Bio::Graphics installation steps for Debian 12, Ubuntu 24.04, and derivative distros

[ernstki]

I'll be closing this issue as soon as opening it, because it's not an issue, per se. It's just to give others something to search for in the issue tracker, and so I have something to link to from our internal documentation.

See also: #396.

Steps required to get Bio::Graphics installed on Debian 12 or Ubuntu 24.04

These steps will probably work with other Debian/Ubuntu-derived distros, and other related Bio::Whatever packages, too.

The below steps assume you are root, or are running in a Docker container.¹ It is true that you're not supposed to install things with cpan as root.² As an alternative, use local::lib and run cpan or cpanm under your own user account.

apt update && apt full-upgrade -y

# these packages preempt numerous `cpanm` build failures without them
apt install --no-install-recommends -y \
    gcc make git libc6-dev cpanminus bioperl libgd-perl \
    libxml-libxml-perl libclass-dbi-perl libwww-perl libapache-dbi-perl \
    liblist-moreutils-perl liblist-moreutils-xs-perl libcgi-pm-perl

# isn't properly picked up as a dependency, so install manually
cpan -T Bio::DB::SeqFeature::Store

# finally
cpan -T Bio::Graphics

Did you want to run the tests? If you use http_* environment variables for a local proxy setup, see #337 and do this for the time being:

# until https://github.com/bioperl/bioperl-live/issues/337 is resolved
HTTP_PROXY= http_proxy= cpan -T Bio::DB::SeqFeature::Store

Finally, test to make sure the desired module actually got installed:³

# perl -MBio::Graphics -e'print $INC{"Bio/Graphics.pm"} . "\n"'
/usr/local/share/perl/5.38.2/Bio/Graphics.pm

References

• Fix test suite with libxml2 2.13.0 shlomif/perl-XML-LibXML#87 - the patch here can be used to patch XML::LibXML to pass all its tests when using the distro-supplied libxml or libxml2, if not using a distro package version of this and not skipping tests
• https://stackoverflow.com/a/78965715 - included the helpful suggestion of installing the distro's libxml library plus development headers preemptively

Footnotes

1. …even though it seems like cpanm should've been able to figure this out that this was a dependency on its own ¯\_(ツ)_/¯ ↩

2. See Bio::Graphics installation steps for Rocky Linux 9 or other EL-like distros #396 if you doubt this will ever be a problem. I didn't necessarily doubt it, but had never seen it go wrong with my own eyes until now. ↩

3. Thanks to https://modfoss.com/find-a-perl-modules-path.html for this tip. ↩