Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    Saving and restoring the list of packages installed on a Debian system using aptitude or deborphan

    18th October 2013

    The usual, or even classical way is to create the list of installed packages with sudo dpkg --get-selections > package_list, and then restore when/if necessary with cat package_list | xargs sudo apt-get -y install.

    As VihangD points out in his serverfault answer, the same can be achieved with aptitude, while also excluding dependent, automatically installed packages (which are included by the classical method). To create the list of packages, run aptitude search -F '%p' '~i!~M' > package_list. Here, -F '%p' asks aptitude to only print package names (instead of the default output, which also contains package state and description); search term ‘~i!~M’ asks for all non-automatically installed packages.

    To install packages using the created list, run xargs aptitude --schedule-only install < package_list; aptitude install. The first of these two commands instructs aptitude to mark all the packages from the list as scheduled for installation. The second command actually performs the installation.

    Hamish Downer suggests an alternative way of getting the initial package_list: using the deborphan utility, deborphan -a --no-show-section > package_list. This command asks deborphan to show a list of packages, which have no dependencies on them. Sounds very similar to what we did with aptitude above, but using deborphan will most likely result in a much shorter list of packages (on my system, deborphan printed 291 package names, aptitude printed 847, and dpkg printed 3650 package names). One more potentially important difference between aptitude- and deborphan-produced package lists is that aptitude only specifies package architecture when it is different from native (e.g. 'googleearth:i386' on a 64-bit system), while deborphan specifies architectures for all the packages (resulting in e.g. 'google-talkplugin:amd64' and 'googleearth-package:all' on a 64-bit system).

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    rtorrent-enhanced with ipfilter and GeoIP: Debian Squeeze amd64 package

    1st April 2011

    rtorrent-eyecandy
    rtorrent is an excellent ncurses rtorrent client.

    There are a few highly-popular patches, which haven’t yet made it into the Squeeze’s rtorrent version 0.8.6.

    Note: ArchLinux already has an rtorrent-extended package, so you may want to look at that one (instead of my Debian package below). I might use Arch’s patchset next time to generate a truly extended rtorrent package.

    I’ve incorporated 3 of such patches (#239 ipfilter, #2064 GeoIP support, and #2171 colours/eyecandy), and built a squeeze amd64 rtorrent-enhanced package.

    A few excerpts to explain how these extra features are to be configured and used (all come from the above-mentioned trac tickets, some were edited/extended).

    ipfilter

    ipfilter allows to selectively blacklist/whitelist peers – based on IP address range files (so-called ipfilter files). The ipfilter files may, for example, come from bluetack.co.uk. Each line of the file contains a record in this format: range_description:start_IP-end_IP, where start_IP should be less than or equal to end_IP. Multiple files can be used. Overlapping ranges are merged automatically. Both incoming and outgoing connections are checked against the filter. Exclusions are not supported, so connection to/from IPs in all the loaded ranges will be disallowed and dropped.

    Include “ip_filter=” directive in .rtorrent.rc. For example (paths are specified relative to user’s home directory):
    ip_filter=ipfilter/level1,ipfilter/level2

    It is probably a good idea to reload ipfilter files once in a while, so you can also include “reload_ip_filter” directive on schedule to refresh the filter. The same files named in “ip_filter” will be reloaded.

    schedule = filter,18:30:00,24:00:00,reload_ip_filter=

    To support the feature you may want to setup cron job to reload and unzip files from bluetack. Examples here and here.

    GeoIP

    In the Peers view of each torrent a new column – CC, country code – is added, which shows peer’s country code. When examining each peer, you will see more data from the GeoIP database (if you have the relevant files installed): AS num and city. At the very least, you need to have geoip-database installed. You can get free “lite” versions of city/AS-databases, rename them (removing “lite”) and put into an appropriate location to make rtorrent+geoip use them as well. Geop-isp data support isn’t integrated into this rtorrent package.

    Colours

    This patch somewhat changes the way rtorrent shows torrents. Seeding torrents have bold titles, there are no half-displayed torrents at the top/bottom when scrolling, and you can configure colours for active/done torrents (ticket libtorrent.rakshasa.no/ticket/1382, which seems to be gone now). Source code and testing hint at these configurable colours: done_fg_color, done_bg_color, active_fg_color, active_bg_color, and at these possible values: 1 (red), 2 (green), 3 (yellow).

    Geek’s cellar
    A related (though not used in any way for the preparation of the package) resource is rtorrent mods page.

    Relatively schematically, applying patches and building the package was performed in these steps (starting within some newly-created directory):

    1. sudo aptitude install cdbs devscripts [and whatever else you find you're missing]
    2. apt-get source rtorrent
    3. dpkg-source -x rtorrent_0.8.6-1.dsc
    4. cd rtorrent-0.8.6
    5. cdbs-edit-patch 01-ipfilter.patch
    6. patch -p1 < /path/to/patch/239
    7. exit 0
    8. cdbs-edit-patch 02-geoip.patch
    9. patch -p1 < /path/to/patch/2064-after-ipfilter
    10. exit 0
    11. cdbs-edit-patch 03-eyecandy.patch
    12. patch -p1 < /path/to/patch/2171-mod-with-canvas
    13. exit 0 [you could do all 3 patches together, but I prefer cleaner and manageable approaches]
    14. [some weird operation to be explained below]
    15. dpkg-buildpackage

    Weird operation: I didn’t know how to make dpkg-buildpackage run autorun.sh (which is required for one of the patches I’ve used) before configure (could someone enlighten me how to do that?), so I started a new patch with cdbs-edit-patch, then ran one by one `autoreconf -if`, `./autorun.sh`, `./configure`, exited with zero status and was done with that problem. The resulting “patch” was 2MB large :)

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    Chandler 1.0.3 package for Debian testing amd64

    25th January 2010

    Recently, I have come across the Chandler project. Chandler is a sophisticated organizer, including tasks, calendar, appointments, invitations, and many more.

    The project does provide a 64-bit package for Ubuntu 8.10 “Intrepid Ibex”, but it has a dependency on python-zope-interface – which in Debian testing is a virtual package, currently provided by python-zope.interface. That single dependency made my aptitude complain all the time, so I edited the .deb-file, renaming depends/python-zope-interface to depends/python-zope.interface (following nice and simple instructions). After that – no more aptitude complaints, and Chandler works fine.

    Download the modified Chandler 1.0.3 Debian testing amd64 package (md5: 239071715977bea2eb75f3bb54491a02).

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    Posted in *nix, Software | 1 Comment »

    Debian-Med Project

    3rd September 2008

    There’s a Debian-Med project, aiming to

    develop Debian into an operating system that is particularly well fit for the requirements for medical practice and research

    Debian-Med has several web sites/pages: one at Debian.org (descriptive), and the actual project’s website at debian-med.alioth.debian.org. There’s also debian-med wiki (for developers).

    As of nowadays, Debian-Med has released a number of Debian packages, which are grouped into respective Debian Med Tasks. The Biology-dev task, for example, contains MCL and libsbml packages (among many others).

    Check this project out – you might find that the software you need is already available as Debian package.

    This post was stimulated by Steffen’s comment.

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