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1 Provides galaxy tools for Complete Genomics' cgatools package - http://www.completegenomics.com
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2
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3 This repository provides tools to execute functions of cgatools from Complete Genomics, Inc.
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4 and includes the cgatools 1.6 executable.
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5
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6 Reference genomes files for cgatools can be downloaded from Complete Genomics' ftp site:
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7 ftp://ftp.completegenomics.com/ReferenceFiles/build37.crr
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8 ftp://ftp.completegenomics.com/ReferenceFiles/build36.crr
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9
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10 Calibration files for cgatools can be downloaded from Complete Genomics' ftp site:
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11 ftp://ftp.completegenomics.com/ScoreCalibrationFiles/var-calibration-v2.tgz
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12
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13 After copying the files in the desired locations follow the instructions below to register
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14 the reference files with galaxy.
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15
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16
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17
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18
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19 AUTOMATIC INSTALL
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20
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21 When prompted for a tool panel section to contain the installed tools create a new section
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22 called 'Complete Genomics - cgatools 1.6'.
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23
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24 After install create a cg_ccr_files.loc file in the tool-data directory of your Galaxy
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25 instance by copying the cg_ccr_files.loc.sample file. In cg_ccr_files.loc edit the path
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26 for the reference genome files (.crr files) downloaded from Complete Genomics' ftp site.
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27
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28 Restart Galaxy instance after editing cg_crr_files.loc.
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29
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30
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31
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32
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33 MANUAL INSTALL
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34
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35 For manual install from compressed files move/copy the following files into your Galaxy instance:
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36 directory tools/cgatools_1.6 to tools/
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37 file lib/galaxy/datatypes/completegenomics.py to lib/galaxy/datatypes/
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38 file tool-data/cg_crr_files.loc.sample to tool-data/cg_crr_files.loc
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39
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40 In cg_ccr_files.loc edit the path for the reference genome files (.crr files) downloaded
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41 from Complete Genomics' ftp site.
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42
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43 Paste from tool_config.xml.sample into the tool_config.xml of your Galaxy instance:
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44 <!--
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45 Copy the following section to tool_conf.xml file in your Galaxy distribution if you are
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46 adding Complete Genomics tools manually to your Galaxy instance
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47 -->
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48 <section name="Complete Genomics - cgatools 1.6" id="cg_cgatools1.6">
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49 <tool file="cgatools_1.6/listvariants.xml" />
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50 <tool file="cgatools_1.6/testvariants.xml" />
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51 <tool file="cgatools_1.6/listtestvariants.xml" />
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52 <tool file="cgatools_1.6/calldiff.xml" />
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53 <tool file="cgatools_1.6/snpdiff.xml" />
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54 <tool file="cgatools_1.6/junctiondiff.xml" />
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55 <tool file="cgatools_1.6/join.xml" />
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56 <tool file="cgatools_1.6/varfilter.xml" />
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57 <tool file="cgatools_1.6/mkvcf.xml" />
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58 <tool file="cgatools_1.6/evidence2sam.xml" />
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59 </section>
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60 <!-- End of copied section -->
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61
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62 Paste from tool_data_table_config.xml.sample into the tool_data_table_config.xml of your Galaxy instance:
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63 <!-- Start location of cgatools crr files -->
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64 <table name="cg_crr_files" comment_char="#">
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65 <columns>value, dbkey, name, path</columns>
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66 <file path="tool-data/cg_crr_files.loc" />
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67 </table>
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68 <!-- End Location of cgatools crr files -->
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69
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70 Paste from datatypes_conf.xml into the datatypes_conf.xml of your Galaxy instance:
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71 <!--
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72 Copy the following section to datatypes_conf.xml file in your Galaxy distribution if you are adding Complete Genomics tools manually to your Galaxy instance
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73 -->
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74 <!-- Start Complete Genomics Datatypes -->
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75 <datatype extension="cg_var" type="galaxy.datatypes.completegenomics:CG_Var" display_in_upload="true" />
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76 <datatype extension="cg_mastervar" type="galaxy.datatypes.completegenomics:CG_MasterVar" display_in_upload="true" />
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77 <datatype extension="cg_gene" type="galaxy.datatypes.completegenomics:CG_Gene" display_in_upload="true" />
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78 <!-- End Complete Genomics Datatypes -->
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79 <!-- End of copied section -->
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80
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81 Restart Galaxy instance. |
