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diff --git a/academic/staden/README b/academic/staden/README index 58460934c6..ccb3223dcf 100644 --- a/academic/staden/README +++ b/academic/staden/README @@ -2,26 +2,30 @@ The programs part of the Staden package provide a fully developed set of DNA sequence assembly, editing, analysis and more. Some of its features include: -GAP4 - Performs assembly, contig joining, assembly checking, repeat search, - experiment suggestion, read pair analysis and contig editing. -GAP5 - The new development version of Gap4, designed to work with the large - volumes of data attainable through the newer sequencing technologies. -PREGAP4 - Provides a graphical user interface to set up the processing - required to prepare trace data for assembly or analysis. -SPIN - Compares pairs of sequences in many ways, often presenting its results - graphically and has a sliding sequence window linked to the plots. -TREV - A rapid and flexible viewer and editor for ABI, ALF or SCF trace files. +GAP4 - Performs assembly, contig joining, assembly checking, repeat + search, experiment suggestion, read pair analysis and contig + editing. +GAP5 - The new development version of Gap4, designed to work with the + large volumes of data attainable through the newer sequencing + technologies. +PREGAP4 - Provides a graphical user interface to set up the processing + required to prepare trace data for assembly or analysis. +SPIN - Compares pairs of sequences in many ways, often presenting its + results graphically and has a sliding sequence window linked to + the plots. +TREV - A rapid and flexible viewer and editor for ABI, ALF or SCF + trace files. -For more information and citing, visit Staden's web page and check the +For more information and citing, visit Staden's web page and check the "References" file in the documentation. This requires io_lib and tklib. Notes: 1) You should run the SlackBuild in real root environment (su -)! -2) Make sure you have Emacs and Tetex installed, as they are needed - to generate the documentation. -3) Slackware's TCL and TK sources are expected to be in /tmp at build - time. The SlackBuild will unpack them in the build directory and - create the necessary symlinks in /tmp. You can safely delete the - symlinks when the build is complete. +2) Make sure you have Emacs and Tetex installed at build time. +3) Although unsupported at the moment, SPIN can provide a GUI for the + EMBOSS suite programs. If you want to give it a try, run as root + "create_emboss_data" (EMBOSS should be installed, of course). This + generates some files in /usr/share/staden/tcl/spin_emboss/acdtcl, + so remember to manually clean them if you later uninstall staden. |