Murali-group · alexmorinvt · Feb 21, 2026 · Feb 21, 2026 · Feb 21, 2026 · Feb 21, 2026
diff --git a/.gitignore b/.gitignore
@@ -1,7 +1,9 @@
-inputs/
-__pycache__/
+# Common env outputs
+__pycache__
+.vscode
+
+# BEELINE specific files
+configs/
 outputs/
-src/.*
-*.ipynb_checkpoints*
-.DS_Store
-.idea/
+inputs/
+plotting_examples/
diff --git a/Algorithms/BTR/Dockerfile b/Algorithms/BTR/Dockerfile
@@ -1,6 +1,6 @@
 FROM r-base:3.5.3
 
-LABEL maintainer = "Aditya Pratapa <adyprat@vt.edu>"
+LABEL maintainer="Aditya Pratapa <adyprat@vt.edu>"
 
 USER root
 
@@ -16,9 +16,6 @@ RUN R -e "install.packages('https://cran.r-project.org/src/contrib/BTR_1.2.4.tar
 
 RUN mkdir data/
 
-WORKDIR data/
+WORKDIR /data/
 
 COPY runBTR.R /data/runBTR.R
-
-
-
diff --git a/Algorithms/GRISLI/Dockerfile b/Algorithms/GRISLI/Dockerfile
@@ -1,6 +1,6 @@
 FROM ubuntu:18.04
 
-LABEL Maintainer = "Aditya Pratapa <adyprat@vt.edu>"
+LABEL maintainer="Aditya Pratapa <adyprat@vt.edu>"
 
 USER root
 
@@ -20,9 +20,9 @@ RUN mkdir runGRISLI
 
 COPY runGRISLI/ /runGRISLI/
 
-WORKDIR runGRISLI/
+WORKDIR /runGRISLI/
 
-ENV LD_LIBRARY_PATH /opt/mcr/v96/runtime/glnxa64:/opt/mcr/v96/bin/glnxa64
+ENV LD_LIBRARY_PATH=/opt/mcr/v96/runtime/glnxa64:/opt/mcr/v96/bin/glnxa64
 
 RUN mkdir -p /root/.mcrCache9.6/GRISLI0/GRISLI/
 

diff --git a/Algorithms/GRNVBEM/Dockerfile b/Algorithms/GRNVBEM/Dockerfile
@@ -1,6 +1,6 @@
 FROM ubuntu:18.04
 
-LABEL Maintainer = "Aditya Pratapa <adyprat@vt.edu>"
+LABEL maintainer="Aditya Pratapa <adyprat@vt.edu>"
 
 USER root
 
@@ -20,9 +20,9 @@ RUN mkdir VBEM/
 
 COPY VBEM/ /VBEM/
 
-WORKDIR VBEM/
+WORKDIR /VBEM/
 
-ENV LD_LIBRARY_PATH /opt/mcr/v96/runtime/glnxa64:/opt/mcr/v96/bin/glnxa64
+ENV LD_LIBRARY_PATH=/opt/mcr/v96/runtime/glnxa64:/opt/mcr/v96/bin/glnxa64
 
 RUN mkdir data/
 

diff --git a/Algorithms/JUMP3/Dockerfile b/Algorithms/JUMP3/Dockerfile
@@ -1,6 +1,6 @@
 FROM ubuntu:18.04
 
-LABEL Maintainer = "Aditya Pratapa <adyprat@vt.edu>"
+LABEL maintainer="Aditya Pratapa <adyprat@vt.edu>"
 
 
 RUN apt-get -qq update && apt-get -qq install -y unzip xorg wget curl libstdc++6
@@ -19,10 +19,10 @@ RUN mkdir JUMP3/
 
 COPY J3p/ /JUMP3/
 
-WORKDIR JUMP3/
+WORKDIR /JUMP3/
 
-ENV LD_LIBRARY_PATH /opt/mcr/v96/runtime/glnxa64:/opt/mcr/v96/bin/glnxa64
+ENV LD_LIBRARY_PATH=/opt/mcr/v96/runtime/glnxa64:/opt/mcr/v96/bin/glnxa64
 
 RUN mkdir data/
 
-RUN apt-get install time
+RUN apt-get install time
diff --git a/Algorithms/LEAP/Dockerfile b/Algorithms/LEAP/Dockerfile
@@ -1,16 +1,18 @@
-# FROM r-base:4.2.2
-FROM r-base:4.5.1
+FROM r-base:4.2.2
 
