Mercurial > repos > jjohnson > defuse
annotate README @ 4:679a5c7b1294 draft
deFuse version 0.5.0 - Use tool_dependencies.xml
| author | Jim Johnson <jj@umn.edu> |
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| date | Fri, 04 Jan 2013 13:29:03 -0600 |
| parents | 4245c2b047de |
| children | 3bd1087db05e |
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deFuse version 0.5.0 - Use tool_dependencies.xml
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1 The DeFuse galaxy tool is based on DeFuse_Version_0.5.0 |
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deFuse version 0.5.0 - Use tool_dependencies.xml
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2 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page |
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| 4 DeFuse is a software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. The software also employs a number of heuristic filters in an attempt to reduce the number of false positives and produces a fully annotated output for each predicted fusion. | |
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| 7 Manual: | |
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deFuse version 0.5.0 - Use tool_dependencies.xml
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8 http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.4.2 |
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deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
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9 |
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679a5c7b1294
deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
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10 The included tool_dependencies.xml will download and install the defuse code. |
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679a5c7b1294
deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
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11 It will set the environment variable: "DEFUSE_PATH" to the location of the defuse install. |
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deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
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14 The defuse.pl command relies on a configuration file to specifiy options, the location of reference data, and other applications that it depends upon: bowtie, bowtie-build, samtools, blat, fatotwobit, R, and Rscript. |
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deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
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15 |
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679a5c7b1294
deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
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16 The DeFuse galaxy tool can either construct the config.txt file that is mentioned in the defuse manual, or select an existing config.txt file in the users history. |
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deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
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17 When constructing the config.txt file, the DeFuse tool uses the values selected in: tool-data/defuse.loc |
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679a5c7b1294
deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
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18 The dictionary field in the tool-data/defuse.loc can be used to set fields in the config.txt file, including the site specific location of reference data and the paths to the other application binaries. |
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679a5c7b1294
deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
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19 The "Defuse parameter settings" are used to alter options in the config.txt file. |
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deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
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20 |
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679a5c7b1294
deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
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21 The DeFuse galaxy tool also generates a bash script to run defuse. |
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679a5c7b1294
deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
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22 That script will attempt to edit the config.txt file to specifiy any unset paths to applications that defuse relies upon: |
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679a5c7b1294
deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
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23 bowtie, bowtie-build, samtools, blat, fatotwobit, R, and Rscript |
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679a5c7b1294
deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
changeset
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24 The script uses the using the shell "which" command to discover the application path, so the required applications should in PATH environment variable. |
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deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
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4245c2b047de
Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
Jim Johnson <jj@umn.edu>
parents:
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27 Generate Reference Datasets as described in the Manual: |
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4245c2b047de
Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
Jim Johnson <jj@umn.edu>
parents:
1
diff
changeset
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deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
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29 The manual has detailed instructions on how to set up reference datasets for Human hg19 and hg18. |
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deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
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diff
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30 We were able to follow the same basic procedures to set up a reference for Mouse mm9. |
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4245c2b047de
Changes for defuse-0.4.3, modifications for non-human genomes no longer required, defuse.xml searches for location of scripts/defuse.pl
Jim Johnson <jj@umn.edu>
parents:
1
diff
changeset
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679a5c7b1294
deFuse version 0.5.0 - Use tool_dependencies.xml
Jim Johnson <jj@umn.edu>
parents:
2
diff
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32 These datasets should be referenced in the tool-data/defuse.loc file. |
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