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comparison cgatools/README.txt @ 0:3b8b80827fbe draft default tip

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author greg
date Fri, 22 Jun 2012 14:25:22 -0400
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1 Provides galaxy tools for Complete Genomics' cgatools package - http://www.completegenomics.com
2
3 This repository provides tools to execute functions of cgatools from Complete Genomics, Inc.
4 and includes the cgatools 1.5 executable.
5
6 Reference genomes files for cgatools can be downloaded from Complete Genomics ftp site:
7 ftp://ftp.completegenomics.com/ReferenceFiles/build37.crr
8 ftp://ftp.completegenomics.com/ReferenceFiles/build36.crr
9 After copying the files in the desired locations follow the instructions below to register
10 the reference files with galaxy.
11
12
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15 AUTOMATIC INSTALL
16
17 When prompted for a tool panel section to contain the installed tools create a new section
18 called 'Complete Genomics - cgatools 1.5'.
19
20 After install create a cg_ccr_files.loc file in the tool-data directory of your Galaxy
21 instance by copying the cg_ccr_files.loc.sample file. In cg_ccr_files.loc edit the path
22 for the reference genome files (.crr files) downloaded from Complete Genomics' ftp site.
23
24 Restart Galaxy instance after editing cg_crr_files.loc.
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29 MANUAL INSTALL
30
31 For manual install from compressed files move/copy the following files into your Galaxy instance:
32 directory tools/cgatools_v1.5 to tools/
33 file lib/galaxy/datatypes/completegenomics.py to lib/galaxy/datatypes/
34 file tool-data/cg_crr_files.loc.sample to tool-data/cg_crr_files.loc
35
36 In cg_ccr_files.loc edit the path for the reference genome files (.crr files) downloaded
37 from Complete Genomics' ftp site.
38
39 Paste from tool_config.xml.sample into the tool_config.xml of your Galaxy instance:
40 <!--
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
42 -->
43 <section name="Complete Genomics - cgatools v1.5" id="cg_cgatools1.5">
44 <tool file="cgatools_v1.5/listvariants.xml" />
45 <tool file="cgatools_v1.5/testvariants.xml" />
46 <tool file="cgatools_v1.5/listtestvariants.xml" />
47 <tool file="cgatools_v1.5/calldiff.xml" />
48 <tool file="cgatools_v1.5/snpdiff.xml" />
49 <tool file="cgatools_v1.5/junctiondiff.xml" />
50 <tool file="cgatools_v1.5/join.xml" />
51 <tool file="cgatools_v1.5/varfilter.xml" />
52 </section>
53 <!-- End of copied section -->
54
55 Paste from tool_data_table_config.xml.sample into the tool_data_table_config.xml of your Galaxy instance:
56 <!-- Start location of cgatools crr files -->
57 <table name="cg_crr_files" comment_char="#">
58 <columns>value, dbkey, name, path</columns>
59 <file path="tool-data/cg_crr_files.loc" />
60 </table>
61 <!-- End Location of cgatools crr files -->
62
63 Paste from datatypes_conf.xml into the datatypes_conf.xml of your Galaxy instance:
64 <!--
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
66 -->
67 <!-- Start Complete Genomics Datatypes -->
68 <datatype extension="cg_var" type="galaxy.datatypes.completegenomics:CG_Var" display_in_upload="true" />
69 <datatype extension="cg_mastervar" type="galaxy.datatypes.completegenomics:CG_MasterVar" display_in_upload="true" />
70 <datatype extension="cg_gene" type="galaxy.datatypes.completegenomics:CG_Gene" display_in_upload="true" />
71 <!-- End Complete Genomics Datatypes -->
72 <!-- End of copied section -->
73
74 Restart Galaxy instance.