Bug 114096 – An ebuild for the science program: RepeatMasker

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Brady Catherman 2005-11-30 19:11:31 UTC]

I have no clue what this program does. I was asked to install it on our cluster
so I went ahead and made an ebuild for it.

This package has a fetch restriction.

(From the packages webpage)
RepeatMasker is a program that screens DNA sequences for interspersed repeats
and low complexity DNA sequences. The output of the program is a detailed
annotation of the repeats that are present in the query sequence as well as a
modified version of the query sequence in which all the annotated repeats have
been masked (default: replaced by Ns). It requiers an executable called
cross_match to run. Cross_match can be found in another application called
Phrap. Both Repeatmasker and Phrap have limited availablty.

(Phrap was submitted a bit ago)

[Comment 1 Jakub Moc (RETIRED) 2005-12-01 00:10:15 UTC]

*** Bug 114097 has been marked as a duplicate of this bug. ***

[Comment 2 Brady Catherman 2005-12-01 08:22:47 UTC]

Created attachment 73892 [details]
The Ebuild.

Sorry about the duplicate.. my system here started lagging out and such. Here
is the build.

[Comment 3 Andrey Kislyuk (RETIRED) 2006-11-12 14:30:33 UTC]

Created attachment 101785 [details]
RepeatMasker-3.1.6.ebuild

New version: 3.1.6, change dependencies and file installation. Portage 2.1.2 should be installed to avoid clobbering PERL5LIB

[Comment 4 Andrey Kislyuk (RETIRED) 2006-11-12 14:33:10 UTC]

Created attachment 101786 [details]
RepeatMasker-3.1.6.ebuild

clean up a bit

[Comment 5 Andrey Kislyuk (RETIRED) 2007-04-20 21:22:46 UTC]

Created attachment 116858 [details]
repeatmasker-3.1.7.ebuild

The latest version will be available at

http://overlays.gentoo.org/proj/sunrise/browser/sunrise/sci-biology/repeatmasker

[Comment 6 Andrey Kislyuk (RETIRED) 2007-04-20 21:23:27 UTC]

Created attachment 116860 [details]
repeatmasker-libraries-20061006.ebuild

The latest version will be available at

http://overlays.gentoo.org/proj/sunrise/browser/sunrise/sci-biology/repeatmasker-libraries

[Comment 7 George Shapovalov (RETIRED) 2007-12-15 22:01:02 UTC]

Andrey:
The ebuild in sunrise is looking Ok. However it is fetch restricted (with registration requirement), so I'll skip to the next bug. You can process it yourself when you get full dev status ;).

Arranging deps and reassigning to myself for the recruitment period.

George

[Comment 8 Andrey Kislyuk (RETIRED) 2008-07-08 19:25:36 UTC]

Version 3.2.5 now available in the science overlay.

[Comment 9 Andrey Kislyuk (RETIRED) 2009-02-27 00:20:14 UTC]

In gentoo-x86.