Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    How to easily install any PyPi/easy_install python module on Debian

    16th February 2011

    Imagine you need to install pycassa (which uses easy_install). Here are the 2 (at maximum) very simple steps to have it properly debianized and installed on your Debian/Ubuntu:

    • if you don’t have the python-stdeb package: sudo aptitude install python-stdeb
    • pypi-install pycassa

    That’s it.

    Refer to stdeb readme for more information. You will need that if there are dependencies – which might not be resolved automatically by stdeb.

    Before stdeb, it wasn’t exactly trivial to make a .deb from python module.

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    Posted in *nix, how-to, Notepad, Python, Software | 1 Comment »

    How to relay outgoing postfix emails via another mail server (e.g. your ISP)

    4th December 2010

    Here’s a simple and clear guide for gmail, which also definitely works with other relay hosts. I’ve used it to configure my ISP’s mail relay (they block outgoing port 25) on a Debian Squeeze laptop.

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    Posted in *nix, how-to, Links, Notepad, Software | No Comments »

    ask.debian.net: stackoverflow for Debian with Shapado

    19th October 2010

    ask.debian.net is a StackOverflow-like Q&A website built with OSS Shapado.

    That’s my first encounter of Shapado, so it was interesting to read Shapado authors’ justification and a related question on meta.SO.

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    Posted in Links, Misc, Software, Web | No Comments »

    Linux server remote backup options

    3rd October 2010

    Recently I finally managed to configure remote (aka off-site) backup for my Debian server. As always, I started with a comparison of existing solutions.

    Debian has a number of packages enabling remote (over the network) backup: backupPC, backupninja, backup-manager, dirvish, duplicity, luckybackup, rdiff-backup, and some others.

    Read the rest of this entry »

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    Posted in *nix, Links, Software | 1 Comment »

    ntfstruncate binary for Debian (resetting NTFS bad clusters counter)

    1st March 2010

    There is an excellent step-by-step instruction on resetting the bad clusters counter of an NTFS partition with linux-ntfs tools. I’ve checked – it works as expected:

    1. Back up important data from partition just in case
    2. Find out size of ‘$Bad’ attribute in $Badclus using ntfsinfo -i 8 partition (partition is for example /dev/sda1). It will be the “Allocated size” value in the “Dumping attribute $DATA (0x80)” (there will be two 0x80 attributes. Only one has an “Allocated size” line). Let us write down (remember) this size as ntfs_size.
    3. Use ntfstruncate partition 8 0x80 ‘$Bad’ 0 to set $Bad’s attribute length to zero.
    4. Use ntfstruncate partition 8 0x80 ‘$Bad’ ntfs_size to set $Bad’s attribute length back to proper value ntfs_size which was recorded in step 2.
    5. Boot into Windows and run chkdsk -f diskname. It will find errors and should fix them.

    However, Debian’s ntfsprogs package does not have the ntfstruncate binary.

    Here’s how you can easily build one yourself (you may need a few extra packages with build tools for that):
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    Posted in *nix, how-to, Software | 3 Comments »

    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 »

    R under Debian testing/i386: permanently set pdfviewer option

    21st October 2009

    If you get this message when opening vignettes:

    Error in openPDF(vif) :
    getOption(‘pdfviewer’) is ”; please use ‘options(pdfviewer=…)’

    and you are tired of running this command every time:

    > options(pdfviewer=”okular”)

    then you should check if your system-wide Renviron file has proper PDF viewer set:
    Read the rest of this entry »

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