Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add alternative key servers for R #1

Merged
merged 2 commits into from
Feb 20, 2024
Merged

Add alternative key servers for R #1

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
46ca93e
Add alternative key servers for R
arine Feb 16, 2024
5d7e32a
Replace hpo with HP:0000001 if empty
arine Feb 20, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 5 additions & 1 deletion Dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,11 @@ RUN apt install wget
RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc

# add the R 4.0 repo from CRAN -- adjust 'focal' to 'groovy' or 'bionic' as needed
RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 || \
apt-key adv --keyserver ha.pool.sks-keyservers.net --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 || \
apt-key adv --keyserver pgp.mit.edu --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 || \
apt-key adv --keyserver hkp://p80.pool.sks-keyservers.net:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 || \
apt-key adv --keyserver keyserver.pgp.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
RUN add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"

RUN apt install -y r-base r-base-core r-recommended r-base-dev
Expand Down
6 changes: 6 additions & 0 deletions run/proc.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,12 @@ else
REF_GEN="GRCh38"
fi

#Check if hpo.txt is empty or has no valid HPO ID
if [[ -z $(egrep 'HP:[0-9]{7}' /input/hpo.txt) ]] ; then
#Replace it with HP:0000001
echo "HP:0000001" > /input/hpo.txt
fi


echo "VCF pre-processing"
#annotate with new chromosomes and preserve original coordinates in ID
Expand Down