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Attached is an ebuild for the Gibbs motif sampler developed at NCBI (National Center for Biotechnology Information). The Gibbs motif sampler uses a statistical method (Gibbs sampling) to discover subtle sequence signals (motifs) in a given list of proteins. The Gibbs motif sampler is an application for bioinformaticists, so app-sci is probably a fine home for it. It is a text-mode-only application. References: - http://www.people.fas.harvard.edu/~junliu/index1.html#Publications - Neuwald, Liu, & Lawrence (1995) "Gibbs motif sampling: detection of bacterial outer membrane protein repeats" Protein Science 4, 1618-1632. - Lawrence, Altschul, Boguski, Liu, Neuwald & Wootton (1993) "Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment" Science 262:208-214.
Created an attachment (id=17776) [edit] Tarball containing the gibbs-1995.9.ebuild and its associated files (metadata.xml, Changelog etc.)
Created an attachment (id=17777) [edit] License file for the gibbs-1995.9.ebuild (New license for /usr/portage/licenses)
The attached tarball contains the gibbs-1995.9.ebuild and its associated files. It emerges fine on my machine. Also attached is the corresponding new license file for /usr/portage/licenses. Cheers, Frank Vernaillen.
** TESTCASE ** After "emerge gibbs" it can be verified that the gibbs sampler works fine by running it on an example provided by the authors, and comparing your output to theirs. Run /usr/share/gibbs-1995.9/demo > mydemo.out 2> mydemo.err and then compare mydemo.out with /usr/share/gibbs-1995.9/demo.out. The only difference will be some timing statistics.
Created an attachment (id=31925) [edit] gibbs-1995.9-r1.ebuild - Revised ebuild - Compiles using the user's CFLAGS. - Uses "-lm" for libraries rather than "-lm -ll" (avoids ld failure). - Installs the demo as gibbs-demo in /usr/bin, not /usr/share. - Updated file names in the demo script accordingly. - A message informs the user of the existence of a testcase script. Testcase succeeds on my computers.
Created an attachment (id=31926) [edit] gibbs-demo - Updated demo Goes with 31925 - Uses #!/bin/bash rather than #!/bin/csh - Uses absolute paths for example files - It think it is better than a patch since the file is so small the patch is actually bigger that it's target.
Created an attachment (id=31927) [edit] ChangeLog Goes with 31925
Created an attachment (id=31928) [edit] metadata.xml - Updated Goes with 31925 (Added long description.)
The license looks more like "public-domain" to me, don't think we need something seperate here. Thank you, guys!
