FlashPCA projection fix for single sample Projection (#9)

Author: kachulis

ImputationPipeline/ScoringPart.wdl

@@ -203,7 +203,7 @@ task ProjectArray {
 	}
 
 	runtime {
-		docker: "skwalker/flashpca:v1"
+		docker: "quay.io/ckachuli/flashpca@sha256:85e9ee91bc552e46a0d69cc851b893419c8de6588c696458fc770eee526e381d" # a special version of flashpca which allows to project a single sample without erroring out at an unnecessary check
 		disks: "local-disk 400 HDD"
 		memory: mem + " GB"
 	} 

ImputationPipeline/flashpca_docker/Dockerfile

@@ -0,0 +1,36 @@
+FROM ubuntu:bionic
+RUN apt-get update && \
+   apt-get -y install python2.7 python-pip libboost1.62-all-dev \
+   libeigen3-dev git gnupg2 sudo wget ca-certificates
+RUN echo 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/' \
+   > /etc/apt/sources.list.d/cran.list
+RUN apt-key adv --keyserver keyserver.ubuntu.com \
+   --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
+RUN apt-get update
+RUN DEBIAN_FRONTEND=noninteractive apt-get -y install tzdata
+RUN ln -fs /usr/share/zoneinfo/Australia/Melbourne /etc/localtime && \
+   dpkg-reconfigure --frontend noninteractive tzdata
+RUN apt-get install -y r-base r-base-dev
+RUN apt-get install -y vim
+RUN useradd -m flashpca-user
+RUN chpasswd flashpca-user:password
+WORKDIR /home/flashpca-user
+USER flashpca-user
+RUN wget https://github.com/yixuan/spectra/archive/v0.8.1.tar.gz && \
+   tar xvf v0.8.1.tar.gz
+ADD https://api.github.com/repos/kachulis/flashpca/git/refs/heads/ck_project_single_sample \
+   version.json
+RUN git clone https://github.com/kachulis/flashpca.git
+RUN cd flashpca && \
+   git checkout ck_project_single_sample &&\
+   make all \
+   EIGEN_INC=/usr/include/eigen3 \
+   BOOST_INC=/usr/include/boost \
+   SPECTRA_INC=$HOME/spectra-0.8.1/include &&\
+   make flashpca_x86-64 \
+   EIGEN_INC=/usr/include/eigen3 \
+   BOOST_INC=/usr/include/boost \
+   SPECTRA_INC=$HOME/spectra-0.8.1/include
+#RUN R -e "install.packages(c('abind', 'RcppEigen', 'BH', 'RSpectra'))"
+
+