Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

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    Best method to recursively chmod/process files or directories

    8th June 2009

    Found here.

    Recursively set directories only to drwx-rx-rx (755):

    find . -type d -exec chmod 755 {} \;

    Recursively set files only to rwx-r-r (644):

    find . -type f -exec chmod 644 {} \;

    Recursively remove carriage returns (^M) from the end of all *.php files:

    find . -type f -name “*.php” -exec /home/user/ {} \;

    In all these cases, {} is replaced with the filename/directory find has found matching your parameters; \; at the end just stops exec processing.


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

    Drupal Views: how to display random nodes/content

    4th May 2009

    Today I had a task of displaying random node in a Views-generated sidebar block.

    This is how to do that in Drupal 7 (Views 3):

    1. edit the view which makes the block available (follow
    2. in the Sort Criteria section (under Filter), look for and add Global:Random.

    This is how to do that in Drupal 6 (Views 2):

    1. edit the view which makes the block available (follow
    2. in the Sort Criteria section, add the Random criteria.

    It can’t be simpler than that.


    Posted in Drupal, Notepad, Software | 13 Comments »

    Linux: how to remove trailing ^M (carriage return)

    30th March 2009

    Imagine you have some styles.css transferred from Win machine to Linux via FTP in binary mode instead of ASCII mode; then

    cat styles.css | tr -d "\r" > styles-nocarriage.css

    will create styles-nocarriage.css with ^M’s removed.

    Alternative syntax:

    tr -d "\r" < styles.css > styles-nocarriage.css

    Most editors have global replace features which allow to get rid of control characters using regular expressions (exact instructions are editor-specific).

    For multiple files, try this:

    for f
    mv $f ${f}~ && tr -d "\r" <${f}~ >$f
    rm ${f}~

    Save this shell script as a file (e.g., then do ./ . This script accepts wildcards (e.g. ./ *.php), so be careful!


    Posted in *nix, how-to, Notepad | 3 Comments »

    Intel i915 integrated graphics under Debian: how to get rid of sluggish 2D performance

    2nd March 2009

    I assume you already have configured and working desktop environment, but want to improve performance.

    First of all, sudo aptitude install mesa-utils. Then run in a Terminal/Konsole glxgears, and wait for ~15 seconds; if your FPS is ~400 or less, then you do have sluggish video performance (usually manifesting itself as slow scrolling in Firefox/Iceweasel, slow window switching/minimziing/maximizing etc).

    After reading through several forums and bug reports and blog posts, I’ve ended with the following modifications to my /etc/X11/xorg.conf:
    Read the rest of this entry »


    Posted in *nix, Hardware, how-to | 5 Comments »

    gitosis: how to add new repository

    20th February 2009

    I assume that you already have your gitosis-admin repository working (this is described elsewhere).

    1. cd gitosis-admin && git pull – enter your gitosis administrative repository and ensure it is up-to-date
    2. $EDITOR gitosis.conf
    3. add [group newreponame] section (newreponame is the name of your new repository being added); add yourself with members = yourlogin@yourhost line; also add writable = newreponame line:

      [group newreponame]
      members = yourlogin@yourhost
      writable = newreponame

    4. based on my assumption of a correctly setup gitosis-admin repository, you should already have the appropriate public key in the keydir directory, but if not – copy your user’s ssh public key to keydir in the form of, then do git add keydir/
    5. git commit -am ‘new repository: newreponame’; git push;
    6. now that you have the new repo permissions configured, let’s actually create it. Navigate to the directory holding the files of your project (e.g. cd ~/newreponame), and do git init; git add . – this initializes empty git repository, and then adds all the files to it. If you have no files – you can skip the ‘git add .’ command, as it will do nothing for you.
    7. git commit -m ‘initial commit’. If you had no files added to the commit, git will complain that it cannot create an empty commit. In this case use the command git commit ––allow-empty -m ‘initial commit’
    8. git remote add origin ssh://gitosis@yourGitosisServerName/newreponame.git
    9. git push ––all
    10. final thing: git config ––add branch.master.remote origin && git config ––add branch.master.merge refs/heads/master; alternatively, cd .git && $EDITOR config, and then add these lines:

      [branch "master"]
      remote = origin
      merge = refs/heads/master

      Without these lines, you won’t be able to git pull.


    Posted in *nix, how-to, Software | 16 Comments »

    WordPress and Google Analytics external nofollow problem in comment links

    13th February 2009

    Since some WP release, the comment author’s link in comments is broken – it has ‘ external nofollow’ attached straight to the href attribute (which breaks the link).

    I assume that the problem is caused by Google Analytics, namely the “track outgoing clicks” feature (as recalled, might be inaccurate feature name). “Track outgoing links” adds some JavaScript code to all outgoing links, and that script has tick characters like this one ‘ which, incidentally, are also used for delimiting the values of comment anchor tags.

    To fix:
    Read the rest of this entry »


    Posted in CMS, how-to, PHP, Programming, Software, Web | 2 Comments »

    Git: how to remove file and commit from history

    13th February 2009

    Once I accidentally added circa 300 MiB of archive files to one of my git repositories (which was as small as 5 MiB). I removed those files as soon as I noticed them, but the .git directory still preserved commits with those files, and still occupied over 300 MiB.

    I have found the solution at stackoverflow (see also this question).

    This method worked for me, but I couldn’t push my rebased repository to the gitosis. I would need to re-init the gitosis repository from my rebased, but I’m not yet prepared to do that.

    There is also a slightly different method (which relies on a temporary tag instead of a temporary branch), documented in Git online manual pages; I prefer the temporary branch method.

    Below is a full copy-paste of the winning answer by Charles Bailey:

    # create and check out a temporary branch at the location of the bad merge
    git checkout -b tmpfix

    # remove the incorrectly added file
    git rm somefile.orig

    # commit the amended merge
    git commit –amend

    # go back to the master branch
    git checkout master

    # replant the master branch onto the corrected merge
    git rebase tmpfix

    # delete the temporary branch
    git branch -d tmpfix

    Also, in my case this thread at stackoverflow was highly useful. I start enjoying the concise and compact style of Charles Bailey :) :
    Read the rest of this entry »


    Posted in how-to, Links, Programming | 2 Comments »