changed nim

Dockerfile

+FROM alpine:3.11.5
+#FROM alpine:20190925
+
+ENV CFLAGS="-fPIC -O3"
+
+RUN apk add wget git xz bzip2-static musl m4 autoconf tar xz-dev bzip2-dev build-base libpthread-stubs libzip-dev gfortran \
+	    openssl-libs-static openblas-static pcre-dev curl llvm-dev curl-static bash
+
+RUN mkdir -p /usr/local/include && \
+    git clone --depth 1 https://github.com/ebiggers/libdeflate.git && \
+    cd libdeflate && make -j4 CFLAGS="-fPIC -O3" install && \
+    cd .. && rm -rf libdeflate && \
+    git clone https://github.com/cloudflare/zlib cloudflare-zlib && \
+    cd cloudflare-zlib && ./configure && make install && \
+    cd .. && \
+    rm -rf cloudflare-zlib
+
+RUN cd / && \
+    git clone -b v1.2.6 git://github.com/nim-lang/nim nim && \
+    cd nim &&  \
+    sh ./build_all.sh && \
+    rm -rf csources && \
+    echo 'PATH=/nim/bin:$PATH' >> ~/.bashrc && \
+    echo 'PATH=/nim/bin:$PATH' >> ~/.bash_profile && \
+    echo 'PATH=/nim/bin:$PATH' >> /etc/environment 
+
+RUN apk add cmake openssl-dev && \
+	wget https://libzip.org/download/libzip-1.6.1.tar.gz && \
+	tar xzvf libzip-1.6.1.tar.gz && \
+	cd libzip-1.6.1 && \
+	mkdir build && cd build && \
+	cmake -DBUILD_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=/usr/local/ ../ && \
+	make -j4 CFLAGS="-fPIC -O3" install && \
+	cd ../../ && rm -rf libzip-1.6.1*
+
+
+ENV PATH=:/root/.nimble/bin:/nim/bin/:$PATH	
+
+RUN \
+    git clone https://github.com/samtools/htslib && \
+    cd htslib && git checkout 1.11 && autoheader && autoconf && \
+    ./configure --disable-s3 --disable-libcurl --with-libdeflate && \
+    make -j4 CFLAGS="-fPIC -O3" install && \
+    cd ../ && \
+    git clone https://github.com/samtools/bcftools && \
+    cd bcftools && git checkout 1.10.2 && autoheader && autoconf && \
+    ./configure --disable-s3 --disable-libcurl --with-libdeflate && \
+    make -j4 CFLAGS="-fPIC -O3" install && \
+    cd ../ && rm -rf htslib bcftools
+
+ADD . /src/
+
+RUN nimble install -y https://gitlab.svi.edu.au/biocellgen-public/sscocaller.git
+
+RUN ls ~/.nimble/lib/
+ENV LD_LIBRARY_PATH=:/root/.nimble/lib/:$LD_LIBRARY_PATH
+
+RUN cp /root/.nimble/bin/sscocaller /usr/bin/
+
+RUN /usr/bin/sscocaller
\ No newline at end of file

README.md

@@ -78,6 +78,6 @@ docker run -it svirlyu/sscocaller
 ```
 
 
-### Static builds
+### Static builds (WIP)
 
-The static bianry can be simply downloaded which works for GNU/Linux type OS:
\ No newline at end of file
+The static bianry can be simply downloaded which works for GNU/Linux type OS:

src/sscocaller.nim

@@ -13,7 +13,11 @@ import hts
 import tables
 import sequtils
 import math
+<<<<<<< HEAD
 import distributions/rmath
+=======
+from distributions/rmath import dbinom
+>>>>>>> 7c0fd54896b7218781289237b99b0cd26eec98a3
 import streams
 
 #echo paramCount(), " ", paramStr(1)

sscocaller.nimble

@@ -10,7 +10,7 @@ bin           = @["sscocaller"]
 
 # Dependencies
 
-requires "nim >= 1.2.0","docopt","hts >= 0.3.4"
+requires "nim >= 1.0.0","docopt","hts >= 0.3.4"
 requires "https://github.com/ruqianl/distributions.git"
 
 # task test, "run the tests":