Re: [EMBOSS] emma and clustalw2
Hi Mahmut, Thanks it works nicely this way. So, move back to external: "clustalw" and use EMBOSS_CLUSTALW variable. 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' -- Sébastien 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/ ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] emma and clustalw2
Dear Sebastien, On 31/01/2013 16:04, Moretti Sébastien 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 ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] emma and clustalw2
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' ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
[EMBOSS] emma and clustalw2
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 -- Sébastien 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/ ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
