Update conda environment: this fixes an error "assert_that: assertion must...

Update conda environment: this fixes an error "assert_that: assertion must return a logical value", presumably due to a new version of r-assertthat. Also, add scipy (needed for ploidy estimation script) and whatshap (needed for haplotagging).

Update conda environment: this fixes an error "assert_that: assertion must...
Update conda environment: this fixes an error "assert_that: assertion must return a logical value", presumably due to a new version of r-assertthat. Also, add scipy (needed for ploidy estimation script) and whatshap (needed for haplotagging).
ecaa9332 · Tobias Marschall · 878eb1cb · ecaa9332
Commit ecaa9332 authored 6 years ago by Tobias Marschall
--- a/conda-environment.yml
+++ b/conda-environment.yml
 name: strandseqnation
 channels:
- bioconda
- conda-forge
- defaults
- r
+  - bioconda
+  - conda-forge
+  - defaults
+  - r
 dependencies:
- bcftools=1.6=0
- bioconductor-biobase=2.38.0=r3.4.1_0
- bioconductor-biocgenerics=0.24.0=r3.4.1_0
- bioconductor-biocinstaller=1.28.0=r3.4.1_0
- bioconductor-biocparallel=1.12.0=r3.4.1_0
- bioconductor-biostrings=2.46.0=r3.4.1_0
- bioconductor-bsgenome=1.46.0=r3.4.1_0
- bioconductor-bsgenome.hsapiens.ucsc.hg38=1.4.1=r3.4.1_2
- bioconductor-delayedarray=0.4.1=r3.4.1_0
- bioconductor-fastseg=1.24.0=r3.4.1_0
- bioconductor-genomeinfodb=1.14.0=r3.4.1_0
- bioconductor-genomeinfodbdata=1.0.0=r3.4.1_1
- bioconductor-genomicalignments=1.14.0=r3.4.1_0
- bioconductor-genomicranges=1.30.0=r3.4.1_0
- bioconductor-iranges=2.12.0=r3.4.1_0
- bioconductor-rsamtools=1.30.0=r3.4.1_0
- bioconductor-rtracklayer=1.38.0=r3.4.1_0
- bioconductor-s4vectors=0.16.0=r3.4.1_0
- bioconductor-summarizedexperiment=1.8.0=r3.4.1_0
- bioconductor-xvector=0.18.0=r3.4.1_0
- bioconductor-zlibbioc=1.24.0=r3.4.1_0
- filechunkio=1.6=py36_0
- ftputil=3.2=py36_0
- htslib=1.6=0
- pysftp=0.2.9=py36_0
- r-data.table=1.10.4=r3.4.1_0
- r-peer=1.3=r3.4.1_0
- samtools=1.5=1
- snakemake=4.4.0=py36_0
- urllib3=1.12=py36_0
- aioeasywebdav=2.2.0=py36_0
- aiohttp=2.0.7=py36_0
- appdirs=1.4.3=py_0
- asn1crypto=0.22.0=py36_0
- async-timeout=1.2.1=py36_0
- boost=1.65.1=py36_0
- boost-cpp=1.65.1=0
- bzip2=1.0.6=1
- ca-certificates=2017.11.5=0
- cairo=1.14.6=4
- certifi=2017.11.5=py36_0
- cffi=1.11.2=py36_0
- chardet=3.0.4=py36_0
- cmake=3.10.0=4
- configargparse=0.12.0=py36_0
- cryptography=2.1.4=py36_0
- curl=7.54.1=0
- docutils=0.14=py36_0
- dropbox=7.3.1=py36_0
- expat=2.2.5=0
- fontconfig=2.12.1=4
