[EMBOSS] Embassy tools

[Sumit Middha]

Hello Alan,
Thanks for your help on that.

I tried downloading and installing mse-1.0. The make was going fine 
until this error. A similar thing happened with MYEMBOSS-3.0. I used the 
--prefix option for emboss. So I untarred these to someplace and used 
.configure with --prefix option.
Am I doing something wrong?
Thanks.

mse.c:18:18: ajax.h: No such file or directory
In file included from mse.c:29:
../h/mse.h:203: error: parse error before "AjPSeqout"
mse.c:40: error: parse error before "seqset"
mse.c: In function `LoadSeqWithseqset':
mse.c:43: error: syntax error before "tempname"
mse.c:45: error: `seqset' undeclared (first use in this function)
mse.c:45: error: (Each undeclared identifier is reported only once
mse.c:45: error: for each function it appears in.)
mse.c:51: warning: passing arg 2 of `strcpy' makes pointer from integer 
without a cast
mse.c:54: warning: assignment makes pointer from integer without a cast
mse.c:77: error: `tempname' undeclared (first use in this function)
mse.c:79: warning: passing arg 2 of `strcpy' makes pointer from integer 
without a cast
mse.c: At top level:
mse.c:100: error: parse error before "AjPSeqout"
mse.c: In function `DoSave':
mse.c:104: error: `AjPSeq' undeclared (first use in this function)
mse.c:104: error: parse error before "seqnew"
mse.c:105: error: `AjPStr' undeclared (first use in this function)
mse.c:106: error: `AjPSeqout' undeclared (first use in this function)
.........
*** Error code 1
make: Fatal error: Command failed for target `mse.o'
Current working directory /bioportal/build/MSE-1.0.0/source
*** Error code 1
make: Fatal error: Command failed for target `all-recursive'

for MYEMBOSS:

myseq.c:22:20: emboss.h: No such file or directory
myseq.c: In function `main':
myseq.c:33: error: `AjPSeq' undeclared (first use in this function)
myseq.c:33: error: (Each undeclared identifier is reported only once
myseq.c:33: error: for each function it appears in.)
.........


ajb at ebi.ac.uk wrote:

>There are also instructions at:
>  http://emboss.sourceforge.net/docs/faq.html
>
>Look for "Q) Installing associated software PHYLIP". You need the
>instructions
>in part 'b)' of that question as you are not using the CVS version of EMBOSS.
>
>To summarise what's there in case it was that documentation which
>confused you, if you installed EMBOSS-3.0.0 using:
>
>    ./configure --prefix=/usr/local/emboss [and any other options you chose]
>    make
>    make install
>
>Then you install PHYLIP using:
>
>   ./configure --prefix=/usr/local/emboss  [and any other options you chose]
>   make
>   make install
>
>
>
>There is only one exception and that is if you installed EMBOSS-3.0.0 using:
>
>   ./configure
>   make
>   make install
>
>(i.e. you didn't supply a --prefix). In this case you have to supply
>an extra flag to the EMBASSY package configuration i.e.
>
>   ./configure --enable-localforce
>   make
>   make install
>
>We recommend that you use the first approach (i.e supply a --prefix)
>to have EMBOSS installed in a directory of its own.
>The instructions at the URL above were updated last night and replace
>those in the EMBOSS-3.0.0/FAQ file.
>
>HTH
>
>Alan
>
>
>  
>

-- 
Sumit Middha, MS in Bioinformatics
Assistant Staff Scientist
The Center for Genomics and Bioinformatics
Indiana University, Jordan Hall
Bloomington, IN 47405-3700