Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    Archive for March, 2011

    How to truncate git history (sample script included)

    28th March 2011

    Under a few assumptions (most importantly – you do not have any non-merged branches,), it is very easy to throw away git repository commits older than an arbitrarily-chosen commit.

    Here’s a sample script (call it e.g. git-truncate and put into your ~/bin or whichever location you have in PATH).


    #!/bin/bash
    git checkout --orphan temp $1
    git commit -m "Truncated history"
    git rebase --onto temp $1 master
    git branch -D temp
    # The following 2 commands are optional - they keep your git repo in good shape.
    git prune --progress # delete all the objects w/o references
    git gc --aggressive # aggressively collect garbage; may take a lot of time on large repos

    Invocation: cd to your repository, then git-truncate refspec, where refspec is either a commit’s SHA1 hash-id, or a tag.

    Expected result: a git repository starting with “Truncated history” initial commit, and continuing to the tip of the branch you were on when calling the script.

    If you truncate repositories often, then consider adding an optional 2nd argument (truncate-commit message) and also some safeguards against improper use – currently, even if refspec is wrong, the script will not abort after a failed checkout.

    Thanks for posting any improvements you may have.

    Source: Tekkub’s post on github discussions.
    See also: how to remove a single file from all of git’s commits.

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    Posted in how-to, Notepad | 11 Comments »

    How to fix: Nokia Ovi Suite could not connect to the Nokia account server

    10th March 2011

    I’ve been getting this message for a long while, when trying to log into Ovi from within my Ovi Suite:

    Nokia Ovi Suite could not connect to the Nokia account server. Make sure the internet connection is working properly and try again.

    However, both my internet connection, and logging into ovi.com using a browser work fine. Even looking for updates from within Ovi Suite works fine!

    Here’s the solution (tested on Nokia Ovi Suite 3.0.0.290):
    Read the rest of this entry »

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    Posted in how-to, Misc | 21 Comments »

    Amazonia! 6462 human microarray datasets

    6th March 2011

    Amazonia!Amazonia! – explore the jungle of microarray results

    Paradoxically, the tremendous downpour of microarray results prevents a simple use of expression data. Therefore, we propose a thematic entry to public transcriptomes: you may for instance query a gene on a “Stem Cells page”, where you will see the expression of your favorite gene across selected microarray experiments related to stem cell biology. This selection of samples can be customized at will among the 6462 samples currently present in the database.

    Every transcriptome study results in the identification of lists of genes relevant to a given biological condition. In order to include this valuable information in any new query in the Amazonia! database, we indicate for each gene in which lists it is included. This is a straightforward and efficient way to synthesize hundreds of microarray publications.

    A special feature of Amazonia! is the field of human stem cells, notably embryonic stem cells.

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    Posted in Bioinformatics, Links, Science | No Comments »