fix static builds

Dockerfile

@@ -1,39 +1,35 @@
 FROM alpine:3.10
 
-ENV CFLAGS="-DCURL_STATICLIB -fPIC -O3"
+ENV CFLAGS="-fPIC -O3"
 
-RUN apk add wget git xz bzip2 musl m4 autoconf tar xz-dev bzip2-dev \
-	    build-base libpthread-stubs libssh2-dev \
-            openssl-dev nghttp2-static \
-	    curl-dev curl-static libssh2-static && \
-    mkdir -p /usr/local/include && \
+RUN apk add wget git xz bzip2 musl m4 autoconf tar xz-dev bzip2-dev build-base libpthread-stubs # gcc abuild binutils binutils-doc gcc-doc
+
+RUN mkdir -p /usr/local/include && \
     git clone --depth 1 https://github.com/ebiggers/libdeflate.git && \
-    cd libdeflate && make -j 2 libdeflate.a && \
-    cp libdeflate.a /usr/local/lib && cp libdeflate.h /usr/local/include && \
+    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 v0.20.2 git://github.com/nim-lang/nim nim && \
+    git clone -b v1.0.0 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 
 
-ENV PATH=/nim/bin:/root/.nimble/bin:$PATH
+ENV PATH=:/root/.nimble/bin:/nim/bin/:$PATH	
 
 RUN \
     git clone https://github.com/samtools/htslib && \
     cd htslib && git checkout 1.9 && autoheader && autoconf && \
-    CFLAGS="-fPIC -O3 -DCURL_STATICLIB" ./configure --enable-libcurl --with-libdeflate CFLAGS="-fPIC -O3 -DCURL_STATICLIB" && \
-    make -j4 CFLAGS="-fPIC -O3 -DCURL_STATICLIB" install && \
+    ./configure --disable-s3 --disable-libcurl --with-libdeflate && \
+    make -j4 CFLAGS="-fPIC -O3" install && \
     cd ../ && rm -rf htslib
 
-#nimble install -y c2nim@#3ec45c24585ebaed && \
 ADD . /src/
 RUN cat /src/docker/docker.nim.cfg >> /nim/config/nim.cfg && \
     source ~/.bashrc && cd /src/ && nimble install -y && \

docker/docker.nim.cfg

@@ -3,24 +3,25 @@
 @if nsb_static:
   passC:"-static"
   passl:"-static"
+  passl:"-no-pie"
 
-  passl:"/usr/local/lib/libhts.a"
   passl:"/usr/lib/libm.a"
-  #passl:"/usr/local/lib/libnghttp2.a"
+  passl:"/usr/local/lib/libhts.a"
   passl:"/usr/local/lib/libdeflate.a"
   passl:"/usr/lib/liblzma.a"
-  passl:"/usr/lib/libcurl.a"
   passl:"/usr/local/lib/libz.a"
   passl:"/usr/lib/libbz2.a"
   passl:"/usr/lib/libpthread.a"
   passl:"/usr/lib/libdl.a"
   passl:"/usr/lib/libc.a"
   passl:"/usr/lib/librt.a"
 
-  passl:"/usr/lib/libssl.a"
-  passl:"/usr/lib/libcrypto.a"
-  passl:"/usr/lib/libssh2.a"
-  passl:"/usr/lib/libnghttp2.a"
+#  passl:"/usr/local/lib/libnghttp2.a"
+#  passl:"/usr/lib/libcurl.a"
+#  passl:"/usr/lib/libssl.a"
+#  passl:"/usr/lib/libcrypto.a"
+#  passl:"/usr/lib/libssh2.a"
+#  passl:"/usr/lib/libnghttp2.a"
 
   dynlibOverride:"hts"
 @end

hts.nimble

@@ -17,7 +17,7 @@ skipFiles = @["teloage.nim"]
 import ospaths,strutils
 
 task test, "run the tests":
-  exec "nim c --lineDir:on --debuginfo -r tests/all"
+  exec "nim c  -d:useSysAssert -d:useGcAssert --lineDir:on --debuginfo -r tests/all"
 
 #before test:
 #  exec "c2nim src/hts/private/hts_concat.h"