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INSTALL

build modules

pysam

pysam requires Cython, load it first and easybuild too

module use $RESIF_ROOTINSTALL/lcsb/modules/all
module load lang/Cython/0.22-goolf-1.4.10-Python-2.7.3
module load base/EasyBuild

cd ~/easybuild

sometimes Cython is not found, reload cache by doing module spider Cython

paleomix

Dependencies

'nose>=1.3.0' 'flexmock>=0.9.7' 'coverage>=4.0.0'

solving pysam and nose was sufficient

eb nose-1.3.7-goolf-1.4.10-Python-2.7.3.eb eb pysam-0.9.1-goolf-1.4.10-Python-2.7.3.eb

Need to add the path where pysam and nose are since paleomix depends on it eb -r /home/users/aginolhac/easybuild paleomix-1.2.5-goolf-1.4.10-Python-2.7.3.eb

AdapterRemoval

version 2 is now published

eb AdapterRemoval-2.1.7-goolf-1.4.10.eb`

jar

picard and GATK can be used from resif

mapDamage

eb -r /home/users/aginolhac/easybuild mapDamage-2.0.6-goolf-1.4.10-Python-2.7.3.eb

load modules

module load bio/AdapterRemoval
module load bio/paleomix
module load bio/SAMtools/0.1.19-goolf-1.4.10
module load bio/BWA
module load bio/mapDamage

module load bio/AdapterRemoval
module load bio/paleomix
module load bio/SAMtools/0.1.19-goolf-1.4.10
module load bio/BWA
module load bio/mapDamage

IGV install locally

can be connected to the galaxy server to display bams / bigwig etc.

set-up ssh keys on Windows

FIXME: convert to ppk before for all students

download putty, puttygen and pageant here

puttygen will be useless once ppk keys are available.

  1. Open puttygen to convert keys to .ppk format.
    • load private key, should say imported with success
    • save private key with .ppk extension
  2. Open pageant and open the ssh key in ppk format
  3. Open putty with a new session
    • host: `access-gaia.uni.lu
    • port: 8022
    • save as gaia
  4. load the gaia session, a prompt asks for the login student?? and should do

Remenber galaxy works only with internal wi-fi

FIXME: external PhD cannot connect

Test from a student account

using the ssh keys provided

ssh -p 8022 -i ./student06.key [email protected]

student01 = Jonathan student02 = Julia student03 = Daniela student04 = Xiabong student05 = Turkan student06 = test student07 = Jonas student08 = Nicolas

mkdocs

set-up done in mkdocs.yml

deploy

publish on github

mkdocs gh-deploy --clean

convert to pdf

install convertion to pandoc

pip install mkdocs-pandoc

convert to PDF and EPUB

mkdocs2pandoc > mydocs.pd
pandoc --toc -f markdown+grid_tables+table_captions -o chip-seq_AG.pdf mydocs.pd
pandoc --toc -f markdown+grid_tables -t epub -o chip-seq_AG.epub mydocs.pd