Mercurial > repos > saskia-hiltemann > cgatools_v17

comparison README @ 1:3a2e0f376f26 draft

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Minor change to tv2vcf.xml to allow for workflow automation
author dgdekoning
date Wed, 21 Oct 2015 10:09:15 -0400
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0:751b62d30ae1 1:3a2e0f376f26
1 installation instructions cgatools:
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4 reference data
5 ------------------------
6 Get .crr files from CG ftp site:
7 - ftp://ftp.completegenomics.com/ReferenceFiles/build36.crr
8 - ftp://ftp.completegenomics.com/ReferenceFiles/build37.crr
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10 Get calibration root file:
11 - ftp://ftp.completegenomics.com/ScoreCalibrationFiles/var-calibration-v2.tgz
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13 Get other reference file from CG ftp site:
14 - ftp://ftp.completegenomics.com/AnnotationFiles/gene36.tsv.gz
15 - ftp://ftp.completegenomics.com/AnnotationFiles/rmsk36.tsv.gz
16 - ftp://ftp.completegenomics.com/AnnotationFiles/segdup36.tsv.gz
17 - ftp://ftp.completegenomics.com/AnnotationFiles/gene37.tsv.gz
18 - ftp://ftp.completegenomics.com/AnnotationFiles/rmsk37.tsv.gz
19 - ftp://ftp.completegenomics.com/AnnotationFiles/segdup37.tsv.gz
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22 And unzip them to desired location.
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25 Adjust cgatools.loc file (included in repository) to reflect the locations of the reference files you dowloaded.
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28 datatypes
29 ------------------------
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31 <!-- Start Complete Genomics Datatypes -->
32 <datatype extension="cg_var" type="galaxy.datatypes.completegenomics:CG_Var" display_in_upload="true" />
33 <datatype extension="cg_mastervar" type="galaxy.datatypes.completegenomics:CG_MasterVar" display_in_upload="true" />
34 <datatype extension="cg_gene" type="galaxy.datatypes.completegenomics:CG_Gene" display_in_upload="true" />
35 <!-- End Complete Genomics Datatypes -->
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