Bug 20184 – ncbi-tools ebuild fixes

• Status: RESOLVED FIXED
• Product: Gentoo Linux

[Description Stephen Diener (RETIRED) 2003-04-29 16:08:59 UTC]

New ebuild for the NCBI bioinformatics tools...

[Comment 1 Stephen Diener (RETIRED) 2003-04-29 16:11:53 UTC]

Created attachment 11306 [details]
ncbi_tools-04222003.ebuild

This program requires a config file (.ncbirc) in the home directory of each
user.  I wasn't sure how to handle that properly so I just added a note at the
end of the ebuild for each user to create a .ncbirc file.

- Steve

[Comment 2 Stephen Diener (RETIRED) 2003-04-29 16:29:46 UTC]

We should change the date/version to be ncbi_tools-2003.04.22.ebuild so that upgrading will work properly.

- Steve

[Comment 3 Jon Portnoy (RETIRED) 2003-05-02 15:04:35 UTC]

Does this deprecate the separate BLAST ebuild?

[Comment 4 Stephen Diener (RETIRED) 2003-05-02 18:40:25 UTC]

I guess we should drop that one.  I only started with that one because I 
had run into a lot of problems with building this toolkit on redhat but that, 
apparantly, was just a redhat problem.  It builds without a problem on 
gentoo.    

- Steve

[Comment 5 Jon Portnoy (RETIRED) 2003-05-02 18:43:26 UTC]

Okay, thanks - I'll get this in tonight or tomorrow depending on time constraints.

[Comment 6 Jon Portnoy (RETIRED) 2003-05-02 18:44:20 UTC]

*** Bug 19865 has been marked as a duplicate of this bug. ***

[Comment 7 Jon Portnoy (RETIRED) 2003-05-03 22:37:28 UTC]

Committed as ncbi-tools (naming policy is to avoid _ in names), thanks :)

[Comment 8 Gontran Zepeda 2003-05-05 08:14:04 UTC]

Per my discussion with Stephen last week, I've tried out the ncbi tools
ebuild.  A couple of additions to the DEPEND to get it to work out of
the box here:  added app-shells/tcsh so the ncbi csh configuration
script will run, also added a libpng dependency for when X is in use.

Also, from prior experience with blast-bin on a gentoo system, I've
modified the post install section and included two additional files for
/etc/skel and /etc/env.d

Have tested using emerge works ok.  Need to find a way to get
optimization settings into the build.  Unfortunately the setup is
resaonably complex to make this time consuming.

Will submit diff, newfile and files/* momentarily.

Cheers.

[Comment 9 Gontran Zepeda 2003-05-05 08:16:08 UTC]

Created attachment 11512 [details]
dot-ncbirc for filesdir

[Comment 10 Gontran Zepeda 2003-05-05 08:18:39 UTC]

Created attachment 11513 [details]
env.d file

[Comment 11 Gontran Zepeda 2003-05-05 08:52:29 UTC]

Created attachment 11514 [details, diff]
ncbi-tools.diff

diff to current ebuild

[Comment 12 Gontran Zepeda 2003-05-05 08:53:16 UTC]

Created attachment 11515 [details]
ncbi-tools-2003.04.02-r1.ebuild

applied diff above

[Comment 13 Jon Portnoy (RETIRED) 2003-05-05 09:17:57 UTC]

Okay, will commit in a few.

[Comment 14 Jon Portnoy (RETIRED) 2003-05-05 15:32:18 UTC]

Committed - by the way, policy is that author credits can't go into ebuilds (only ChangeLogs), so I've moved that.

Thanks, guys :)