[EMBOSS] emma/clustalw PATH problems

Sean.Maceachern at dpi.vic.gov.au Sean.Maceachern at dpi.vic.gov.au
Thu Aug 18 23:01:53 UTC 2005

I have had a simillar problem with eprimer3, a temporary fix will be to
modify your path so that it can find the clustalw binary


export PATH=$PATH:/home/sm82/primer3_1.0.0/src

                      anders.nister at lcb.uu.se                                                                                                
                      Sent by:                       To:       emboss at emboss.open-bio.org                                                    
                      emboss-bounces at emboss.o        cc:                                                                                     
                      pen-bio.org                    Subject:  [EMBOSS] emma/clustalw PATH problems                                          
                      19/08/2005 12:46 AM                                                                                                    

I am trying to run emma, and for certain reasons i don't have clustalw in

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

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