User:Lindenb/Notebook/UMR915/20100608
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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 )
<settings xmlns="http://maven.apache.org/SETTINGS/1.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0 http://maven.apache.org/xsd/settings-1.0.0.xsd"> <proxies> <localRepository>/GENOTYPAGE/data/maven2/repository</localRepository> <proxy> <active>true</active> <protocol>http</protocol> <host>xxxxxhost</host> <port>xxxxxport</port> <nonProxyHosts>localhost</nonProxyHosts> </proxy> </proxies> </settings>
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