[EMBOSS] emma/clustalw PATH problems

George Magklaras george.magklaras at biotek.uio.no
Thu Aug 18 15:15:57 UTC 2005

How about placing the clustalw binary ( I assume that you have compiled 
this separately) into the same directory where you have the emboss 
binaries? If every other aspect of your EMBOSS install is OK then that 
should work?


George B. Magklaras

Senior Computer Systems Engineer/UNIX Systems Administrator
The Biotechnology Centre of Oslo,
University of Oslo

EMBnet Norway: http://www.biotek.uio.no/EMBNET/

Anders Nistér wrote:

>I am trying to run emma, and for certain reasons i don't have clustalw in my
>Running emma produces this error:
>   EMBOSS An error in ajsys.c at line 398:
>cannot find program 'clustalw'
>Looking through the manual for emma there is a mention of EMBOSS_CLUSTALW:
>   "cannot find program 'clustalw'" - means that the ClustalW program has
>   not been set up on your site or is not in your environment (i.e. is
>   not on your path). The solutions are to (1) install clustalw in the
>   path so that emma can find it with the command "clustalw", or (2)
>   define a variable (an environment variable of in emboss.defaults or
>   your .embossrc file) called EMBOSS_CLUSTALW containing the command
>   (program name or full path) to run clustalw if you have it elsewhere
>   on your system.
>So I'm supposed to be able to specify the full path to clustalw through
>Setting this variable to the full path of clustalw produces a similar error
>to the one before.
>   EMBOSS An error in ajsys.c at line 398:
>cannot find program '/usr/local/bin/clustalw'
>Looking through the emma source code I can see that ajSystemEnv is used to
>execute clustalw, this function will always look through the PATH env
>variable for the executable it is trying to run, so specifying a full path
>does absolutely nothing to get around the problem.
>Is the documentation wrong or is this a bug ?
>Has anyone got a workaround ?
>Is there any emboss function for executing an external program directly,
>without it being present in PATH ?
>/Anders Nistér
>EMBOSS mailing list
>EMBOSS at emboss.open-bio.org

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