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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 1.5 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 After copying the files in the desired locations follow the instructions below to register
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10 the reference files with galaxy.
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11
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12
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13
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14
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15 AUTOMATIC INSTALL
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16
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17 When prompted for a tool panel section to contain the installed tools create a new section
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18 called 'Complete Genomics - cgatools 1.5'.
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19
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20 After install create a cg_ccr_files.loc file in the tool-data directory of your Galaxy
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21 instance by copying the cg_ccr_files.loc.sample file. In cg_ccr_files.loc edit the path
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22 for the reference genome files (.crr files) downloaded from Complete Genomics' ftp site.
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23
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24 Restart Galaxy instance after editing cg_crr_files.loc.
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25
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26
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27
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28
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29 MANUAL INSTALL
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30
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31 For manual install from compressed files move/copy the following files into your Galaxy instance:
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32 directory tools/cgatools_v1.5 to tools/
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33 file lib/galaxy/datatypes/completegenomics.py to lib/galaxy/datatypes/
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34 file tool-data/cg_crr_files.loc.sample to tool-data/cg_crr_files.loc
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35
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36 In cg_ccr_files.loc edit the path for the reference genome files (.crr files) downloaded
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37 from Complete Genomics' ftp site.
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38
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39 Paste from tool_config.xml.sample into the tool_config.xml of your Galaxy instance:
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40 <!--
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41 Copy the following section to tool_conf.xml file in your Galaxy distribution if you are adding Complete Genomics tools manually to your Galaxy instance
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42 -->
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43 <section name="Complete Genomics - cgatools v1.5" id="cg_cgatools1.5">
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44 <tool file="cgatools_v1.5/listvariants.xml" />
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45 <tool file="cgatools_v1.5/testvariants.xml" />
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46 <tool file="cgatools_v1.5/listtestvariants.xml" />
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47 <tool file="cgatools_v1.5/calldiff.xml" />
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48 <tool file="cgatools_v1.5/snpdiff.xml" />
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49 <tool file="cgatools_v1.5/junctiondiff.xml" />
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50 <tool file="cgatools_v1.5/join.xml" />
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51 <tool file="cgatools_v1.5/varfilter.xml" />
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52 </section>
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53 <!-- End of copied section -->
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54
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55 Paste from tool_data_table_config.xml.sample into the tool_data_table_config.xml of your Galaxy instance:
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56 <!-- Start location of cgatools crr files -->
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57 <table name="cg_crr_files" comment_char="#">
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58 <columns>value, dbkey, name, path</columns>
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59 <file path="tool-data/cg_crr_files.loc" />
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60 </table>
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61 <!-- End Location of cgatools crr files -->
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62
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63 Paste from datatypes_conf.xml into the datatypes_conf.xml of your Galaxy instance:
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64 <!--
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65 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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66 -->
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67 <!-- Start Complete Genomics Datatypes -->
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68 <datatype extension="cg_var" type="galaxy.datatypes.completegenomics:CG_Var" display_in_upload="true" />
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69 <datatype extension="cg_mastervar" type="galaxy.datatypes.completegenomics:CG_MasterVar" display_in_upload="true" />
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70 <datatype extension="cg_gene" type="galaxy.datatypes.completegenomics:CG_Gene" display_in_upload="true" />
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71 <!-- End Complete Genomics Datatypes -->
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72 <!-- End of copied section -->
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73
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74 Restart Galaxy instance. |
