253844 – new package sci-biology/cap3-bin: CAP3 is for small-scale assembly of EST sequences

Bug 253844 - new package sci-biology/cap3-bin: CAP3 is for small-scale assembly of EST sequences

Summary: new package sci-biology/cap3-bin: CAP3 is for small-scale assembly of EST seq...

Status:	CONFIRMED

Alias:	None

Product:	Gentoo Linux
Classification:	Unclassified
Component:	New packages (show other bugs)
Hardware:	All Linux

Importance:	High enhancement (vote)
Assignee:	Default Assignee for New Packages

URL:	http://seq.cs.iastate.edu
Whiteboard:
Keywords:	EBUILD

Depends on:
Blocks:

Reported:	2009-01-05 12:56 UTC by Martin Mokrejš
Modified:	2010-11-28 20:59 UTC (History)
CC List:	1 user (show)

See Also:
Package list:
Runtime testing required:	---

Attachments
cap3-bin-20071222.ebuild (cap3-bin-20071222.ebuild,984 bytes, text/plain) 2009-01-05 12:57 UTC, Martin Mokrejš	Details
cap3-bin-20071222.ebuild (cap3-bin-20071222.ebuild,1.11 KB, text/plain) 2009-01-06 19:52 UTC, Martin Mokrejš	Details
cap3-bin-20071221.ebuild (cap3-bin-20071221.ebuild,1.37 KB, text/plain) 2010-11-28 20:59 UTC, Martin Mokrejš	Details
metadata.xml (metadata.xml,391 bytes, application/xml) 2010-11-28 20:59 UTC, Martin Mokrejš	Details
Show Obsolete (2) View All Add an attachment (proposed patch, testcase, etc.)

Note You need to log in before you can comment on or make changes to this bug.

Description Martin Mokrejš 2009-01-05 12:56:53 UTC

Don't know what license it is ... "AS IS" or "public"?
Anyway, working ebuild is here (no source code available?).

# equery files =sci-biology/cap3-bin-20071222
[ Searching for packages matching =sci-biology/cap3-bin-20071222... ]
* Contents of sci-biology/cap3-bin-20071222:
/usr
/usr/bin
/usr/bin/cap3
/usr/bin/formcon
/usr/share
/usr/share/cap3
/usr/share/cap3/example
/usr/share/cap3/example/README
/usr/share/cap3/example/xyz
/usr/share/cap3/example/xyz.con
/usr/share/cap3/example/xyz.qual
/usr/share/cap3/examples
/usr/share/doc
/usr/share/doc/cap3-bin-20071222
/usr/share/doc/cap3-bin-20071222/README.bz2
/usr/share/doc/cap3-bin-20071222/cap3.txt.bz2

Comment 1 Martin Mokrejš 2009-01-05 12:57:57 UTC

Created attachment 177467 [details]
cap3-bin-20071222.ebuild

Comment 2 Martin Mokrejš 2009-01-06 19:52:34 UTC

Created attachment 177590 [details]
cap3-bin-20071222.ebuild

Added support for other arch binaries. But how to distinguish ppc and ppc_64? And how about x86, amd64, amd64_itanium? See the commented URLs in the ebuild for clue what I mean. Hope "64 bit xeon" fits amd64 in Gentoo ARCHs.

Comment 3 Martin Mokrejš 2010-11-28 16:23:05 UTC

Which /usr/portage/licenses/ matches this?

Quoting from http://seq.cs.iastate.edu/:
CAP3 and PCAP are freely available for use at non-profit organizations. CAP3 and PCAP are available for use at company under a licensing agreement from Michigan Tech. For information on a licensing agreement, please contact ...

Comment 4 Martin Mokrejš 2010-11-28 20:59:16 UTC

Created attachment 255759 [details]
cap3-bin-20071221.ebuild

Updated patch (corrected the date), except the LICENSE it is ready to go into the tree. No source code available, has to be cap3-bin. sci-biology/tgicl, or sci-biology/tgi-tools or sci-biology/gicl should DEPEND on this package, although those upstream packages contain it for users convenience cap3 binary.

In theory, a slight improvement of the ebuild could be done. One could parse CFLAGS and if opteron could be inferred then another binary could be installed. Otherwise the one for "64bit Xeon will go" when on any amd64, or of course 32bit for x86. PPC binaries of the very same version used to exist but not available anymore. But probably one could find them in Google's cache, or ask author.

Comment 5 Martin Mokrejš 2010-11-28 20:59:58 UTC

Created attachment 255761 [details]
metadata.xml