update htslib. tag fix for #134

HISTORY.md

@@ -1,3 +1,7 @@
+v0.2.6
+======
++ fix name collisions with cram (#134)
+
 v0.2.5
 ======
 + slight sensitivity increase

cmd/smoove/smoove.go

@@ -8,7 +8,6 @@ import (
 
 	"github.com/brentp/smoove"
 	"github.com/brentp/smoove/annotate"
-	"github.com/brentp/smoove/cnvnator"
 	"github.com/brentp/smoove/duphold"
 	"github.com/brentp/smoove/hipstr"
 	"github.com/brentp/smoove/lumpy"
@@ -26,15 +25,13 @@ type progPair struct {
 }
 
 var progs = []progPair{
-	//"cnvnator": progPair{"call cnvnator and make bedpe files needed by lumpy", cnvnator.Main},
 	progPair{"call", "call lumpy (and optionally svtyper)", lumpy.Main},
 	progPair{"merge", "merge and sort (using svtools) calls from multiple samples", merge.Main},
 	progPair{"genotype", "parallelize svtyper on an input VCF", svtyper.Main},
 	progPair{"paste", "square final calls from multiple samples (each with same number of variants)", paste.Main},
 	progPair{"plot-counts", "plot counts of split, discordant reads before, after smoove filtering", merge.PlotCountsMain},
 	progPair{"annotate", "annotate a VCF with gene and quality of SV call", annotate.Main},
 	progPair{"hipstr", "run hipSTR in parallel", hipstr.Main},
-	progPair{"cnvnator", "run cnvnator in parallel", cnvnator.Main},
 	progPair{"duphold", "run duphold in parallel (this can be done by adding a flag to call or genotype)", duphold.Main},
 }
 

docker/Dockerfile

@@ -2,7 +2,7 @@ FROM ubuntu:16.04
 
 ENV PATH /opt/conda/bin:$PATH
 
-RUN apt-get update --fix-missing && \
+RUN apt-get update --fix-missing &&  \
     apt-get install -qy wget curl git bzip2 ca-certificates procps zlib1g-dev \
     make build-essential cmake libncurses-dev ncurses-dev g++ gcc \
     nfs-common pigz bedtools gawk fuse mdadm time \
@@ -18,14 +18,19 @@ RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda2-4.5.11-Linux-x86
     echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
     echo "conda activate base" >> ~/.bashrc
 
-RUN conda create -n smoove-env -c conda-forge -c bioconda python=2.7 awscli numpy scipy cython pysam toolshed pyvcf pyfaidx cyvcf2 svtyper svtools
-RUN echo "source activate smoove-env" > ~/.bashrc
-ENV PATH /opt/conda/envs/smoove-env/bin:$PATH
 ENV HTSLIB_LIBRARY_DIR /usr/local/lib
 ENV HTSLIB_INCLUDE_DIR /usr/local/include
 ENV LD_LIBRARY_PATH /usr/local/lib
 
+RUN conda update conda
+RUN conda create -n smoove-env -c conda-forge -c bioconda python=2.7 click awscli numpy scipy cython pysam toolshed pyvcf pyfaidx cyvcf2 svtyper svtools
+RUN echo "source activate smoove-env" > ~/.bashrc
+ENV PATH /opt/conda/envs/smoove-env/bin:$PATH
+
+#ENV PATH $PATH
+#:/opt/conda/envs/smoove-env/bin
+#RUN bash -c "conda install click && conda install awscli numpy scipy cython pysam toolshed pyvcf pyfaidx cyvcf2 svtyper svtools"
 COPY ./docker-build.sh .
 RUN bash docker-build.sh
-COPY ./smoove /usr/bin/
+#COPY ./smoove /usr/bin/
 WORKDIR /work/