-LABEL maintainer = "Aditya Pratapa <adyprat@vt.edu>"
+LABEL maintainer="Aditya Pratapa <adyprat@vt.edu>"
 
 USER root
 
 WORKDIR /
 
-RUN R -e "install.packages('https://cran.r-project.org/src/contrib/LEAP_0.2.tar.gz', type = 'source')"
+RUN R -e "install.packages('https://cran.r-project.org/src/contrib/Archive/LEAP/LEAP_0.2.tar.gz', type = 'source')"
 
 COPY runLeap.R /
 
 RUN mkdir data/
 
-RUN apt-get update && apt-get install -y time
+RUN apt-get update -o Acquire::AllowInsecureRepositories=true \
+    && apt-get install -y --allow-unauthenticated debian-archive-keyring \
+    && apt-get update \
+    && apt-get install -y time
diff --git a/Algorithms/PIDC/Dockerfile b/Algorithms/PIDC/Dockerfile
@@ -16,4 +16,3 @@ RUN julia installPackages.jl
 COPY runPIDC.jl /
 
 RUN apt-get update && apt-get install -y time
-
diff --git a/Algorithms/PNI/Dockerfile b/Algorithms/PNI/Dockerfile
@@ -10,13 +10,12 @@ RUN pip2 install pandas==0.21
 
 RUN git clone https://github.com/fionahamey/Pseudotime-network-inference
 
-WORKDIR Pseudotime-network-inference/
+WORKDIR /Pseudotime-network-inference/
 
 RUN git checkout b900655
 
 #RUN python2 booleanRules.py Bptf binary_expression_LMPP.txt 5 LMPP_trajectory_order.txt 2 2 startingNetworkParCor.txt 0.95 0.05
 
 #RUN cat Bptf_boolean_rules_5.txt
 
-
-RUN apt-get install time
+RUN apt-get install time
diff --git a/Algorithms/PPCOR/Dockerfile b/Algorithms/PPCOR/Dockerfile
@@ -1,16 +1,18 @@
-# FROM r-base:4.2.2
-FROM r-base:4.5.1
+FROM r-base:4.2.2
 
-LABEL maintainer = "Aditya Pratapa <adyprat@vt.edu>"
+LABEL maintainer="Aditya Pratapa <adyprat@vt.edu>"
 
 USER root
 
 WORKDIR /
 
-RUN R -e "install.packages('https://cran.r-project.org/src/contrib/ppcor_1.1.tar.gz', type = 'source')"
+RUN R -e "install.packages('ppcor', repos='https://cloud.r-project.org', dependencies=TRUE)"
 
 COPY runPPCOR.R /
 
 RUN mkdir data/
 
-RUN apt-get update && apt-get install -y time
+RUN apt-get update -o Acquire::AllowInsecureRepositories=true \
+    && apt-get install -y --allow-unauthenticated debian-archive-keyring \
+    && apt-get update \
+    && apt-get install -y time
diff --git a/Algorithms/SCINGE/Dockerfile b/Algorithms/SCINGE/Dockerfile
@@ -1,6 +1,6 @@
 FROM ubuntu:18.04
 
-LABEL Maintainer = "Aditya Pratapa <adyprat@vt.edu>"
+LABEL maintainer="Aditya Pratapa <adyprat@vt.edu>"
 
 USER root
 
@@ -21,9 +21,9 @@ RUN mkdir runSCINGE/
 
 COPY runSCINGE/ /runSCINGE/
 
-WORKDIR runSCINGE/
+WORKDIR /runSCINGE/
 
-ENV LD_LIBRARY_PATH /opt/mcr/v96/runtime/glnxa64:/opt/mcr/v96/bin/glnxa64
+ENV LD_LIBRARY_PATH=/opt/mcr/v96/runtime/glnxa64:/opt/mcr/v96/bin/glnxa64
 
 RUN mkdir data/
 

diff --git a/Algorithms/SCNS/Dockerfile b/Algorithms/SCNS/Dockerfile
@@ -15,21 +15,21 @@ RUN apt-get install -y build-essential patch
 RUN apt-get install -y fsharp \ 
 	mono-xbuild
 RUN git clone https://github.com/Z3Prover/z3
-WORKDIR z3
+WORKDIR /z3
 RUN git checkout d6df51951f4cdc95f0dfd3b1297d04a465d8f2ca 
 
 RUN python2 scripts/mk_make.py --python
 RUN cd build && make
 RUN cd build && make install
-WORKDIR ..
+WORKDIR /
 
