raid 0 vs raid 10

http://www.zdnet.com/blog/storage/raid-10-is-the-cadillac-of-raid/131

https://bitcointalk.org/index.php?topic=28411.0

http://www-03.ibm.com/systems/resources/Demartek_IBM_LSI_RAID_Controller_Performance_Evaluation_2009-10.pdf

http://www.dell.com/downloads/global/products/pvaul/en/PERC6_PerfWP_WMD1120.pdf

http://www.tomshardware.com/forum/245704-32-raid-raid

http://www.dell.com/downloads/global/products/pvaul/en/PERC6_PerfWP_WMD1120.pdf

RAID level Sequential Reads (MB/s) Sequential Writes (MB/s) Random Reads (IOPS) Random Writes (IOPS)
RAID 0 Best Best Best Best
RAID 10 Better Better Best Better

http://louwrentius.com/benchmark-results-of-random-io-performance-of-different-raid-levels.html
http://docs.oracle.com/cd/E19691-01/820-1847-20/appendixf.html#50515995_83606

https://www.kernel.org/doc/Documentation/filesystems/ext4.txt

 

One Liners

https://blogs.oracle.com/ksplice/entry/the_top_10_tricks_of

http://www.math.harvard.edu/computing/perl/oneliners.txt

https://wiki.python.org/moin/Powerful%20Python%20One-Liners

 

Report LGC

indel detection

dindel

test mpileup
./samtools-bcftools-htslib-1.0_x64-linux/bin/samtools mpileup MM140738JS.bam -v -u > test.vcf
10:72358747

samtools mpileup -C50 -gf ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam

./samtools-bcftools-htslib-1.0_x64-linux/bin/samtools mpileup -uf /lgc/datasets/hg19/new/hg19/hg19.fa MM140738JS.bam | ./samtools-bcftools-htslib-1.0_x64-linux/bin/bcftools call -mv > var.raw.vcf

http://gatkforums.broadinstitute.org/discussion/3255/indel-calling
https://www.broadinstitute.org/files/shared/mpg/nextgen2011/nextgen2011_delangel.pdf

GATK -glm INDEL

python /lgc/scripts/unifiergenotyper_indel.py -i MM140738JS.bam -t /lgc/datasets/sickkids/AmpliSeqExome.20131001.designed.bed -o MM140738JS.indel.vcf

grep “72358746” *.vcf [ 7:47AM]
raony@mendel{MM140738JS} grep “72358745” *.vcf [ 7:48AM]
MM140738JS.indel.vcf:chr10 72358745 . CA C 1049.73 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.769;DP=84;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=81.36;MQ0=0;MQRankSum=-1.613;QD=12.50;ReadPosRankSum=0.095 GT:AD:DP:GQ:PL 0/1:47,32:81:99:1087,0,1785

 

KDE 5

$ sudo apt-add-repository ppa:neon/kf5
$ sudo apt-get update
$ sudo apt-get install project-neon5-session project-neon5-utils project-neon5-konsole

On startup

raony@einstein ~ $ free -m
total used free shared buffers cached
Mem: 3680 1659 2020 16 155 673
-/+ buffers/cache: 831 2849
Swap: 19072 0 19072

After opening Chrome

raony@einstein ~ $ free -m
total used free shared buffers cached
Mem: 3680 2684 995 26 180 863
-/+ buffers/cache: 1640 2040
Swap: 19072 0 19072

Source: http://arstechnica.com/information-technology/2014/08/kde-plasma-5-for-those-linux-users-undecided-on-the-kernels-future/3/

http://www.tecmint.com/install-kde-plasma-5-in-linux/|

 

Fixing Python 3.4 in Ubuntu Trusty 14.04

Python 3.4 is broken in the new version of Ubuntu 14.04! (Which is a shame and should now happen! 😛 )

When you try to create a new virtual environment with “pyvenv venv” you get the following message:

pyvenv-3.4 test
Error: Command '['/home/raony/development/test_py3/test/bin/python3.4', '-Im', 'ensurepip', '--upgrade', '--default-pip']' returned non-zero exit status 1

I think this is because ensurepip is not included with python in the new version of Ubuntu 14.04 trusty.

You can read the discussion about this bug in here:

https://bugs.launchpad.net/ubuntu/+source/python3.4/+bug/1290847

So for me the solution was to install two ssl-packages and python3.4 from source with the following commands:

sudo apt-get install libssl-dev openssl
wget https://www.python.org/ftp/python/3.4.0/Python-3.4.0.tgz
tar -zxvf Python-3.4.0.tgz
cd Python-3.4.0
./configure
make
sudo make install

And them you can finally start creating your virtual environments again with the new venv module that comes with python 3.4 (https://docs.python.org/3/library/venv.html) ! 🙂

pyvenv venv
source venv/bin/activate
pip install -r requirements.txt

And now I can finally start migrating my django projects from python 2.7 to python 3.4! Uhuuu!