User:Lindenb/Notebook/UMR915/20100608

=Download SIFT=

wget "http://sift.jcvi.org/www/sift4.0.3.tar.gz"

"Human variation databases should be downloaded from the ftp location ftp://ftp.jcvi.org/pub/data/sift/Human_db_36/, unzipped and placed in the directory SIFT_HOME/db/Human_db_version/"

ln -s Human_db_36 to the storage area

for C in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y ; do wget "ftp://ftp.jcvi.org/pub/data/sift/Human_db_36/Human_CHR${C}.sqlite.gz"; done =Polyphen=

wget "http://genetics.bwh.harvard.edu/pph2/dokuwiki/_media/polyphen-2.0.22r308.tar.gz"

=Maven=

added in ~/${HOME}/.m2/settings.xml (cf. http://maven.apache.org/guides/mini/guide-proxies.html )  /GENOTYPAGE/data/maven2/repository true http xxxxxhost xxxxxport localhost

=mvn for taverna= /usr/local/package/apache-maven-2.2.1/bin/mvn -B archetype:generate -DarchetypeRepository=http://www.mygrid.org.uk/maven/repository/ \ -DgroupId=fr.inserm.umr915 -DartifactId=taverna01  -Dpackage=fr.inserm.umr915.taverna01  \ -DarchetypeGroupId=net.sf.taverna.t2.archetypes \ -DarchetypeArtifactId=taverna-activity-archetype \ -DarchetypeVersion=1.0