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

[DH-178] remove some python packages from bio and timing for R installation #5219

Merged
merged 10 commits into from
Nov 15, 2023
Merged

[DH-178] remove some python packages from bio and timing for R installation #5219

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
10 commits
Select commit Hold shift + click to select a range
0e3bb01
remove some python packages
shaneknapp Nov 14, 2023
618fc91
time the R installation and rm-ing of temp files
shaneknapp Nov 14, 2023
d87475b
time python package installs
shaneknapp Nov 14, 2023
c5d5dca
install time, add quotes
shaneknapp Nov 14, 2023
b18c624
shell gymnastics ftl
shaneknapp Nov 14, 2023
d28e05f
moar shell gymnastics ftl
shaneknapp Nov 14, 2023
2f63e41
moar shell gymnastics ftl le sigh
shaneknapp Nov 14, 2023
21af23b
and i quote, help me escape from this bash hell
shaneknapp Nov 15, 2023
30fc0d7
time ALL the things that take time
shaneknapp Nov 15, 2023
60f5257
remove timing code
shaneknapp Nov 15, 2023
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: 4 additions & 2 deletions deployments/biology/image/Dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -169,7 +169,9 @@ USER ${NB_USER}
COPY environment.yml /tmp/
COPY infra-requirements.txt /tmp/

RUN mamba env update -p ${CONDA_DIR} -f /tmp/environment.yml && mamba clean -afy
RUN mamba env update -p ${CONDA_DIR} -f /tmp/environment.yml && \
mamba clean -afy

RUN jupyter contrib nbextensions install --sys-prefix --symlink && \
jupyter nbextensions_configurator enable --sys-prefix

Expand All @@ -187,7 +189,7 @@ RUN r -e "install.packages('IRkernel', version='1.2')" && \
# Install R packages, cleanup temp package download location
COPY install.R /tmp/install.R
RUN r /tmp/install.R && \
rm -rf /tmp/downloaded_packages/ /tmp/*.rds
rm -rf /tmp/downloaded_packages/ /tmp/*.rds

# install bio1b packages
COPY bio1b-packages.bash /tmp/bio1b-packages.bash
Expand Down
6 changes: 3 additions & 3 deletions deployments/biology/image/environment.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ dependencies:
- nb_conda_kernels=2.3.1

# Packages from bioconda for IB134L
- bwa=0.7.12
# - bwa=0.7.12
- samtools=1.3.1
- mafft=7.471
- emboss=6.6.0
Expand All @@ -23,8 +23,8 @@ dependencies:
- fastqc=0.11.9
- phyml=3.3.20200621
- sra-tools=2.11
- hisat2=2.2.1
- subread=2.0.1
# - hisat2=2.2.1
# - subread=2.0.1
- plink=1.90b6.21

- syncthing==1.18.6
Expand Down