 RUN export PATH="$PATH:/z3/build/"
 
 RUN  git clone https://github.com/swoodhouse/SCNS-Toolkit
-WORKDIR SCNS-Toolkit
+WORKDIR /SCNS-Toolkit
 RUN git checkout 27cb7a349f239d450a9571b270abc38b053ad6b2
 
-WORKDIR SynthesisEngine
+WORKDIR /SCNS-Toolkit/SynthesisEngine
 
 RUN xbuild SynthesisEngine.sln
 

diff --git a/Algorithms/SCODE/Dockerfile b/Algorithms/SCODE/Dockerfile
@@ -1,29 +1,28 @@
-# FROM r-base:4.2.2
-FROM r-base:4.5.1
+FROM r-base:4.2.2
 
-LABEL maintainer = "Aditya Pratapa <adyprat@vt.edu>"
+LABEL maintainer="Aditya Pratapa <adyprat@vt.edu>"
 
 USER root
 
 WORKDIR /
 
-
-RUN apt-get update && apt-get install -y  gcc
+RUN apt-get update -o Acquire::AllowInsecureRepositories=true \
+    && apt-get install -y --allow-unauthenticated debian-archive-keyring \
+    && apt-get update \
+    && apt-get install -y gcc
 
 RUN apt-get install -y git
 
 RUN apt-get install -y ruby
 
 RUN git clone https://github.com/hmatsu1226/SCODE
 
-WORKDIR SCODE/
+WORKDIR /SCODE/
 
 RUN git checkout a0512f8ec29aac188c9c27a8e89ddd2464e6d84d
 
-RUN R -e "install.packages('https://cran.r-project.org/src/contrib/MASS_7.3-51.3.tar.gz', type = 'source')"
+RUN R -e "install.packages('https://cran.r-project.org/src/contrib/Archive/MASS/MASS_7.3-51.3.tar.gz', type = 'source')"
 
 # RUN ruby run_R.rb data/exp_train.txt data/time_train.txt out 100 4 356 100 2
 
-
-
-RUN apt-get install -y time
+RUN apt-get update && apt-get install -y time
diff --git a/Algorithms/SCRIBE/Dockerfile b/Algorithms/SCRIBE/Dockerfile
@@ -1,19 +1,12 @@
-FROM bioconductor/release_base2:R3.5.3_Bioc3.8
+FROM bioconductor/bioconductor_docker:RELEASE_3_14
 
-LABEL maintainer = "Aditya Pratapa <adyprat@vt.edu>"
+LABEL maintainer="Aditya Pratapa <adyprat@vt.edu>"
 
 USER root
 
 WORKDIR /
 
-Run R -e "BiocManager::install('devtools',version=3.8)"
-
-RUN echo "deb http://archive.debian.org/debian stretch main contrib non-free" > /etc/apt/sources.list
-
-RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 04EE7237B7D453EC
-RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 648ACFD622F3D138
-RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys EF0F382A1A7B6500
-RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 0E98404D386FA1D9
+RUN R -e "install.packages('devtools')"
 
 RUN apt-get update && apt-get install -y libhdf5-dev \
 libxml2-dev \
@@ -24,51 +17,51 @@ libfreetype6-dev
 
 RUN DEBIAN_FRONTEND=noninteractive apt-get -y install xorg \
 libx11-dev \
-libglu1-mesa-dev 
+libglu1-mesa-dev
 
-RUN apt-get install -y r-cran-rgl
+RUN R -e "install.packages('rgl')"
 
 
-RUN R -e "BiocManager::install('HiveR',ref = 3.8)"
+RUN R -e "BiocManager::install('HiveR', update = FALSE)"
 
-RUN R -e "BiocManager::install(c('lattice','Matrix','irlba'),ref = 3.8, update = FALSE)"
+RUN R -e "BiocManager::install(c('lattice','Matrix','irlba'), update = FALSE)"
 
-RUN R -e "BiocManager::install(c('cluster','dplyr'), ref = 3.8, update = FALSE)"
+RUN R -e "BiocManager::install(c('cluster','dplyr'), update = FALSE)"
 
-# Needs monocle 2.8
+# monocle 2.x — available in Bioconductor 3.14 as version 2.22.0
 
-RUN R -e "BiocManager::install('monocle', ref = 2.8)" 
+RUN R -e "BiocManager::install('monocle', update = FALSE)"
 
 RUN git clone https://github.com/cole-trapnell-lab/RANNinf
 
-WORKDIR RANNinf/
+WORKDIR /RANNinf/
 
 RUN git checkout 9d4a3d781c8b74a01ec2018ca7137b22a0e583b6
 
 WORKDIR /
 
 RUN R CMD build RANNinf
 
-RUN R -e "BiocManager::install('RcppArmadillo', ref = 3.8, update = FALSE)"
+RUN R -e "BiocManager::install('RcppArmadillo', update = FALSE)"
 
 RUN R -e "install.packages('RANNinf_2.5.0.99.tar.gz', repo = NULL, type ='source')"
 
 RUN git clone https://github.com/cole-trapnell-lab/Scribe
 
-WORKDIR Scribe/
+WORKDIR /Scribe/
 
 RUN git checkout 4ba98500764adbce4a59be508d94b279bbfcfb31
 
-RUN R -e "BiocManager::install(c('cowplot','lpSolveAPI'), ref = 3.8, update = FALSE)"
+RUN R -e "BiocManager::install(c('cowplot','lpSolveAPI'), update = FALSE)"
 
 RUN R -e "install.packages('Scribe_0.1.tar.gz', repo = NULL, type ='source')"
 
 WORKDIR /
 
-RUN R -e "BiocManager::install(c('optparse'), ref = 3.8, update = FALSE)"
+RUN R -e "BiocManager::install(c('optparse'), update = FALSE)"
 
 RUN mkdir data/
 
 COPY runScribe.R /
 
-RUN apt-get install -y time
+RUN apt-get update && apt-get install -y time
diff --git a/Algorithms/SINCERITIES/Dockerfile b/Algorithms/SINCERITIES/Dockerfile
@@ -1,30 +1,33 @@
-# FROM r-base:4.2.2
-FROM r-base:4.5.1
+FROM r-base:4.2.2
 
-LABEL maintainer = "Aditya Pratapa <adyprat@vt.edu>"
+LABEL maintainer="Aditya Pratapa <adyprat@vt.edu>"
 
 USER root
 
 WORKDIR /
 
 RUN R -e "install.packages('https://cran.r-project.org/src/contrib/versions_0.3.tar.gz', type='source')"
-RUN R -e "install.packages('https://cran.r-project.org/src/contrib/Archive/glmnet/glmnet_2.0-13.tar.gz', type='source')"
-RUN R -e "install.packages('https://packagemanager.posit.co/cran/latest/src/contrib/Archive/kSamples/kSamples_1.2-9.tar.gz', type='source')"
-RUN R -e "install.packages('https://cran.r-project.org/src/contrib/ppcor_1.1.tar.gz', type='source')"
+RUN R -e "install.packages(c('Matrix', 'foreach', 'iterators'), repos='https://cloud.r-project.org')"
+RUN R -e "install.packages('https://cran.r-project.org/src/contrib/Archive/glmnet/glmnet_2.0-13.tar.gz', type='source', repos=NULL)"
+RUN R -e "install.packages('SuppDists')"
+RUN R -e "install.packages('https://cran.r-project.org/src/contrib/Archive/kSamples/kSamples_1.2-9.tar.gz', type='source')"
+RUN R -e "install.packages('ppcor', repos='https://cloud.r-project.org', dependencies=TRUE)"
 RUN R -e "install.packages('https://cran.r-project.org/src/contrib/Archive/pracma/pracma_2.2.9.tar.gz', type='source')"
 RUN R -e "install.packages('https://cran.r-project.org/src/contrib/Archive/R.matlab/R.matlab_3.6.2.tar.gz', type='source')"
 RUN R -e "install.packages('https://cran.r-project.org/src/contrib/Archive/cvTools/cvTools_0.3.2.tar.gz', type='source')"
 
-
 RUN ls
 
 COPY SINCERITIES.zip /
 
 
 RUN unzip SINCERITIES.zip -d SINCERITIES
 
-WORKDIR SINCERITIES/
+WORKDIR /SINCERITIES/
 
 RUN mkdir data/
 
-RUN apt-get update && apt-get install -y time
+RUN apt-get update -o Acquire::AllowInsecureRepositories=true \
+    && apt-get install -y --allow-unauthenticated debian-archive-keyring \
+    && apt-get update \
+    && apt-get install -y time
Original file line number	Diff line number	Diff line change
Expand Up		@@ -16,4 +16,3 @@ RUN julia installPackages.jl
		COPY runPIDC.jl /

		RUN apt-get update && apt-get install -y time