Lennart's weblog

Notes about open source software, computers, other stuff.

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ProbABEL v0.4.2 released

13 January 2014 / / 0 Comments

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).

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Puppet commands change when upgrading to v3.0.0

27 December 2013 / / 0 Comments

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

To show a list of clients waiting for signing of their certificates run the following on the master:

puppet cert list

instead of puppet ca -l. To list all certificates, run (on the master):

puppet cert list --all

To completely remove a client’s certificate on the master run:

puppet cert clean client.localdomain

and to sign a client certificate on the master run:

puppet cert sign client.localdomain

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Permantly ban an IP address with fail2ban

12 December 2013 / / 0 Comments

Over the last few days I noticed in my logwatch e-mails that one IP address kept trying to log in to my server, even though it was blocked regularly by fail2ban.

Here’s a post that explains how to simply add a list of IP addresses to block permanently. There’s only one catch: the listing provided there contains an error, the word <name> is missing in the iptables command, probably due to HTML conversion. This is the correct line to be insterted into the actionstart section of /etc/fail2ban/action.d/iptables-multiport.conf:

cat /etc/fail2ban/ip.blacklist | while read IP; do iptables -I fail2ban-<name> 1 -s $IP -j DROP; done

Use the following command to check if the IP address is indeed banned:

$ sudo iptables  -L fail2ban-ssh
Chain fail2ban-ssh (1 references)
target     prot opt source               destination         
DROP       all  --  192.168.20.25        anywhere            
RETURN     all  --  anywhere             anywhere

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Replacing a character in a Bash variable name

4 December 2013 / / 0 Comments

Today I needed to replace a : in a bunch of file names with a -, so I wanted to write a Bash for-loop to do just that. I vaguely remembered that you can do character replacements within variables, but couldn’t remember the details.

This is how it’s done:

for filename in *; do
    mv "$filename" "${filename/:/-}"
done

I put the variables in double quotes, because the file names contained spaces.

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How to start a LaTeX enumerate environment with a different number

10 October 2013 / / 0 Comments

I keep forgetting how to do this, so here’s a quick post that shows how to start a LaTeX enumerate environment with a different number.

By default enumerate environments start counting from 1 (obviously). To start with a different number you simply need to change the value of a counter:

\begin{enumerate}
   \setcounter{enumi}{2}
   \item This will be item 3
   \item Item 4 will be here
\end{enumerate}

If you have nested enumerate environments, the counters are enumii and enumiii.

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Showing other users (from LDAP) in the LightDM greeter

23 September 2013 / / 0 Comments

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:

sudo /usr/lib/lightdm/lightdm-set-defaults --show-manual-login true

This will disable the user list. It adds the line

greeter-show-manual-login=true

to the lightdm.conf file.
If you only want to see the “Other” entry run:

sudo /usr/lib/lightdm/lightdm-set-defaults --hide-users true

And lastly you can turn off guest:

sudo /usr/lib/lightdm/lightdm-set-defaults --allow-guest false

Thanks to mfish at askubuntu.com!

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Doing a quick fixed-effects meta-analysis using the Rmeta package

3 September 2013 / / 0 Comments

This is a quick example of how to do a fixed meta-analysis using the R package Rmeta, just so I dont have to look it up again next time:

## Create data frame containing betas and standard errors
df <- data.frame()
df <- rbind(df, c(2., 0.2))
df <- rbind(df, c(2.5, 0.4))
df <- rbind(df, c(2.2, 0.2))
 
## Add study names
df <- cbind(df, c("study 1", "study 2", "study 3"))
 
colnames(df) <- c("beta", "se_beta", "name") 
 
## Do the meta-analysis 
ms <- meta.summaries(df$beta, df$se_beta, names=df$name)
 
## Add some colors
mc <- meta.colors(summary="darkgreen", zero="red")
 
## Make a forest plot
plot(ms, xlab=expression(beta ~ " (mmol/l)"), 
     ylab="Study", colors=mc, zero=2.6)

The resulting plot looks like this:
Forest plot of fake data

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ProbABEL v0.4.1 released

3 September 2013 / / 0 Comments

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 \chi^2 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.

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Using BibTeX from org-mode

22 August 2013 / / 1 Comment

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)

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"))

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Growing XFS and still not able to write files, enough free space

19 August 2013 / / 1 Comment

One of the XFS filesystems at work almost ran out of space recently, so I extended the Logical Volume it was on, followed by xfs_growfs. This worked fine, df -h showed enough free space for the upcoming data. In the XFS FAQ I read that by default all inodes are placed in the first 1 TB of disk, which could lead to problem. Therefore, I added the inode64 option to the mount options and ran 

mount -o remount

on the partition.

While reviewing my log messages this morning I noticed a lot of

No space left on device

messages for that filesystem. Having this inode64 option in mind I wondered what went wrong. Although df -h and df -i showed enough free space and free inodes, respectively, I still couldn’t create a file. Again the XFS FAQ had an entry for that, but it puzzled me, because I was already using the inode64 option. Since the filesystem wasn’t in use I decided to completely unmount it and then mount it again. That worked. Apparently -o remount is not enough to enable the inode64 option.

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