After upgrading my Ubuntu 13.10 installation to 14.04, I noticed that the output of several git commands (e.g. git diff and git log) didn’t show colours as they used to, but showed ESC[ ANSI codes instead.
A quick internet search lead to this post on unix.stackexchange.com where the LESS environment variable was ‘blamed’. Indeed, I have my LESS variable (re-) defined in my .bashrc and .zshrc files.
The solution was to add -R to the environment variable, which allows raw control characters to be displayed. I now have the environment variable defined as:
Note to self: if you want to be able to upgrade WordPress via the web interface using SSH, you need to have the libssh2-php package installed on Debian/Ubuntu Linux.
Don’t forget to restart Apache after installing the package. Reload the WordPress admin pages and you’ll see the SSH option added.
After upgrading to Ubuntu 13.10 some time ago I noticed that my compose key (i.e. the key that you press followed by e.g. c and , to create a ç) didn’t work anymore in Emacs. I found two bug reports on this issue [1, 2], both effectively suggesting the same solution: start Emacs like this
XMODIFIERS=@im=none emacs
XMODIFIERS=@im=none emacs
So I added the following line to my ~/.zshrc and ~/.bashrc files:
aliasemacs='XMODIFIERS=@im=none emacs'
alias emacs='XMODIFIERS=@im=none emacs'
(of course somewhere before I set my EDITOR variable). I also changed the command in the launcher I use (GLX-Dock/Cairo-Dock).
This doesn’t make it a system-wide (or even user-wide) fix, e.g. the Firefox add-on “It’s all text” doesn’t get it, but it covers most of my use cases.
During the Christmas holidays I released a new version of ProbABEL (v0.4.2). The official release announcement can be found here. ProbABEL is a toolset that allows running GWAS (Genome-Wide Association Studies) in a fast and efficient manner. It implements regression using the linear, logistic or Cox proportional hazards models.
This version is mostly a bug fix release. The most important user-visible change is the fact that the ‘official’ name for the wrapper script that runs a GWAS over a range of chromosomes is now called probabel instead of probabel.pl. This change was induced by my attempts to get ProbABEL packaged in the Debian Linux repositories. One of the warnings that occurred during the package creation process was a Lintian warning that said that scripts with ‘language extensions’ are not allowed. There are several reasons for that, but the one I found most compelling was the fact that the user shouldn’t be concerned with the programming/scripting language we used to write it in. Moreover, being ‘agnostic’ in this matter also allows us to write such a script in a different language.
Of course, we have left the original name in place (via a symlink) in order not to disrupt any current pipelines. If the user runs the script with the old name a warning appears, urging him/her to start using the new name and that the old name will be deprecated in the future.
In the mean time, ProbABEL v0.4.1 has been accepted in Debian (unstable) and as of today it is also available in Debian ‘testing’. Lots of thanks to the Debian Med team that helped me a lot in preparing the .deb package. Note that the package has been split up in probabel (architecture-dependent files) and probabel-examples (with architecture independent files: the examples). See the Debian Package Tracking System page for ProbABEL for more details of the package.
From Debian the package has trickled down to Ubuntu as well (Launchpad page here), so it will be available by default in the next Ubuntu release (14.04, a.k.a. Trusty Tahr).
After upgrading Puppet from versions < v3 to version 3.0.0 or higher, the main commands have changed, keep this in mind when reading my earlier post. From the ChangeLog:
Pre-2.6
Post-2.6
puppetmasterd
puppet master
puppetd
puppet agent
puppet
puppet apply
puppetca
puppet cert
ralsh
puppet resource
puppetrun
puppet kick
puppetqd
puppet queue
filebucket
puppet filebucket
puppetdoc
puppet doc
pi
puppet describe
Some examples
To run puppet on a client puppetd --test is changed to:
puppet agent --test
puppet agent --test
To show a list of clients waiting for signing of their certificates run the following on the master:
puppet cert list
puppet cert list
instead of puppet ca -l. To list all certificates, run (on the master):
puppet cert list --all
puppet cert list --all
To completely remove a client’s certificate on the master run:
puppet cert clean client.localdomain
puppet cert clean client.localdomain
and to sign a client certificate on the master run:
Ubuntu Linux uses the LightDM greeter (the login screen you see after booting). Since I’m using an LDAP server to store my user accounts and LightDM by default only shows local users I needed to tell LightDM to give me an ‘other user’ option where I can enter a user name and password (I first checked to see if my LDAP connection work by logging in with an LDAP user from the console (tty1).
LightDM is configured in /etc/lightdm/lightdm.conf, but also provides command line tools to set the options. To show the ‘other user’ use:
Last week I released v0.4.1 of ProbABEL, just a few days after releasing v0.4.0, which contained a small, but irritating bug.
This release took quite some time to create, but features quite a few bug fixes, including a major one: for the first time since the filevector format was introduced somewhere in 2009/2010, the Cox proportional hazards regression module works with filevector/DatABEL files. This is a major step forward, because up till now we had to maintain two branches of code: trunk, with all the regular updates and improvements, and the old branch that contained the Cox PH module that was only capable of reading text files.
Another notable change is the incorporation of values in the output files. At the moment these are based on the LRT (likelihood ratio test), except where that doesn’t make sense (e.g. when using the --mmscore option. The implementation was relatively easy, because part of the code was still there from previous versions; it was disabled however, because it didn’t deal with missing genotype data. Now it does. Using the LRT is also easier in the case of the 2df (or genotypic) genetic model, where using the Wald test is not straightforward.
The third user-visible change was a change in the [code]probabel.pl[/code] script that hides some of the details (e.g. the location of the files with genotype data) of running a regression for the user. Previously, using the -o option meant that the output file name was constructed from the name of the phenotype file, the argument of the -o option and a fixed extension that depends on the model(s) being run. Starting with v.0.4.0 this behaviour has changed. If the -o option is specified its argument is used as the start of the output file name, with only the fixed extension appended to it. This allows users to specify output in a different directory than the one where the phenotype file was created.
Packages for Ubuntu Linux (or one of its derivatives and probably also Debian) can be found in the GenABEL PPA (personal package archive). Previously we also released pre-compiled Windows binaries, but I’ve stopped doing that. They were never tested anyway, and I think there isn’t much demand for them anyway. Most people who do genome-wide association studies use Linux servers anyway.
Development of ProbABEL (and other members of the GenABEL suite) takes place on this R-forge page. If you are in search of an open source project to contribute to, feel free to contact us!
User support for the GenABEL suite can be found at our forum.
I use Emacs‘ org-mode a lot for writing notes, todo lists, presentations and writing short reports. Recently I started writing a larger report which I normally would have done in LaTeX. This time, since the notes related to the project were already in org format, I decided to write the whole report in org-mode. The one thing I needed for that was using BibTeX bibliographies (and RefTeX) from org-mode. A quick web search revealed that that can easily be done by adding the following to your .emacs file:
;; Configure RefTeX for use with org-mode. At the end of your;; org-mode file you need to insert your style and bib file:;; \bibliographystyle{plain};; \bibliography{ProbePosition};; See http://www.mfasold.net/blog/2009/02/using-emacs-org-mode-to-draft-papers/(defun org-mode-reftex-setup ()(load-library "reftex")(and(buffer-file-name)(file-exists-p (buffer-file-name))(reftex-parse-all))(define-key org-mode-map (kbd "C-c )") 'reftex-citation))(add-hook 'org-mode-hook 'org-mode-reftex-setup)
;; Configure RefTeX for use with org-mode. At the end of your
;; org-mode file you need to insert your style and bib file:
;; \bibliographystyle{plain}
;; \bibliography{ProbePosition}
;; See http://www.mfasold.net/blog/2009/02/using-emacs-org-mode-to-draft-papers/
(defun org-mode-reftex-setup ()
(load-library "reftex")
(and (buffer-file-name)
(file-exists-p (buffer-file-name))
(reftex-parse-all))
(define-key org-mode-map (kbd "C-c )") 'reftex-citation)
)
(add-hook 'org-mode-hook 'org-mode-reftex-setup)
After that, RefTeX works, but exporting the org document to PDF (via LaTeX) didn’t include the bibliography entries. A quick look at the error log showed that bibtex hadn’t been run, so the question was: how to tell org-mode to do that too when exporting. The answer is to tell org-mode to use the latexmk Perl script (on Debian/Ubuntu it is easily installed from the package repositories) when exporting to PDF. I added the following lines to my .emacs file:
;; Use latexmk for PDF export(setq org-latex-to-pdf-process (list"latexmk -pdf -bibtex %f"))
;; Use latexmk for PDF export
(setq org-latex-to-pdf-process (list "latexmk -pdf -bibtex %f"))
Today I tried to clone my laptop’s harddrive to a new drive (thanks to Lenovo for sending me a replacement since the old drive was showing signs of breaking down). At first I tried dd, but that failed at around 90%, either because the old disk is indeed failing or because something fishy with the USB connection or enclosure in which I put the new disk. So I started gparted to check which partitions were copied OK and which weren’t. It turns out that all partitions were fine, except for my (encrypted) swap partition. gparted didn’t even recognise the partition type (on the original drive!). So after I replaced the harddrive I wanted to recreate the encrypted swap partition. It turn’s out to be easy if you follow the steps outlined in this blog post from Puny Geek. Thanks Puny Geek!
For some time (probably after an upgrade, I actually don’t remember anymore) we had problems with the NFS check in Nagios on our Ubuntu 12.04 servers. The check would return UNKNOWN: RPC program nfs udp is not running. When running the actual check from the command line:
the output would be: Can't fork for rpcinfo.
It turns out that the file /usr/lib/nagios/plugins/utils.pm has the wrong path to the rpcinfo binary. Instead of /usr/sbin/rpcinfo it lists /usr/bin/rpcinfo. So, like most of the times, the fix is easy, but pinpointing the exact problem isn’t.
Don’t forget to restart Nagios after changing the path as utils.pm needs to be reloaded.
As Ubuntu is based on Debian, I expect this fix to work there as well. According to this Launchpad bug report this issue was fixed in January in version 1.4.16-1ubuntu1 of the nagios-plugins package, which is not in Ubuntu 12.04.
values in the output files. At the moment these are based on the LRT (likelihood ratio test), except where that doesn’t make sense (e.g. when using the