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Exploratory results for inferCNV on non-ETP samples (SCPCP000003) #838

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merged 21 commits into from
Nov 5, 2024
Merged

Exploratory results for inferCNV on non-ETP samples (SCPCP000003) #838

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412d8fb
adding inferCNV part
UTSouthwesternDSSR Oct 23, 2024
b802413
Merge remote-tracking branch 'origin/main' into UTSouthwesternDSSR/no…
UTSouthwesternDSSR Oct 23, 2024
c3c6b8c
Merge branch 'AlexsLemonade:main' into main
UTSouthwesternDSSR Oct 23, 2024
9a33d0b
Add jags to system dependencies installation
jaclyn-taroni Oct 25, 2024
7f532da
Add Rhtslib installation step separately to Dockerfile
jaclyn-taroni Oct 25, 2024
a059dde
update scripts structure
UTSouthwesternDSSR Oct 29, 2024
0f075ed
Merge remote-tracking branch 'origin/main' into UTSouthwesternDSSR/no…
UTSouthwesternDSSR Oct 29, 2024
e31ab64
added marker genes table in final submission format
UTSouthwesternDSSR Oct 29, 2024
692be0d
change directory structure
UTSouthwesternDSSR Oct 30, 2024
33b2be0
change name
UTSouthwesternDSSR Oct 30, 2024
3588896
add script for rerun copykat
UTSouthwesternDSSR Oct 30, 2024
32423db
final submission script
UTSouthwesternDSSR Oct 30, 2024
151559d
Add new scripts to CI/CD
jaclyn-taroni Oct 30, 2024
514a06d
update final submission
UTSouthwesternDSSR Oct 30, 2024
d56c5d6
Merge remote-tracking branch 'origin/main' into UTSouthwesternDSSR/no…
UTSouthwesternDSSR Oct 30, 2024
b3478c7
update submission script and output
UTSouthwesternDSSR Oct 31, 2024
8d9dd4c
Merge branch 'main' into main
jashapiro Oct 31, 2024
7bde7e5
update scripts and readme
UTSouthwesternDSSR Oct 31, 2024
9b36d48
Merge remote-tracking branch 'origin/main' into UTSouthwesternDSSR/no…
UTSouthwesternDSSR Oct 31, 2024
74d9cad
exploration plots for CopyKat prediction with fine-tuned B cells
UTSouthwesternDSSR Oct 31, 2024
c3a7a7e
Merge branch 'main' into main
jaclyn-taroni Nov 5, 2024
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3 changes: 2 additions & 1 deletion .github/workflows/run_cell-type-nonETP-ALL-03.yml
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Expand Up @@ -59,7 +59,8 @@ jobs:
libfontconfig1-dev \
libharfbuzz-dev \
libfribidi-dev \
libtiff5-dev
libtiff5-dev \
jags

- name: Set up renv
uses: r-lib/actions/setup-renv@v2
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3 changes: 3 additions & 0 deletions analyses/cell-type-nonETP-ALL-03/Dockerfile
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Expand Up @@ -52,6 +52,9 @@ RUN conda-lock install -n ${ENV_NAME} conda-lock.yml \
# Copy the renv.lock file from the host environment to the image
COPY renv.lock renv.lock

# Temporarily install Rhtslib separately
RUN Rscript -e 'BiocManager::install("Rhtslib")'

# restore from renv.lock file and clean up to reduce image size
RUN Rscript -e 'renv::restore()' \
&& rm -rf ~/.cache/R/renv \
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