Archive for the ‘Linux’ Category

Software update

November 30, 2013 Leave a comment

Picards tools

The classical one 😉

GATK 2.7-4

A new experimental feature to assess PK for reference site. Plus some bug fixing


A new version of the algorithm. Shortened arguments flags. New sides tools (data checking and graph handling).


A new version released 2.12 :  faster and with additional feature. Note a GCTA forum is now available for discussion and technical problem.


A more flexible way to define reference population and the way data are handled. Multi-threading available during sampling step.

Delly 0.12

Apart from translocation detection removal (not for long ?), this version ship a lot of awaited features like vcf output.

Varscan 2.3.6

Still some work on vcf compatibility improvement.

Categories: Linux, NGS, QTL-detection, SNP

Software update

August 18, 2013 Leave a comment

Picards tools

The classical one 😉  Note that some changes were done for java 7 compatibility. So, after GATK, turning to java 7 as default may be on its way.

Beagle 4

Another update (r1128), not documented so far.


The new version now use all variants in the reference panel (snp, indels, SV)

Open MP

The openmp specification 4.0 are out ! Now support Fortran2003 and prepare the support for accelerator. Note the next intel compiler version already support a large number of the new specifications.


This library now in its version 1.4 . Support for new GPUs were added as well as additional subroutines. I wish more Fortran interface were added…maybe next time !

Cuda 5.5

As previously mentioned, the last version of cuda is now available as rpm/deb package (allowing a much easier install).

Categories: emacs, Linux, NGS

Software update

July 25, 2013 Leave a comment

So what are the last noticeable update of this latest months ?

GATK 2.6-5

At last HaplotypeCaller is now a real alternative for Big project ! <grumpy> The bad thing <\grumpy> is that now GATK need java7, which is still not so common nowadays and (thanks to oracle) no that easy to install !

I am actually running it on a batch of 100 bulls  @12&+X(so far so good, I will complete a whole genome variant calling in 2 weeks).

Beagle 4
Now allowing imputation ! And this just make everything so simple !


This tool has been released in its 5.0 version.


This is the yearly release. Not a lot of new things but it’s always worthy to upgrade.

Categories: emacs, Linux, NGS

Serial snapshots with IGV batch

July 16, 2013 Leave a comment

IGV is a very handy tool. Nevertheless, scrolling from one position to another may be fastidious. Second, the bad aspect of this very user-friendly software, is that you can spend hours looking here and there, with at last no backtrack of your discoveries.

Thankfully, IGV can run in batch mode, allowing, for a targeted list of positions, to take screenshots and store the later in a folder. We’ll illustrate in the following with a small example :

Setting up a session

To test our script, we will first download some publicly available data.

#Download a vcf file (on beagle4 website, you may have to change file name according to last release)
gunzip test.r1099.vcf.gz
#Create an index
igvtools index test.r1099.vcf
#(You can alternatively prefer to use igvtools from igv GUI)
#Launch igv

To check if everything is right, load the vcf file test.r1099.vcf. Then move to positions chr22:20,000,000-20,100,000.


Set everything to your taste, and save the session :  File, save session, you should obtain a xml file.

Running IGV in batch mode

Now, let’s consider you are interested in some particular position. Let’s say we’ve stored several positions of interest in a csv file. Our aim is to create an IGV batch file.

Basically, we’ll have to load the session, set a directory to store the screenshots, and then move from one position to the other. A very crude version could therefore be. (I know : Why csv ? Because a lot of person still use excel 😦 )

#Create a fake positions list
cat >Liste.csv <<EOF

#Create a ss directory
mkdir IMG
#Write the header of the script
cat >Batch.igv <<EOF
load igv_session.xml
snapshotDirectory IMG
#Now parse the csv file
gawk -F ";" -v R=10000 '{print "goto "$1":"$2 -R"-"$2 + R"\nsnapshot Screen"NR".png"}END{print "exit"}' Liste.csv >>Batch.igv

From, igv, go to Tools, Run a batch script. Load Batch.igv, when all the process will be done, IGV will terminate and you’ll find your screenshots in IMG.

For an even more automated version you can use the script “” available in the scriptotheque

Software update

June 18, 2013 Leave a comment

Another month, another software update

samtools 0.1.19

I missed it in the last posts (this version was released in March). Multi-thread is now available. I play a bit with the the different displays (Html, Curse and Text) of tview, (pretty handy). I may need more time to get acustomed to bamcheck/plot-bamcheck output.

Delly 0.0.11

Some small fixes, a new progress bar to control process, better temporary file handling, and BWA-mem support…more here

BWA 0.7.5a

Several small fixes

Picard tools 1.93

Small bug fixes. Released some hours ago (I had to compensate samtools glitch)

llvm 3.3

Still some efficiency enhancement, clang is now totally C++11 complient. New Arch support…and more. Release announcement is still pending, but binary are already available.


Apparently computing speed improvement are the newsworthy point of this release.

Coming soon…

I’ve had access to both next cuda 5.5 RC and Intel compiler….and so far the good new is that both now offer a simplified install procedure. Cuda 5.5 is available as a deb file, Intel compiler as a script with a GUI. I am eager to test these RC.

Software update

May 1, 2013 1 comment

April’s quick review of software’s updates :

GATK 2.5

Still some speed improvement, our bug got finally fixed ! Just wonder how broad’s staff will manage to make Haplotype Caller faster than Unified genotyper ! Wait and see.

BWA 0.7.4

After some small bugs, this version offer the same stability for BWA-MEM than for BWA-backtrack, nice to hear.

Picard-Tools 1.90

Still on the same releases rhythm.

IGV 2.3

The motif finder is a very nice new feature.


Not really an update, but ensembl 71 added sift score for cow.

Categories: Linux, NGS

eMarch 5 : Tramp

March 29, 2013 Leave a comment

We are all living in a modern world, the cloud is everywhere and of course also in emacs. So the closing post of this serie will talk about tramp. Tramp is so rich of features that a post won’t be enough. I’ll focus on the point I’ve used so far.

Basic use

I generally use a lot of ssh connection. Tramp allows me to naviguate through the remote directory as if they were on my local machine. The basic commands C-x D and C-x f just need a special syntax to describe the path to the file directory you want to access to.

With ssh, the syntax is similar to the scp one. Hence to access the file test.txt in your home directory “~” on remote host “rem1” , just do

C-x C-f

To access the directory “/work/you/project” on remote1 “”, ip “”

C-x d

Last, while visiting a remote directory, if you start a shell buffer with “M-x shell”, the later will be started on the remote host. If a shell buffer is already open on your localhost, M-x shell will redirect you to this buffer. The trick here is to use  C-u M-x shell to start a second buffer shell.

Some other hints

Of course the neat way to access remote host is to create a ssh config file. Anyway if your login on the remote host is different from the one you generally use, or if you are using a tunnel with a different port, you ‘ll have to modify your path.

Taking the former example, assuming now that your login is “Name” you want to connect on localhost port 9022 (We are considering an access via an ssh tunnel).

C-x d

Other useful tips and alternative can be found on the emacs wiki tramp page, like :

  • setting a default tramp user with (setq tramp-default-user “ClassicalLogin”)
  • setting a default tramp protocol (setq tramp-default-method “ssh”)
Categories: emacs, Linux, Shell