Mercurial > repos > saskia-hiltemann > cgatools_v17

annotate README @ 10:d53cbccb08a0 draft

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit c475b4222a15cdadc6085865f4d13426249fec25-dirty
author yhoogstrate
date Wed, 11 Nov 2015 04:06:28 -0500
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1 installation instructions cgatools:
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4 reference data
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5 ------------------------
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6 Get .crr files from CG ftp site:
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7 - ftp://ftp.completegenomics.com/ReferenceFiles/build36.crr
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8 - ftp://ftp.completegenomics.com/ReferenceFiles/build37.crr
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10 Get calibration root file:
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11 - ftp://ftp.completegenomics.com/ScoreCalibrationFiles/var-calibration-v2.tgz
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13 Get other reference file from CG ftp site:
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14 - ftp://ftp.completegenomics.com/AnnotationFiles/gene36.tsv.gz
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15 - ftp://ftp.completegenomics.com/AnnotationFiles/rmsk36.tsv.gz
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16 - ftp://ftp.completegenomics.com/AnnotationFiles/segdup36.tsv.gz
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17 - ftp://ftp.completegenomics.com/AnnotationFiles/gene37.tsv.gz
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18 - ftp://ftp.completegenomics.com/AnnotationFiles/rmsk37.tsv.gz
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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
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29 ------------------------
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31 <!-- Start Complete Genomics Datatypes -->
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32 <datatype extension="cg_var" type="galaxy.datatypes.completegenomics:CG_Var" display_in_upload="true" />
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33 <datatype extension="cg_mastervar" type="galaxy.datatypes.completegenomics:CG_MasterVar" display_in_upload="true" />
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34 <datatype extension="cg_gene" type="galaxy.datatypes.completegenomics:CG_Gene" display_in_upload="true" />
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35 <!-- End Complete Genomics Datatypes -->
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