- freetype=2.7=1
- gettext=0.19.7=1
- glib=2.51.4=0
- graphite2=1.3.10=0
- gsl=2.1=2
- harfbuzz=1.4.3=0
- icu=58.2=0
- idna=2.6=py36_1
- jpeg=9b=2
- krb5=1.14.2=0
- libffi=3.2.1=3
- libiconv=1.15=0
- libpng=1.6.34=0
- libssh2=1.8.0=1
- libtiff=4.0.9=0
- libuv=1.11.0=0
- libxml2=2.9.5=0
- multidict=2.1.4=py36_0
- ncurses=5.9=10
- openssl=1.0.2n=0
- pandas=0.22.0=py36_0
- pango=1.40.4=0
- paramiko=2.3.1=py_0
- pcre=8.39=0
- pip=9.0.1=py36_1
- pixman=0.34.0=1
- psutil=5.4.0=py36_0
- pyasn1=0.4.2=py_0
- pycparser=2.18=py36_0
- pynacl=1.1.2=py36_0
- python=3.6.4=0
- python-dateutil=2.6.1=py36_0
- pytz=2017.3=py_2
- pyyaml=3.12=py36_1
- r-assertthat=0.1=r3.4.1_0
- r-base=3.4.1=3
- r-bh=1.65.0_1=r3.4.1_0
- r-bitops=1.0_6=r3.4.1_0
- r-colorspace=1.3_2=r3.4.1_0
- r-cowplot=0.9.1=r3.4.1_0
- r-curl=2.4=r3.4.1_0
- r-devtools=1.13.2=r3.4.1_0
- r-dichromat=2.0_0=r3.4.1_0
- r-digest=0.6.12=r3.4.1_0
- r-futile.logger=1.4.3=r3.4.1_0
- r-futile.options=1.0.0=r3.4.1_0
- r-ggplot2=2.2.1=r3.4.1_0
- r-git2r=0.19.0=r3.4.1_0
- r-gridextra=2.3=r3.4.1_0
- r-gtable=0.2.0=r3.4.1_0
- r-hexbin=1.27.1=r3.4.1_0
- r-httr=1.2.1=r3.4.1_0
- r-jsonlite=1.4=r3.4.1_0
- r-labeling=0.3=r3.4.1_0
- r-lambda.r=1.1.9=r3.4.1_0
- r-lattice=0.20_34=r3.4.1_0
- r-lazyeval=0.2.0=r3.4.1_0
- r-magrittr=1.5=r3.4.1_0
- r-mass=7.3_45=r3.4.1_0
- r-matrix=1.2_7.1=r3.4.1_0
- r-matrixstats=0.52.2=r3.4.1_0
- r-memoise=1.1.0=r3.4.1_0
- r-mime=0.5=r3.4.1_0
- r-munsell=0.4.3=r3.4.1_0
- r-openssl=0.9.7=r3.4.1_0
- r-plyr=1.8.4=r3.4.1_0
- r-r6=2.2.0=r3.4.1_0
- r-rcolorbrewer=1.1_2=r3.4.1_0
- r-rcpp=0.12.13=r3.4.1_0
- r-rcurl=1.95_4.8=r3.4.1_0
- r-reshape2=1.4.2=r3.4.1_0
- r-rlang=0.1.2=r3.4.1_0
- r-rstudioapi=0.7=r3.4.1_0
- r-scales=0.5.0=r3.4.1_0
- r-snow=0.4_2=r3.4.1_0
- r-stringi=1.1.2=r3.4.1_0
- r-stringr=1.2.0=r3.4.1_0
- r-tibble=1.3.3=r3.4.1_0
- r-viridislite=0.2.0=r3.4.1_0
- r-whisker=0.3_2=r3.4.1_0
- r-withr=1.0.2=r3.4.1_0
- r-xml=3.98_1.6=r3.4.1_0
- ratelimiter=1.2.0=py36_0
- readline=7.0=0
- requests=2.13.0=py36_0
- rhash=1.3.4=0
- setuptools=38.4.0=py36_0
- six=1.11.0=py36_1
- sqlite=3.20.1=2
- tk=8.6.7=0
- wheel=0.30.0=py36_2
- wrapt=1.10.11=py36_0
- xz=5.2.3=0
- yaml=0.1.6=0
- yarl=0.10.0=py36_0
- zlib=1.2.11=0
- bcrypt=3.1.4=py36h621fe67_0
- intel-openmp=2018.0.0=hc7b2577_8
- libgcc=7.2.0=h69d50b8_2
- libgcc-ng=7.2.0=h7cc24e2_2
- libgfortran-ng=7.2.0=h9f7466a_2
- libstdcxx-ng=7.2.0=h7a57d05_2
- mkl=2018.0.1=h19d6760_4
- numpy=1.14.0=py36h3dfced4_0
- wget=1.18=0
-prefix: /MMCI/TM/structvar/work/marschal/miniconda3/envs/strandseqnation
