Configuring EMBASSY packages is done using the configure script provided with each package (see the directory listing under Section 1.1.3, “Unpacking the Source Code”). Each EMBASSY package must be configured before it is compiled.
There can be some pitfalls though, so look at the general prerequisites (Section 2.8, “EMBASSY Installation: Platform-specific Concerns”) for your operating system before continuing.
At its most simple all you should need to type (with suitable adjustment to the --prefix option) is:
./configure --prefix=/usr/local/emboss |
In short, you must use exactly the same configuration options with which you configured the main EMBOSS package. There are two exceptions:
You did not supply a --prefix option to the main EMBOSS package configuration or, equivalently, you used --prefix=/usr/local for the main EMBOSS package configuration. In both these cases EMBOSS will have been installed under the /usr/local directory tree. In these cases you must supply an extra option for the EMBASSY packages, namely -enable-localforce, i.e.
./configure --prefix=/usr/local -enable-localforce |
Some of the EMBASSY packages (EMNU and MSE) require an extra system library, namely the Ncurses library. If this library is installed in a non-standard place then you will need to configure with:
./configure --prefix=/usr/local/emboss --with-curses= |
where DIR specifies the location of the Ncurses library. For example, if the Ncurses library is in /opt/lib and the header files are in /opt/include then you would specify --with-curses=/opt.
The use of the --prefix option is vital: it tells the EMBASSY configuration where you installed the main EMBOSS package. If you cannot remember which options you supplied for the EMBOSS configuration then you can look in the config.status file at the top of the EMBOSS source code tree. The config.status file will have been created by the EMBOSS configuration. In the middle of that file you will see something similar to the following lines:
%more config.status.. configured by ./configure, generated by GNU Autoconf 2.63, with options \"'--prefix=/usr/local/emboss'\" ..
You need only specify the compilation options you used for the main EMBOSS package. The CBS packages chlorop, lipop, netnglyc, netoglyc, netphos, prop, signalp, tmhmm and yinoyang are required for the corresponding EMBOSS wrappers provided by CBSTOOLS.
You need only specify the compilation options you used for the main EMBOSS package.
You need only specify the compilation options you used for the main EMBOSS package.
You need only specify the compilation options you used for the main EMBOSS package.
You need to specify both the configuration options used for the main EMBOSS package and may also require the --with-curses=DIR option. See the Platform-specific notes (Section 2.8, “EMBASSY Installation: Platform-specific Concerns”) for Ncurses.
EMNU was written as a simple text-based interface before the advent of GUIs for EMBOSS. Various interfaces are now available (see the EMBOSS Users Guide).
You need only specify the compilation options you used for the main EMBOSS package. The sim4 package is required.
You need only specify the compilation options you used for the main EMBOSS package. The hmmer package is required.
You need only specify the compilation options you used for the main EMBOSS package. The InterProScan package is required. The CBS packages signalp and tmhmm can optionally be installed.
You need only specify the compilation options you used for the main EMBOSS package. The meme package is required.
You need only specify the compilation options you used for the main EMBOSS package. The mira package is required.
You need to specify both the configuration options used for the main EMBOSS package and you may also need the --with-curses=DIR option. See the platform-specific notes (Section 2.8, “EMBASSY Installation: Platform-specific Concerns”) for Ncurses.
You need only specify the compilation options you used for the main EMBOSS package. Note that this package is meant to be installed only by EMBOSS developers. Each must have their own copy. It is not the job of the system administrator to install this package.
You need only specify the compilation options you used for the main EMBOSS package.
You need only specify the compilation options you used for the main EMBOSS package.
You need only specify the compilation options you used for the main EMBOSS package.