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Fix mhcflurry docker permission problem #52

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merged 3 commits into from
Sep 8, 2020
Merged

Fix mhcflurry docker permission problem #52

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0def7b5
Fix mhcflurry docker permission problem
skrakau Sep 1, 2020
a0505a9
Update CHANGELOG
skrakau Sep 1, 2020
62b7915
Merge branch 'dev' into fix_mhcflurry_dir
christopher-mohr Sep 8, 2020
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -25,7 +25,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Fixed`

- [#79](https://github.com/nf-core/epitopeprediction/pull/39) - Fix display of prediction tool version [#36](https://github.com/nf-core/epitopeprediction/issues/36)
- [#55](https://github.com/nf-core/epitopeprediction/pull/52) - Fix MHCflurry permission problem when run with docker profile [#51](https://github.com/nf-core/epitopeprediction/issues/51)
- [#39](https://github.com/nf-core/epitopeprediction/pull/39) - Fix display of prediction tool version [#36](https://github.com/nf-core/epitopeprediction/issues/36)

## v1.0.0 - purple-nickel-shrimp - 2019-12-05

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6 changes: 6 additions & 0 deletions main.nf
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Expand Up @@ -409,6 +409,12 @@ process peptidePrediction {
def ref_prot = params.proteome ? "--proteome ${params.proteome}" : ""
def wt = params.wild_type ? "--wild_type" : ""
"""
# create folder for MHCflurry downloads to avoid permission problems when running pipeline with docker profile and mhcflurry selected
mkdir -p mhcflurry-data
export MHCFLURRY_DATA_DIR=./mhcflurry-data
# specify MHCflurry release for which to download models, need to be updated here as well when MHCflurry will be updated
export MHCFLURRY_DOWNLOADS_CURRENT_RELEASE=1.4.0

epaa.py ${input_type} --identifier ${inputs.baseName} \
--alleles $alleles \
--mhcclass ${params.mhc_class} \
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