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The European Molecular Biology Open Software Suite (clone of git://anonscm.debian.org/debian-med/emboss.git)
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General Users. ------------- GCC and CC compilers -------------------- The 'configure' script looks for a working GNU C compiler (gcc) and uses it by default if it is found. You can force 'configure' to use the standard C compiler (cc) by either adding a line to the 'configure' script: CC=cc or by defining an environment variable: setenv CC cc The file 'config.cache' seems to retain the value for this option. If you have already run 'configure' you may need to delete the 'config.cache' file when changing back to the gcc compiler. Shared libraries ---------------- By default, the configure script builds shared libraries using libtool. While this is very nice for making usable binaries, it can be a pain when trying to debug a program. For that reason, compilation of shared libraries can be turned off by specifying the '--disable-shared' option to 'configure'. PLplot graphics --------------- EMBOSS now comes with a stripped down version of PLPlot which is now compiled under the same system as EMBOSS. The full PLplot can be obtained from http://www.plplot.org/ and by FTP from ftp://plplot.sourceforge.net/pub/plplot/ PLplot is a scientific graphics library distributed under the GNU Library license. This license is a requirement to integrate a graphics library into EMBOSS while allowing third party packages (for example PHYLIP) to be integrated with the EMBOSS libraries. We are interested in any other GNU Library licensed scientific graphics packages. The only major thing to know about PLplot for the normal user are the device types. These consist of various plotters e.g. "xterm","xwin","ps" (postscipt) ,"psc" (colour postscript). X devices. ---------- To get xterm you must have X installed or else PLplot will not build the required driver. PNG driver. ----------- To get the PNG driver you will need to have installed the z, png and gd libraries. In particular gd version >= 2.0.28 must be used. If for some reason you do not have the required libraries and your system support group will not update these then install all three latest versions (z, gd, png) to a new directory and then add this new directory to your configure line for EMBOSS. ./configure --with-pngdriver=my_dir as gd (and the others) were installed using --prefix=my_dir in their ./configure commands. On Linux distributions the above is not usually necessary as PNG graphics will be detected automatically as long as both the library and development RPMs/PKGs have been installed. Other graphics libraries ------------------------ We have considered other graphics libraries, including the GNU libplot library. The problem with GNU libplot currently is that it uses the full GNU license which is not suitable for the non-EMBOSS applications. We understand that there will be a future release of GNU libplot under the GNU Library license. We also intend separating graphics by making the applications produce XML output which can then be rendered using a separate OpenGL-based graphics engine. Third party applications ------------------------ A few applications are wrappers to third-party applications which must be installed and in one case customised. clustalw release 1.8.0 or later, or 2 or later, should be installed in the path with the name clustalw. EMBOSS application emma is a wrapper to launch clustalw. primer3 from the Whitehead institute must be installed in one or two versions. EMBOSS application eprimer3 launches primer3_core and expects this to be version 1.x of the program. EMBOSS application eprimer32 launches primer32_core and expects this to be a renamed primer3_core from version 2.x of the program. primer3's configuration files also need to be installed. The original application looks by default in /opt/primer3_config Installation. ------------- If you have copied the binaries to another directory instead, or made other changes to the file locations, you can also use environment variables or the embossrc file(s) to tell the programs where to look You will need to use this command: setenv EMBOSS_ACDROOT $(prefix)/share/EMBOSS/acd or in your site emboss.default file (in the share/EMBOSS install directory or under emboss/ in the original source directory) or in ~/.embossrc file put env emboss_acdroot $(prefix)/share/EMBOSS/acd Compilation problems for the CVS developers version --------------------------------------------------- On some systems there may be compatibility problems with different automake, autoconf or libtool versions. Always make sure that you keep up to date with releases of these tools and let us know of any problems you experience (firstname.lastname@example.org). If a libtool problem does arise you can try deleting the following files: config.cache ltmain.sh ltconfig libtool and then type aclocal -I m4 autoconf automake -a and then retry the make.