Bug 28808 – app-sci/gibbs-1995.9.ebuild (New package)

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Frank Vernaillen 2003-09-15 10:41:24 UTC]

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.

[Comment 1 Frank Vernaillen 2003-09-15 11:16:40 UTC]

Created attachment 17776 [details]
Tarball containing the gibbs-1995.9.ebuild and its associated files (metadata.xml, Changelog etc.)

[Comment 2 Frank Vernaillen 2003-09-15 11:19:34 UTC]

Created attachment 17777 [details]
License file for the gibbs-1995.9.ebuild (New license for /usr/portage/licenses)

[Comment 3 Frank Vernaillen 2003-09-15 11:24:40 UTC]

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.

[Comment 4 Frank Vernaillen 2003-09-15 11:34:42 UTC]

** 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.

[Comment 5 Olivier Fisette (RETIRED) 2004-05-23 20:54:01 UTC]

Created attachment 31925 [details]
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.

[Comment 6 Olivier Fisette (RETIRED) 2004-05-23 20:56:06 UTC]

Created attachment 31926 [details]
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.

[Comment 7 Olivier Fisette (RETIRED) 2004-05-23 20:56:31 UTC]

Created attachment 31927 [details]
ChangeLog

Goes with 31925

[Comment 8 Olivier Fisette (RETIRED) 2004-05-23 20:57:22 UTC]

Created attachment 31928 [details]
metadata.xml - Updated

Goes with 31925 (Added long description.)

[Comment 9 Patrick Kursawe (RETIRED) 2004-05-27 05:29:27 UTC]

The license looks more like "public-domain" to me, don't think we need something seperate here. Thank you, guys!