Author Archives: Thomas Cokelaer

okular: export annotations in the PDF file

Tweet One open source software to add annotations under Linux is okular ( One can add annotations easily (go to Tools, tick review, or just type F6). Then, it is time to save your document or to send it to … Continue reading

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No more space left on /tmp under Fedora

Tweet Under Fedora, one of my software requires more than 4Gb of temporary space and I realised that the /tmp directory is limited to 4Gb. In order to increase the /tmp directory, just edit the /etc/fstab file and add this … Continue reading

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blasr (pacbio) installation on fedora box

Tweet I wanted to use blasr tool for Pacbio mapping and had difficulties in using or installing the tool. I first use a local installation of the tool on the provided cluster and it look like the installation was quite … Continue reading

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swapping two columns with awk keeping tabulation

Tweet Assuming you have a data file with N columns and you want to swap the first and second one, just type:

To keep the tabulation intact, you need to specify the separator. Incoming separator is defined by -F … Continue reading

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set a default version to an environment module

Tweet Context: “The environment modules package provides for an easy dynamic modification of a user’s environment via modulefiles. which typically instruct the module command to alter or set shell environment variables such as PATH, MANPATH, etc. as well as define … Continue reading

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fedora aeroplane mode always on

Tweet Under Fedora 23, somehow the aeroplane mode went on (plane icon shown in top right corner). I tried to switch it off but could not. After a reboot, the aeroplane is still switch on and there is no way … Continue reading

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packet_write_wait: Connection to XXX : Broken pipe

Tweet In general, I can connect to a remote machine via SSH without any troubles but occasionally in some particular setup, although I can connect to the remote machine and type commands in a shell, the connection is broken after … Continue reading

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pytest-cov collects no data on Travis

Tweet I recently switched from nosetests to pytest and pytest-cov for one of my Python project ( Locally, everything seemed to work fine and once on Travis, all tests passed as expected. Yet, before the coverage report, I noticed this … Continue reading

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Remove extension in a bash script

Tweet Imagine a bunch of files with extension fastq.dsrc, the following script will decompress the files by looping over the N files. One issue was to remove the extension in the script. See below the usage of //

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git synchronisation of a forked repository

Tweet Let us assume you have forked a repository (from You now have a local version at a given time of the repository repository_name.

Time flyes and you come back to the local repository and you are not … Continue reading

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