User:Lindenb/Notebook/UMR915/20100608

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Contents

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
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