1General Users. 2------------- 3 4 5GCC and CC compilers 6-------------------- 7 8The 'configure' script looks for a working GNU C compiler (gcc) and uses it 9by default if it is found. You can force 'configure' to use the 10standard C compiler (cc) by either adding a line to the 'configure' 11script: 12 13 CC=cc 14 15or by defining an environment variable: 16 17 setenv CC cc 18 19The file 'config.cache' seems to retain the value for this option. If you 20have already run 'configure' you may need to delete the 'config.cache' file 21when changing back to the gcc compiler. 22 23 24Shared libraries 25---------------- 26 27By default, the configure script builds shared libraries using 28libtool. While this is very nice for making usable binaries, it can be 29a pain when trying to debug a program. For that reason, compilation of 30shared libraries can be turned off by specifying the 31'--disable-shared' option to 'configure'. 32 33PLplot graphics 34--------------- 35 36EMBOSS now comes with a stripped down version of PLPlot which 37is now compiled under the same system as EMBOSS. 38 39The full PLplot can be obtained from http://www.plplot.org/ 40and by FTP from ftp://plplot.sourceforge.net/pub/plplot/ 41 42PLplot is a scientific graphics library distributed under the GNU 43Library license. This license is a requirement to integrate a graphics 44library into EMBOSS while allowing third party packages (for example 45PHYLIP) to be integrated with the EMBOSS libraries. We are interested 46in any other GNU Library licensed scientific graphics packages. 47 48The only major thing to know about PLplot for the normal user are the 49device types. These consist of various plotters e.g. 50"xterm","xwin","ps" (postscipt) ,"psc" (colour postscript). 51 52X devices. 53---------- 54 55To get xterm you must have X installed or else PLplot will not build the 56required driver. 57 58PNG driver. 59----------- 60 61To get the PNG driver you will need to have installed the z, png and 62gd libraries. In particular gd version >= 2.0.28 must be used. If for 63some reason you do not have the required libraries and your system 64support group will not update these then install all three latest 65versions (z, gd, png) to a new directory and then add this new 66directory to your configure line for EMBOSS. 67 68 ./configure --with-pngdriver=my_dir 69 70as gd (and the others) were installed using --prefix=my_dir 71in their ./configure commands. On Linux distributions the 72above is not usually necessary as PNG graphics will be detected 73automatically as long as both the library and development 74RPMs/PKGs have been installed. 75 76 77 78Other graphics libraries 79------------------------ 80 81We have considered other graphics libraries, including the GNU libplot 82library. The problem with GNU libplot currently is that it uses the 83full GNU license which is not suitable for the non-EMBOSS applications. 84We understand that there will be a future release of GNU libplot under 85the GNU Library license. We also intend separating graphics by making 86the applications produce XML output which can then be rendered using 87a separate OpenGL-based graphics engine. 88 89Third party applications 90------------------------ 91 92A few applications are wrappers to third-party applications which must 93be installed and in one case customised. 94 95clustalw release 1.8.0 or later, or 2 or later, should be installed in 96the path with the name clustalw. EMBOSS application emma is a wrapper 97to launch clustalw. 98 99primer3 from the Whitehead institute must be installed in one or two versions. 100 101EMBOSS application eprimer3 launches primer3_core and expects this to 102be version 1.x of the program. 103 104EMBOSS application eprimer32 launches primer32_core and expects this 105to be a renamed primer3_core from version 2.x of the program. 106 107primer3's configuration files also need to be installed. The original 108application looks by default in /opt/primer3_config 109 110Installation. 111------------- 112 113If you have copied the binaries to another directory instead, or 114made other changes to the file locations, you can also use 115environment variables or the embossrc file(s) to tell the programs 116where to look 117 118You will need to use this command: 119 120 setenv EMBOSS_ACDROOT $(prefix)/share/EMBOSS/acd 121 122or in your site emboss.default file (in the share/EMBOSS install 123directory or under emboss/ in the original source directory) or in 124~/.embossrc file put 125 126 env emboss_acdroot $(prefix)/share/EMBOSS/acd 127 128 129Compilation problems for the CVS developers version 130--------------------------------------------------- 131 132On some systems there may be compatibility problems with different 133automake, autoconf or libtool versions. Always make sure that you keep 134up to date with releases of these tools and let us know of any 135problems you experience (emboss-bug@emboss.open-bio.org). If a libtool problem 136does arise you can try deleting the following files: 137 138 config.cache 139 ltmain.sh 140 ltconfig 141 libtool 142 143and then type 144 145 aclocal -I m4 146 autoconf 147 automake -a 148 149and then retry the make. 150