasts You may need to set the '-find' option. Getorf assumes the sequence is a fragment, so all ORFs are already open until a stop codon is reached. -find 1 requires a start codon in the sequence to open an ORF. If the start codon you are looking for is in an already open reading frame this may be the option you need to translate it as methionine. Hope this helps Peter Rice EMBOSS Team From stefanielager at gmail.com Tue Jan 29 10:19:00 2013 From: stefanielager at gmail.com (Stefanie Lager) Date: Tue, 29 Jan 2013 12:19:00 +0200 Subject: [EMBOSS] Wildcard problem Message-ID: Hi, I have a wildcard problem, which I don't know if it's really an EMBOSS problem? I try to run e.g. seqret *.seq:seqname And this works fine on a linux machine in bash with Emboss 6.3.1, but it does not work in linux running tcsh with Emboss 6.5.7.0 "seqret: No match." Has anyone seen any similar problem? Regards, Stefanie Lager From ricepeterm at yahoo.co.uk Tue Jan 29 11:20:08 2013 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Tue, 29 Jan 2013 11:20:08 +0000 Subject: [EMBOSS] Wildcard problem In-Reply-To: References: Message-ID: <5107B068.4030608@yahoo.co.uk> On 29/01/2013 10:19, Stefanie Lager wrote: > Hi, > > I have a wildcard problem, which I don't know if it's really an EMBOSS > problem? I try to run e.g. It is a shell problem .. but it does show up another EMBOSS problem. > seqret *.seq:seqname > > And this works fine on a linux machine in bash with Emboss 6.3.1, but > it does not work in linux running tcsh with Emboss 6.5.7.0 > > "seqret: No match." > > Has anyone seen any similar problem? That would be a shell problem, not an EMBOSS problem. Using tcsh the shell tries to expand *.seq into a list of filenames on the command line. This can give unwanted effects, for example with two files matching *.seq you could get a valid seqret command line where the second file becomes the output file and is overwritten (note that seqret has a valid output file name and does not prompt for an output file in the example below). % ls -l *.seq total 2 -rw-r--r-- 1 pmr None 30 Jan 29 10:45 abc.seq -rw-r--r-- 1 pmr None 26 Jan 29 10:45 xyz.seq % seqret *.seq % ls -l *.seq total 2 -rw-r--r-- 1 pmr None 30 Jan 29 10:45 abc.seq -rw-r--r-- 1 pmr None 30 Jan 29 10:48 xyz.seq The solution should be to put quotes around any wildcards - in filenames or in any other options, because the shell may try to expand them into filenames. However, if you put quotes around the "*.seq" wildcard filename to keep the shell form interpreting it, EMBOSS fails to read the sequence. It should be able to find the identifier 'seqname' in one of the files. This worked in EMBOSS 6.3.1 but seems to have been broken when the query language was rewritten. I will take a look and make a patch for the latest release any other releases affected. regards, Peter Rice EMBOSS Team From sebastien.moretti at unil.ch Thu Jan 31 16:04:11 2013 From: sebastien.moretti at unil.ch (=?ISO-8859-1?Q?Moretti_S=E9bastien?=) Date: Thu, 31 Jan 2013 17:04:11 +0100 Subject: [EMBOSS] emma and clustalw2 Message-ID: <510A95FB.3040103@unil.ch> Hi I try to use emma (v 6.5.7.0) with clustalw2 (v 2.1) on Linux x86_64. My environment contains both clustalw and clustalw2, that's why clustalw2 binary is called clustalw2. Accordingly I have changed this line in the emma.acd file (before compilation): external: "clustalw2" instead of external: "clustalw" When I try to run emma, I get this error message: Multiple sequence alignment (ClustalW wrapper) Warning: Cannot find 'clustalw', no ACD external definition found Error: Failed to open filename '00011120B' Problem writing out EMBOSS alignment file Error: File 'msf::00011120B' remove failed, error:2 'No such file or directory' Do you know how to solve this ? Regards -- S?bastien Moretti SIB Vital-IT EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4079/4221 http://www.vital-it.ch/ http://myhits.vital-it.ch/ From uludag at ebi.ac.uk Thu Jan 31 16:37:37 2013 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Thu, 31 Jan 2013 16:37:37 +0000 Subject: [EMBOSS] emma and clustalw2 In-Reply-To: <510A95FB.3040103@unil.ch> References: <510A95FB.3040103@unil.ch> Message-ID: <510A9DD1.4020303@ebi.ac.uk> Hi Sebastien, It looks if I set EMBOSS_CLUSTALW environment variable to point to clustalw2 executable, as in the following example, i don't need to modify the emma.acd file. export EMBOSS_CLUSTALW=~/esbin/clustalw-2.1/bin/clustalw2 Regards, Mahmut > I try to use emma (v 6.5.7.0) with clustalw2 (v 2.1) on Linux x86_64. > My environment contains both clustalw and clustalw2, that's why > clustalw2 binary is called clustalw2. > Accordingly I have changed this line in the emma.acd file (before > compilation): > external: "clustalw2" > instead of > external: "clustalw" > > > When I try to run emma, I get this error message: > > Multiple sequence alignment (ClustalW wrapper) > Warning: Cannot find 'clustalw', no ACD external definition found > Error: Failed to open filename '00011120B' > Problem writing out EMBOSS alignment file > Error: File 'msf::00011120B' remove failed, error:2 'No such file or > directory' From ricepeterm at yahoo.co.uk Thu Jan 31 17:04:20 2013 From: ricepeterm at yahoo.co.uk (Peter Rice) Date: Thu, 31 Jan 2013 17:04:20 +0000 Subject: [EMBOSS] emma and clustalw2 In-Reply-To: <510A95FB.3040103@unil.ch> References: <510A95FB.3040103@unil.ch> Message-ID: <510AA414.4040901@yahoo.co.uk> Dear Sebastien, On 31/01/2013 16:04, Moretti S?bastien wrote: > I try to use emma (v 6.5.7.0) with clustalw2 (v 2.1) on Linux x86_64. > My environment contains both clustalw and clustalw2, that's why > clustalw2 binary is called clustalw2. > Accordingly I have changed this line in the emma.acd file (before > compilation): > external: "clustalw2" > instead of > external: "clustalw" The name is fixed within emma source code in a call to ajAcdGetPathC, so changing it in the ACD file will not work. You can define EMBOSS_CLUSTALW to point to clustalw2 in your emboss.default file (for all users), in your personal ~/.embossrc file (only for yourself), or as an environment variable for the current session. > When I try to run emma, I get this error message: > > Multiple sequence alignment (ClustalW wrapper) > Warning: Cannot find 'clustalw', no ACD external definition found This is because emma is looking for "clustalw" explicitly in the path or defined as above. The ACD parser has found an application called "clustalw2" so it completed successfully. However, when emma asks for the path to "clustalw" it is surprised to find that the ACD parser does not know the answer. Hope that helps, Peter Rice EMBOSS Team