What are some good apps for X11? - Page 3

sao · 01-17-2003, 02:34 PM

Don Benot,

I wouldn't recommend to install anything that is not a Fink package in /sw. That's the official Fink advice too. I have read about many problems already from people who wanted to 're-invent' the wheel.

Quote:


	ClarkGoble wrote: There really isn't a problem with putting anything anywhere.

I think that's a bold statement when you had the experience of installing 'only' 15 packages by hand.

I will give the opposite advice to a beginner, especially if they don't know what you know.

Cheers...

ClarkGoble · 01-17-2003, 03:15 PM

Well you did leave out my caveat about version differences with Fink stuff. Further I noted many reasons why you wouldn't want to put them in /sw.

There are excellent reasons for putting things in specific locations. However there is rarely a reason for a program having to go in a specific location. Also, while I've installed 15 non-fink programs in OSX, I've installed far more in Linux, Solaris, and BSD systems. Often I've installed them in their own location and then symlinked executables to one of the various /bin directories. Indeed many installers do this so as to keep the applications clear and easy to upgrade.

With regards to newbies, I'd suggest putting them where the installer wants. Typically that will be /usr/bin. If it doesn't put them anywhere, put them in ~/bin or /mysw/bin.

sao · 01-17-2003, 03:43 PM

ClarkGoble,

From what you said now, I'm sure that you had a lot of experiences. I just wanted to pass the message to keep it simple for beginners.

It could be a good idea you start a thread in Unix beginners about compiling things by hand in /usr/local.

Cheers...

Don Benot · 01-17-2003, 03:49 PM

Yes ClarkGoble, please do that. I'm having some problems with what is probably a simple compile right now. I wasn't sure this thread would be the place for it, even though that's kind of what we've been discussing.

Regards,
Don

Glanz · 01-17-2003, 03:51 PM

Quote:


	Originally posted by ClarkGoble With regards to newbies, I'd suggest putting them where the installer wants. Typically that will be /usr/bin. If it doesn't put them anywhere, put them in ~/bin or /mysw/bin.

I find that most of the X11 dependant apps I install go to /usr/local..... I even opt out of /opt often to redirect to /usr/local.... This keeps interference with a non-X11 system [osx] to a minimum. Although, Unix is Unix, yes, but I like to keep non aqua/quartz stuff away from the base machine system.

Glanz · 01-18-2003, 11:53 AM

here are two applications that I use daily at work in my genome sequencing methodology research....... I did not install them from Fink however they may be launched from Fink via a window manager provided that the path is literal in the menu system.

http://cns.csb.yale.edu/v1.1/

Crystallography & NMR System (CNS) is the result of an international collaborative effort among several research groups. The program has been designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. Highlights include heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data.....

And this one....
http://www.hgmp.mrc.ac.uk/Software/EMBOSS/

EMBOSS is a new, free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.

The EMBOSS suite

Provides a comprehensive set of sequence analysis programs (approximately 100)
Provides a set of core software libraries (AJAX and NUCLEUS)
Integrates other publicly available packages
Encourages the use of EMBOSS in sequence analysis training.
Encourages developers elsewhere to use the EMBOSS libraries.
Supports all common Unix platforms including Linux, Digital Unix, Irix, Tru64Unix and Solaris.

Within EMBOSS you will find around 100 programs (applications). These are just some of the areas covered:

Sequence alignment
Rapid database searching with sequence patterns
Protein motif identification, including domain analysis
Nucleotide sequence pattern analysis, for example to identify CpG islands or repeats.
Codon usage analysis for small genomes
Rapid identification of sequence patterns in large scale sequence sets.
Presentation tools for publication
And much more.

01-17-2003, 03:15 PM	#42
ClarkGoble Triple-A Player Join Date: Jan 2002 Posts: 58	Well you did leave out my caveat about version differences with Fink stuff. Further I noted many reasons why you wouldn't want to put them in /sw. There are excellent reasons for putting things in specific locations. However there is rarely a reason for a program having to go in a specific location. Also, while I've installed 15 non-fink programs in OSX, I've installed far more in Linux, Solaris, and BSD systems. Often I've installed them in their own location and then symlinked executables to one of the various /bin directories. Indeed many installers do this so as to keep the applications clear and easy to upgrade. With regards to newbies, I'd suggest putting them where the installer wants. Typically that will be /usr/bin. If it doesn't put them anywhere, put them in ~/bin or /mysw/bin. Last edited by ClarkGoble; 01-17-2003 at 03:42 PM.

01-18-2003, 11:53 AM	#46
Glanz Major Leaguer Join Date: Aug 2002 Location: Montreal Posts: 373	2 Sci Apps here are two applications that I use daily at work in my genome sequencing methodology research....... I did not install them from Fink however they may be launched from Fink via a window manager provided that the path is literal in the menu system. http://cns.csb.yale.edu/v1.1/ Crystallography & NMR System (CNS) is the result of an international collaborative effort among several research groups. The program has been designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. Highlights include heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data..... And this one.... http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ EMBOSS is a new, free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages. The EMBOSS suite Provides a comprehensive set of sequence analysis programs (approximately 100) Provides a set of core software libraries (AJAX and NUCLEUS) Integrates other publicly available packages Encourages the use of EMBOSS in sequence analysis training. Encourages developers elsewhere to use the EMBOSS libraries. Supports all common Unix platforms including Linux, Digital Unix, Irix, Tru64Unix and Solaris. Within EMBOSS you will find around 100 programs (applications). These are just some of the areas covered: Sequence alignment Rapid database searching with sequence patterns Protein motif identification, including domain analysis Nucleotide sequence pattern analysis, for example to identify CpG islands or repeats. Codon usage analysis for small genomes Rapid identification of sequence patterns in large scale sequence sets. Presentation tools for publication And much more.

01-17-2003, 03:43 PM	#43
sao Moderator Join Date: Jan 2002 Location: Singapore Posts: 4,237	ClarkGoble, From what you said now, I'm sure that you had a lot of experiences. I just wanted to pass the message to keep it simple for beginners. It could be a good idea you start a thread in Unix beginners about compiling things by hand in /usr/local. Cheers...

01-17-2003, 03:49 PM	#44
Don Benot Triple-A Player Join Date: Nov 2002 Location: Kettering, Ohio Posts: 59	Yes ClarkGoble, please do that. I'm having some problems with what is probably a simple compile right now. I wasn't sure this thread would be the place for it, even though that's kind of what we've been discussing. Regards, Don