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Update Dockerfile #125

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Update Dockerfile #125

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f5f2768
Update Dockerfile
VergaJU Feb 28, 2024
de9fa98
added git pull to download large files for reference
VergaJU Feb 28, 2024
c145f73
added to the reference and adapted Dockerfile to download my fork
VergaJU Feb 29, 2024
e83c4b6
Dockerfile clone working branch to correctly update reference
VergaJU Feb 29, 2024
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4 changes: 3 additions & 1 deletion Docker/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,9 @@ RUN apt-get update && \
RUN curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | bash
RUN apt-get install -y git-lfs

RUN git clone https://github.com/RabadanLab/arcasHLA.git
RUN git clone --branch VergaJU-patch-1 https://github.com/VergaJU/arcasHLA.git
RUN conda env create -f /app/arcasHLA/environment.yml
RUN echo "source activate arcas-hla" > ~/.bashrc
ENV PATH /opt/conda/envs/arcas-hla/bin:$PATH
ENV PATH=/app/arcasHLA/:$PATH
RUN arcasHLA reference --update
15 changes: 13 additions & 2 deletions scripts/reference.py
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Original file line number Diff line number Diff line change
Expand Up @@ -85,15 +85,20 @@ def check_ref():
build_fasta()

def fetch_hla_dat():
'''Clones IMGTHLA github to database.'''
'''Clones IMGTHLA github to database. Git lfs pull to be sure to download all needed files'''

if isdir(IMGTHLA):
run_command(['rm', '-rf', IMGTHLA])

command = ['git', 'clone', IMGTHLA_git, IMGTHLA]
run_command(command,
'[reference] Cloning IMGT/HLA database:')


## run git lfs pull
command = ['git', '-C', IMGTHLA, "lfs", "pull"]
run_command(command,
'[reference] pull large files')

def checkout_version(commithash, verbose = True):
'''Checks out a specific IMGTHLA github version given a commithash.'''

Expand All @@ -105,6 +110,12 @@ def checkout_version(commithash, verbose = True):
run_command(command, '[reference] Checking out IMGT/HLA:')
else:
run_command(command)

## run git lfs pull
command = ['git', '-C', IMGTHLA, "lfs", "pull"]
run_command(command,
'[reference] pull large files')


def hla_dat_version(print_version = False):
'''Returns commithash of downloaded IMGTHLA database.'''
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