Mercurial > repos > saskia-hiltemann > cgatools_v17
diff README @ 1:3a2e0f376f26 draft
Minor change to tv2vcf.xml to allow for workflow automation
author | dgdekoning |
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date | Wed, 21 Oct 2015 10:09:15 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Wed Oct 21 10:09:15 2015 -0400 @@ -0,0 +1,38 @@ +installation instructions cgatools: + + +reference data +------------------------ + Get .crr files from CG ftp site: + - ftp://ftp.completegenomics.com/ReferenceFiles/build36.crr + - ftp://ftp.completegenomics.com/ReferenceFiles/build37.crr + + Get calibration root file: + - ftp://ftp.completegenomics.com/ScoreCalibrationFiles/var-calibration-v2.tgz + + Get other reference file from CG ftp site: + - ftp://ftp.completegenomics.com/AnnotationFiles/gene36.tsv.gz + - ftp://ftp.completegenomics.com/AnnotationFiles/rmsk36.tsv.gz + - ftp://ftp.completegenomics.com/AnnotationFiles/segdup36.tsv.gz + - ftp://ftp.completegenomics.com/AnnotationFiles/gene37.tsv.gz + - ftp://ftp.completegenomics.com/AnnotationFiles/rmsk37.tsv.gz + - ftp://ftp.completegenomics.com/AnnotationFiles/segdup37.tsv.gz + + + And unzip them to desired location. + + + Adjust cgatools.loc file (included in repository) to reflect the locations of the reference files you dowloaded. + + +datatypes +------------------------ + + <!-- Start Complete Genomics Datatypes --> + <datatype extension="cg_var" type="galaxy.datatypes.completegenomics:CG_Var" display_in_upload="true" /> + <datatype extension="cg_mastervar" type="galaxy.datatypes.completegenomics:CG_MasterVar" display_in_upload="true" /> + <datatype extension="cg_gene" type="galaxy.datatypes.completegenomics:CG_Gene" display_in_upload="true" /> + <!-- End Complete Genomics Datatypes --> + + +