[EMBOSS] emma/clustalw PATH problems

[Andrew.Mather at dpi.vic.gov.au]

Hi,

You can also put a symlink in the directory with all the Emboss 
executables.

I had to do this to get Emboss Explorer to work, even though both clustalw 
and primer3_core executables were in /usr/local/bin. 

I made a symlink in the Emboss-2.xxxx/bin directory and all was well.

Andrew



Bioinformatics Advanced Scientific Computing, 
Animal Genetics and Genomics, PIRVic Attwood
475 Mickleham Road, Attwood, 3049
ph +61 3 92174342
mob  0413 009 761


----------------
There are 10 kinds of people...those who understand binary and those who 
don't.





Sean.Maceachern at dpi.vic.gov.au
Sent by: emboss-bounces at emboss.open-bio.org
19/08/05 09:01 AM

 
        To:     anders.nister at lcb.uu.se
        cc:     emboss at emboss.open-bio.org
        Subject:        Re: [EMBOSS] emma/clustalw PATH problems



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

eg)

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
my
PATH.

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
EMBOSS_CLUSTALW....

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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