The EMBASSY packages are available on the same FTP server and in the same directory as the primary EMBOSS distribution. Follow the instructions in the EMBOSS chapter for downloading instructions.
You cannot install the EMBASSY packages without first installing the main EMBOSS package, so do that before continuing. The EMBASSY packages can be installed from any temporary directory of your choice.
myemboss is an EMBASSY package designed for use by EMBOSS software developers so you may not wish to install it if your site serves only biologists. myembossdemo contains usage examples of the myemboss package.
You will have downloaded the EMBASSY source code to a suitable directory. Move to whichever directory you chose (e.g. cd /usr/local/src/embassy) and list the directory to make sure.
%lsCBSTOOLS-1.0.0.tar.gz HMMER-2.3.2.tar.gz MYEMBOSSDEMO-6.1.0.tar.gz DOMAINATRIX-0.1.0.tar.gz IPRSCAN-4.3.1.tar.gz PHYLIPNEW-3.68.tar.gz DOMALIGN-0.1.0.tar.gz MEMENEW-4.0.0.tar.gz SIGNATURE-0.1.0.tar.gz DOMSEARCH-0.1.0.tar.gz MIRA-2.8.2.tar.gz STRUCTURE-0.1.0.tar.gz EMNU-1.05.tar.gz MSE-1.0.0.tar.gz TOPO-1.0.0.tar.gz ESIM4-1.0.0.tar.gz MYEMBOSS-6.1.0.tar.gz VIENNA-1.7.2.tar.gz
These EMBASSY files are compressed binary files and require that your UNIX distribution has the gunzip program installed. Check that the command:
which gunzip |
gives a positive response. If not then install the gzip package from whichever freeware site your UNIX distribution uses or, alternatively, compile the source code from the gzip homepage (http://www.gzip.org) which helpfully contains compilation instructions.
Taking DOMAINATRIX as an example, unpack it by typing:
gunzip DOMAINATRIX-0.1.0.tar.gz |
This will create a file called DOMAINATRIX-0.1.0.tar. Such tar files are archive files containing the individual source code files. You must now extract the archive using the tar program:
tar xf DOMAINATRIX-0.1.0.tar |
This will create a new directory, DOMAINATRIX-0.1.0: the exact name will depend on the version of DOMAINATRIX being unpacked.
The tar program on most UNIX distributions will usually perform satisfactorily, however some will not. So, check the platform specific notes (Section 2.8, “EMBASSY Installation: Platform-specific Concerns”) section of this chapter to see whether you need to install the GNU version of the tar program instead.
Enter the directory and type ls to show the files. The directory listing should look something like this:
%cd DOMAINATRIX-0.1.0%lsaclocal.m4 config.sub depcomp ltmain.sh missing AUTHORS configure emboss_acd m4 NEWS ChangeLog configure.in INSTALL Makefile.am README config.guess COPYING install-sh Makefile.in src
If it doesn't then you're in the wrong directory. This unpacking procedure applies to all the EMBASSY packages. You are now ready to build the packages.