Archive

Archive for July, 2012

Evolution

July 26, 2012 Leave a comment

Recently, my attention has been caught by several interesting articles on evolution that (albeit must be taken cautiously), try to support new hypotheses on evolution :

Larson et al nicely  discuss a possible evolution of dog breeds in the light of results obtained with denser SNP chip.

Nature, spotlight Kevin Peterson’s work which use miRNA in phylogeny.

Both  articles point out the necessary distance one must have regarding informations in hand. As instance, markers or miRNA have certain properties (mutation rate, neutrality, abundance….) that should be taken into account as they will drive our conclusion in one way or another. Another feature nicely shown by Larson et al., is the parallel made between the molecular observations, our knowledge of “breed” history , and the probability that genetic events (bottleneck, admixture) occurred.

On another more humorous side, Brian Malow made some good points in one of his video…evolution might be “a slow process”. 😉

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Categories: Agriculture, Funny science, SNP

Software update

July 24, 2012 Leave a comment

Another quick review on some updates :

Emacs 24.1

This version has been released in june. Some visual changes, and a major change with the package manager.
I haven’t really played with it so far, but as emacs is my every day “swiss army knife” i think I’ll soon get used to these new functionalities.

TeXlive 2012

As every year, a new version is available. I haven’t find any striking additional features, but that is part of LaTeX charm, a lot of small new additions that constantly enhanced your final result.

BWA 0.6.2

Mostly a bug fix release.

Picard-Tools 1.73

I realized that my version was outdated (I used the 1.69), but new versions have been delivered on a regular basis (4 in less than 2 months)

GATK 2.0 beta

A lot of change (explaining the version change).

A new website 🙂  a new licence :-(, improvement in base quality score  recalibration and a new file format (reduced BAM)  which should allow handling more files for SNP calling. And last some new tools to call variant. I am eager to test this !

Categories: emacs, Linux, NGS

Remember my name ?

July 19, 2012 Leave a comment

Some SGE options looks apparently useless, but with a second thought turn out to be very powerful. -N is one of such an option This post will try to exemplify the benefit of giving name to your job.

Usage :

To give a name to your job, you just need to add -N Name to qsub, thus to give the name Job1 to a script just type :

qsub -N Job1 Job.sh

…. and that ‘s it ! Ok let’s put it now in a working context.

Usefulness of  -N  : situation 1

Suppose, you submit every  month the same shell script, let say “GenomicEvaluation.sh”. If you submit your job with the same name name every month, with the following command


qsub -N GenomicEvaluation GenomicEvaluation.sh

Then, a simple command as :

qacct -j GenomicEvaluation | gawk '{if($1 ~ "start_time"){$1="";printf "%s , ",$0}; if($1 ~ "maxvmem"){print $2}}'  >MemConsumption.csv

Would create a file reporting the  evolution over time of the memory needed for your job !

Usefulness of  -N  : situation 2

Suppose you have 3 scripts, Job1.sh, Job2.sh and FinalJob.sh, and you don’t want FinalJob.sh to start before the end of the two first scripts. The trick is then to submit your two first with explanatory name.

qsub -N Job1 Job1.sh
qsub -N Job2 Job2.sh

And then submit FinalJob.sh but this time with the -hold_jid option followed by the two first job names

qsub -N FinalJob -hold_jid Job1,Job2   FinalJob.sh

Nice isn’t it ?

In both case, remember that JobID are given by SGE (in order of submission and based on the indication of jobseqnum in ${SGE_ROOT}/default/spool/qmaster) so they can hardly be predicted, whereas name are totally under control !

Usefulness of  -N  : situation 3

A more trivial use of -N can be to pass a variable to your script, in fact within the job environment the name you gave at submission will be assign to JOB_NAME environment variable.

Categories: Linux, SGE, Shell Tags: