For release 0.3 (#175)

* cleanup repo

* remove rs regexp assumption

* fix adapt_flashpca

* remove some unused files

Author: olivierlabayle

.github/workflows/CompatHelper.yml

@@ -10,12 +10,8 @@ CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"
 Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-HypothesisTests = "09f84164-cd44-5f33-b23f-e6b0d136a0d5"
-JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-MKL = "33e6dc65-8f57-5167-99aa-e5a354878fb2"
 Mmap = "a63ad114-7e13-5084-954f-fe012c677804"
 SnpArrays = "4e780e97-f5bf-4111-9dc4-b70aaf691b06"
-TMLE = "8afdd2fb-6e73-43df-8b62-b1650cd9c8cf"
 YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 
 [compat]
@@ -25,9 +21,5 @@ CSV = "0.9, 0.10"
 CategoricalArrays = "0.10"
 Combinatorics = "1.0"
 DataFrames = "1.2"
-HypothesisTests = "0.10"
-JLD2 = "0.4"
-MKL = "0.5"
 SnpArrays = "0.3"
-TMLE = "0.8.2"
 YAML = "0.4"

Project.toml

@@ -31,5 +31,4 @@ For this mode, use the `with-param-files` command and `--param-prefix` option. T
 
 ### MechanismActors strategy
 
-
 For this strategy, use the `with-actors` command. and `--asb-prefix` and `--trans-actors` options. This will generate pairwise interaction parameters between bQTLs output by the [Baal-ChIP pipeline](https://git.ecdf.ed.ac.uk/oalmelid/baal-nf) and trans-actors eQTLs from a CSV file. Additionally, if template parameters configuration files containing extra treatments are provided, nth-order interaction parameters will be generated.

README.md

@@ -45,7 +45,8 @@ function parse_commandline()
             arg_type = Int
             required = false
             help = "Further performance may be obtained by batching phenotypes in a"*
-                   " single Targeted Estimation run"
+                   " single Targeted Estimation run. If not specified, all phenotypes "*
+                   "constitute a batch."
 
         "--positivity-constraint"
             arg_type = Float64

bin/sieve_variance.jl

@@ -6,7 +6,7 @@ ENV TZ=Europe/Amsterdam
 
 ENV JULIA_DEPOT_PATH=/opt
 
-RUN apt-get update && apt-get install -y wget unzip procps libcurl4-openssl-dev libbz2-dev liblzma-dev
+RUN apt-get update && apt-get install -y wget unzip procps
 
 # Install gcta
 
@@ -18,38 +18,8 @@ RUN mv gcta_v1.94.0Beta_linux_kernel_3_x86_64/gcta_v1.94.0Beta_linux_kernel_3_x8
 
 RUN chmod a+x /usr/local/bin/gcta64
 
-# Install R and hal9001
-
-RUN apt-get install -y r-base \
-                    r-base-core \
-                    r-recommended \
-                    r-base-dev
-
-RUN apt-get install -y libssl-dev \
-                libxml2-dev \
-                libcurl4-openssl-dev \
-                libgit2-dev \
-                libfontconfig1-dev \
-                libharfbuzz-dev \
-                libfribidi-dev \
-                libpng-dev \
-                libtiff5-dev \
-                libjpeg-dev
-
-RUN R -e "install.packages('devtools', repos='http://cran.us.r-project.org'); \
-         require(devtools);\
-         install_version('hal9001', version = '0.4.1', repos = 'http://cran.us.r-project.org')"
-
 # Import project, build and precompile
 COPY . /TargeneCore.jl 
 
 RUN julia -q --project=/TargeneCore.jl -e'using Pkg; Pkg.instantiate(); Pkg.resolve(); Pkg.precompile(); using TargeneCore'
 
-# Prepend a writable DEPOT_PATH ($PWD is mounted by default by singularity)
-RUN mkdir $PWD/julia_depot
-
-ENV JULIA_DEPOT_PATH=$PWD/julia_depot:$JULIA_DEPOT_PATH
-
-# RUN julia -q --project build_sysimage.jl
-
-# RUN echo 'alias julia="julia -J TMLEEpistasisSysimage.so"' >> ~/.bashrc

bin/summarize.jl

@@ -1,24 +1,17 @@
 module TargeneCore
 
-if occursin("Intel", Sys.cpu_info()[1].model)
-    using MKL
-end
 using DataFrames
 using CSV
-using TMLE
 using BGEN
-using JLD2
 using SnpArrays
 using Mmap
-using HypothesisTests
 using YAML
 using Combinatorics
 
 ###############################################################################
 # INCLUDES
 
 include("confounders.jl")
-include("sieve_plateau.jl")
 include(joinpath("tmle_inputs", "tmle_inputs.jl"))
 include(joinpath("tmle_inputs", "from_actors.jl"))
 include(joinpath("tmle_inputs", "from_param_files.jl"))
@@ -28,7 +21,6 @@ include(joinpath("tmle_inputs", "from_param_files.jl"))
 # EXPORTS
 
 export filter_chromosome, merge_beds, adapt_flashpca
-export sieve_variance_plateau
 export tmle_inputs
 
 end