Update the samtools/htslib/bcftools versions used by Travis
Pinning 1.7 means Pysam is stuck forever at the broken-openssl/libcrypto
condapocalypse. Pin conda-forge channel for ncurses as the samtools package
currently requires that channel's ncurses build (hat tip
@@ -38,15 +38,17 @@ conda config --add channels bioconda
# pin versions, so that tests do not fail when pysam/htslib out of step
# add htslib dependencies
-conda install -y "samtools=1.7" "bcftools=1.6" "htslib=1.7" xz curl bzip2
+# NB: we force conda-forge:ncurses due to bioconda/bioconda-recipes#13488
+conda install -y "samtools=1.9" "bcftools=1.9" "htslib=1.9" xz curl bzip2 conda-forge:ncurses
# Need to make C compiler and linker use the anaconda includes and libraries:
export PREFIX=~/miniconda3/
export CFLAGS="-I${PREFIX}/include -L${PREFIX}/lib"
export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl --disable-lzma"
+echo "show samtools, htslib, and bcftools versions"
samtools --version
-htslib --version
+htsfile --version
bcftools --version
# Try building conda recipe first
