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authorPetar Petrov <ppetrov@paju.oulu.fi>2012-02-19 14:20:37 -0600
committerRobby Workman <rworkman@slackbuilds.org>2012-02-20 12:20:46 -0600
commitfe3095faf885d66e39a7cf0ff242dce6b3353aef (patch)
tree0684ab050966f1cc52c33842de4e8269a13d3e3b /academic/staden/README
parent63e3433063fed4ed657ea181d933f06cb497b716 (diff)
downloadslackbuilds-fe3095faf885d66e39a7cf0ff242dce6b3353aef.tar.gz
academic/staden: Several fixes/enhancements
I notified upstream that Staden had been added to SlackBuilds.org and got some handy tips. So: 1) The components of the program will now find their documentation directly. 2) The Staden package is now ready to provide a GUI for EMBOSS. 3) The real icons are used (converted from their Mac format). Signed-off-by: Robby Workman <rworkman@slackbuilds.org>
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@@ -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.