docker

README.md

@@ -41,6 +41,13 @@ slivar \
 Note that `slivar` does not give direct access to the genotypes, instead exposing `alts` where 0 is homozygous reference, 1 is heterozygous, 2 is
 homozygous alternate and -1 when the genotype is unknown. It is recommended to **decompose** a VCF before sending to `slivar`
 
+
+## Installation
+
+get the latest binary from: https://github.com/brentp/slivar/releases/latest
+
+or use via docker from: [brentp/slivar:latest](https://cloud.docker.com/repository/docker/brentp/slivar)
+
 ### Attributes
 
  + anything in the INFO is available as e.g. INFO.CSQ

docker/Dockerfile

@@ -27,14 +27,18 @@ RUN cd / && \
     cd nim && \
     chmod +x ./build_all.sh && \
     scl enable devtoolset-2 ./build_all.sh && \
-    export PATH=/nim/bin:$PATH && \
-    echo 'PATH=/nim/bin:$PATH' >> ~/.bashrc && \
-    echo 'PATH=/nim/bin:$PATH' >> ~/.bash_profile && \
-    cd / && \
+    echo 'PATH=/nim/bin:/root/.nimble/bin:$PATH' >> ~/.bashrc && \
+    echo 'PATH=/nim/bin:/root/.nimble/bin:$PATH' >> ~/.bash_profile
+
+RUN cd / && \
+    export PATH=/nim/bin:/root/.nimble/bin:$PATH && \
+    source scl_source enable devtoolset-2  && \
+    nimble install -y nimgen && \
+    cd / && git clone -b dev https://github.com/brentp/duktape-nim && \
+    cd duktape-nim && \
+    nimble install --verbose -y && \
     git clone --depth 1 git://github.com/brentp/slivar.git && \
     cd slivar && \
-    nimble install -y hts && \
-    source scl_source enable devtoolset-2  && \
+    nimble install --verbose -y && \
     nim c -d:release -o:/usr/bin/slivar --passC:-flto src/slivar && \
-    rm -rf /slivar && slivar -h
-
+    rm -rf /slivar /duktape-nim && slivar -h

slivar.nimble

@@ -30,6 +30,7 @@ import ospaths,strutils
 
 task test, "run the tests":
   exec "nim c --lineDir:on --debuginfo -r --threads:on src/slivarpkg/duko"
+  exec "bash tests/functional-tests.sh"
 
 task docs, "Builds documentation":
   mkDir("docs"/"slivar")

src/slivar.nim

@@ -56,10 +56,9 @@ proc newEvaluator*(kids: seq[Sample], expression: TableRef[string, string], info
     quit $msg
   )
 
-
   result = TrioEvaluator(ctx:duk_create_heap(nil, nil, nil, nil, my_fatal))
   result.ctx.duk_require_stack_top(500000)
-  var idx = result.ctx.duk_push_c_function(debug, -1.cint)
+  discard = result.ctx.duk_push_c_function(debug, -1.cint)
   discard result.ctx.duk_put_global_string("debug")
   for k, v in expression:
     result.trio_expressions.add(result.ctx.compile(v))