Bug 135307 – [new ebuild] sci-biology/blat

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Andrey Kislyuk (RETIRED) 2006-06-02 12:07:56 UTC]

BLAT - The BLAST-Like Alignment Tool, a fast genomic sequence aligner

License text, in its entirety:

CONTENTS AND COPYRIGHT

This archive contains the entire source tree for BLAT and
associated utilities.  All files are copyrighted, but license
is hereby granted for personal, academic, and non-profit use.
A license is also granted for the contents of the top level
lib and inc directories for commercial users.  Commercial
users should contact [e-mail] for access to other modules.

[Comment 1 Andrey Kislyuk (RETIRED) 2006-06-02 12:10:03 UTC]

Created attachment 88209 [details]
blat-33.ebuild

This ebuild will need some work on non-x86 platforms due to an unconventional build system.

Also I haven't tested the web server features.

[Comment 2 Andrey Kislyuk (RETIRED) 2006-09-23 18:03:04 UTC]

Created attachment 97908 [details]
blat-33.ebuild

honor user's CFLAGS

[Comment 3 Andrey Kislyuk (RETIRED) 2006-09-23 18:15:07 UTC]

Created attachment 97909 [details]
blat-33.ebuild

forgot to clean up a bit

[Comment 4 Andrey Kislyuk (RETIRED) 2006-09-23 18:26:55 UTC]

Created attachment 97910 [details]
blat-33.ebuild

and a bit more tidying

[Comment 5 Andrey Kislyuk (RETIRED) 2006-09-24 17:11:19 UTC]

Created attachment 97988 [details]
blat-33.ebuild

and more tidying

[Comment 6 Andrey Kislyuk (RETIRED) 2006-12-20 10:00:46 UTC]

The latest version can be found at

http://www.gentoo-sunrise.org/sunrise/browser/reviewed/sci-biology/blat

[Comment 7 Donnie Berkholz (RETIRED) 2006-12-20 10:06:07 UTC]

I'm already in sci-bio.

[Comment 8 Olivier Fisette (RETIRED) 2007-03-09 02:20:27 UTC]

I already watch this bug through the sci-biology alias.

[Comment 9 George Shapovalov (RETIRED) 2007-12-14 23:36:14 UTC]

This one looks rather clean (-34 version, in sunrise now). Just two, or even 1.5 remarks :).

1.     MACHTYPE=$(tc-arch)
    [[ ${MACHTYPE} == "x86" ]] && MACHTYPE="i386"
These lines are duplicated at the beginning src_compile and src_install. Ideally you wouldn't need to do this, but unfortunately this is a known portage bug - that it, somewhat randomly, looses settings between function calls.

2. The ${S}'s at the beginning of file specifications for sed, mkdir and dobin are unnecessary. portage cd's you to ${S} before running the  src_compile and src_install code.

Adding dep and reassigning as well..

George

[Comment 10 Martin Mokrejš 2008-04-28 11:43:12 UTC]

Anybody pls working on this?

[Comment 11 Andrey Kislyuk (RETIRED) 2008-04-28 13:03:14 UTC]

(In reply to comment #10)
> Anybody pls working on this?
> 

Yes, I'm working on it. After I'm done with my exams (May 10 ish) I'll commit it to mainline. Meanwhile, please install the Gentoo Sunrise overlay (http://overlays.gentoo.org/proj/sunrise) and install BLAT from there.

[Comment 12 Andrey Kislyuk (RETIRED) 2008-05-23 19:27:50 UTC]

InCVS

[Comment 13 Martin Mokrejš 2008-05-26 10:51:20 UTC]

Andrey, please provide also ~amd64. It works fine for me there. Thanks.
BTW: No man pages or any docs?

[Comment 14 Andrey Kislyuk (RETIRED) 2008-05-26 14:39:58 UTC]

Keyworded, thanks.

No docs with this package, sorry. Please see the website and the help output for the program.