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Merge branch 'update_docs' into 'develop'
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minro

See merge request tron/addannot!114
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franla23 committed Dec 11, 2020
2 parents b145250 + 84d74be commit 4427a40
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6 changes: 3 additions & 3 deletions docs/source/02_installation.md
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Expand Up @@ -112,12 +112,12 @@ export NEOFOX_REFERENCE_FOLDER=path/to/reference/folder
## Test installation

The user can test if all the installations have been successful by testing NeoFox with some test data. The test data can be downloaded here:
:download:`test file with neoantigen candidates <test_data.txt>`
:download:`test file with patient data <test_patients.txt>`
:download:`test_data.txt <test_data.txt>`
:download:`test_patients.txt <test_patients.txt>`

````commandline
neofox --model-file /path/to/test_data.txt --patient-data /path/to/test_patients.txt --output-folder /path/to/outputfolder --with-short-wide-table --with-tall-skinny-table --with-json --output-prefix test
````

The resulting output files can be compared to the following test output file:
:download:`annotated test file <test_neoantigen_candidates_annotated.tsv>`
:download:`test_neoantigen_candidates_annotated.tsv <test_neoantigen_candidates_annotated.tsv>`

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