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Bug 346957 - [science overlay] sci-biology/gbrowse-2.03: improve webapp_config support and need perl install guru
Summary: [science overlay] sci-biology/gbrowse-2.03: improve webapp_config support and...
Status: RESOLVED WONTFIX
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: New packages (show other bugs)
Hardware: All Linux
: High QA (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard: Science overlay
Keywords:
Depends on:
Blocks:
 
Reported: 2010-11-27 13:30 UTC by Martin Mokrejš
Modified: 2021-05-05 17:20 UTC (History)
1 user (show)

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


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Description Martin Mokrejš 2010-11-27 13:30:26 UTC
I have improved the gbrowse-2.00.ebuild from science overlay and created one for 2.03 and commited it into there as well. GBrowse finally works for me. I sketched in something as a src_test() as well and here are more comments on this functional while still not nice ebuild.

1. I have no experience with this but could webapp_config install the /etc/apache2/vhosts.d/gbrowse.conf automagically?

2. For real use somebody needs to help with something called Apache::Registry, quoting from INSTALL file:
<quote>
    To improve (1), I recommend that you install the mod_perl module for
    Apache. (<http://perl.apache.org>). By configuring an Apache::Registry
    directory and placing gbrowse inside it (rather than in the default
    cgi-bin directory). The overhead for loading Perl and its libraries are
    eliminated, thereby increasing the performance of the script noticeably.

    Be aware that there is a bad interaction between the Apache::DBI module
    (often used to speed up database accesses) and Bio::DB::GFF. This will
    cause the GFF dumper plugin to fail intermittently. GBrowse does not
    need Apache::DBI to achieve performance increases under mod_perl and it
    is suggested that you disable Apache::DBI. If you cannot do this, then
    you should remove the file GFFDumper.pm from the gbrowse.conf/plugins
    directory.
</quote>
Could somebody improve the ebuild in this regard?

3. I have my root username and password to mysql in ~root/.my.cnf in sections [mysql], [client], [defaut]. Somehow, Perl-DBI ignores that and therefore I could not import the test/sample data. I got around by setting an empty password, but it is not ideal. Would somebody try this and fix?

4. I think the demo datasets should be installed as test_* databases instead.

5. Lots of generated image are temporarily stored under /var/tmp/gbrowse2/images/. I propose cronjob through einfo(), however, would somebody more experienced install it as a cron-job directly from the ebuild? Have no idea how to test for various cron deamons.

6. Some variable DO_XS passed to Makefile.PL enables small ANSI C application to be compiled. I did enbale it, it uses automagically i686-pc-linux-gnu-gcc for me but probably should respect CC and other env variables. I haven't inspected this, somebody who understands the Makefile.PL trickery please check. Maybe it is fine, it respects CFLAGS for me and my CC is gcc.

7. There is some startup script to be installed in init.d but should be rewritten to fit gentoo syntax.

8. Somebody understanding apache configs might inspect files/gbrose.conf but also /var/tmp/portage/sci-biology/gbrowse-2.03/work/GBrowse-2.03/install_util/GBrowseInstall.pm because this perl hack contains its templates and does some other trisks. I think some good information could be reverse-engineered from that script so that Gentoo startup will do what is otherwise expected.
Hint: look for the installetc and installconf variables (disabled by the ebuild but we probably have to provide the disabled functionality through Gentoo-specific ways).

9. I suspect the Makefile.PL step does not expected we mess-up with its argumets. There used to be ${D} remnants in the files after qmerge but now they are hopefully all gone (emerge does not report them anymore at least). When some of the arguments to Makefile.PL are omitted, then 'Unitialized value' errors appear during src_install(). Therefore I had to include 
        DATABASES="/var/www/gbrowse2/databases/" \
        TMP="/var/tmp/gbrowse2" \
        INSTALLETC="n" \
        INSTALLCONF="n" \
        WWWUSER="apache" \
in the ebuild. The bad results could be seen in /usr/share/webapps/gbrowse/2.03/htdocs/etc/gbrowse/GBrowse.conf as empty strings in place of variables like $DATABASES, etc. If you fiddle with the build process, watch this file as well.

This following page might be helpful.
http://gmod.org/wiki/GBrowse_2.0_HOWTO#Database_Definitions

10. The way I create the 'i' symlink during src_install is probably ugly but at least we know what the symlink is for, finally. ;)
Comment 2 Jeroen Roovers (RETIRED) gentoo-dev 2010-11-27 15:36:39 UTC
You could have put it in the Summary yourself.
Comment 3 Martin Mokrejš 2010-11-27 15:45:50 UTC
Probably nothing new compared to the current ebuild:
http://gmod.org/wiki/GBrowse_Gentoo_HOWTO

A list of few more requirements/optionals not listed if I remember right in INSTALL plaintext file:
http://gmod.org/wiki/GBrowse_Install_HOWTO#Perl

A list of database adaptors which we should be able to place into DEPEND:
http://gmod.org/wiki/GBrowse#About_Databases
Comment 4 Martin Mokrejš 2011-02-14 18:09:55 UTC
I updated the ebuild in science overlay to 2.26 with some minor improvements, like more lines in GBrowseInstall.pm commented out. ;-)
Comment 5 Andrew Ammerlaan gentoo-dev 2021-05-05 17:20:59 UTC
WONTFIX because package has been removed