-
+  - bcftools=1.8=h4da6232_3
+  - bioconductor-biobase=2.38.0=r3.4.1_0
+  - bioconductor-biocgenerics=0.24.0=r3.4.1_0
+  - bioconductor-biocinstaller=1.28.0=r3.4.1_0
+  - bioconductor-biocparallel=1.12.0=r3.4.1_0
+  - bioconductor-biostrings=2.46.0=r3.4.1_0
+  - bioconductor-bsgenome=1.46.0=r3.4.1_0
+  - bioconductor-bsgenome.hsapiens.ucsc.hg38=1.4.1=r3.4.1_2
+  - bioconductor-delayedarray=0.4.1=r3.4.1_0
+  - bioconductor-fastseg=1.24.0=r3.4.1_0
+  - bioconductor-genomeinfodb=1.14.0=r3.4.1_0
+  - bioconductor-genomeinfodbdata=1.0.0=r3.4.1_1
+  - bioconductor-genomicalignments=1.14.1=r3.4.1_0
+  - bioconductor-genomicranges=1.30.3=r3.4.1_0
+  - bioconductor-iranges=2.12.0=r3.4.1_0
+  - bioconductor-rsamtools=1.30.0=r3.4.1_0
+  - bioconductor-rtracklayer=1.38.3=r3.4.1_0
+  - bioconductor-s4vectors=0.16.0=r3.4.1_0
+  - bioconductor-summarizedexperiment=1.8.0=r3.4.1_0
+  - bioconductor-xvector=0.18.0=r3.4.1_0
+  - bioconductor-zlibbioc=1.24.0=r3.4.1_0
+  - dropbox=5.2.1=py36_0
+  - filechunkio=1.6=py36_0
+  - ftputil=3.2=py36_0
+  - htslib=1.7=0
+  - libdeflate=1.0=h470a237_0
+  - pyfaidx=0.5.4.1=py_0
+  - pynacl=0.3.0=py36_0
+  - pysam=0.14.1=py36hae42fb6_1
+  - pysftp=0.2.9=py36_0
+  - pyvcf=0.6.8=py36_0
+  - r-data.table=1.10.4=r3.4.1_0
+  - r-peer=1.3=r341h470a237_1
+  - samtools=1.8=h46bd0b3_5
+  - snakemake=4.0.0=py36_0
+  - urllib3=1.12=py36_0
+  - whatshap=0.16=py36_0
+  - xopen=0.3.2=py_1
+  - aioeasywebdav=2.2.0=py36_0
+  - aiohttp=3.3.2=py36h14c3975_0
+  - appdirs=1.4.3=py_1
+  - asn1crypto=0.24.0=py36_0
+  - async-timeout=3.0.0=py36_0
+  - attrs=18.1.0=py_1
+  - blas=1.1=openblas
+  - boost=1.67.0=py36h3e44d54_0
+  - boost-cpp=1.67.0=h3a22d5f_0
+  - bzip2=1.0.6=1
+  - ca-certificates=2018.4.16=0
+  - cairo=1.14.10=0
+  - certifi=2018.4.16=py36_0
+  - cffi=1.11.5=py36_0
+  - chardet=3.0.4=py36_0
+  - cmake=3.11.4=0
+  - configargparse=0.12.0=py36_0
+  - cryptography=2.2.1=py36hdffb7b8_1
+  - curl=7.60.0=0
+  - docutils=0.14=py36_0
+  - expat=2.2.5=hfc679d8_1
+  - fontconfig=2.12.6=0
+  - freetype=2.8.1=0
+  - gettext=0.19.8.1=0
+  - glib=2.55.0=0
+  - graphite2=1.3.11=hfc679d8_0
+  - gsl=2.4=blas_openblas_0
+  - harfbuzz=1.7.6=0
+  - icu=58.2=hfc679d8_0
+  - idna=2.7=py36_0
+  - idna_ssl=1.0.0=0
+  - jpeg=9c=h470a237_0
+  - krb5=1.14.6=0
+  - libffi=3.2.1=3
+  - libiconv=1.15=h470a237_1
+  - libpng=1.6.34=ha92aebf_1
+  - libssh2=1.8.0=h5b517e9_2
+  - libtiff=4.0.9=he6b73bb_1
+  - libuv=1.20.3=0
+  - libxml2=2.9.8=h422b904_1
+  - multidict=4.3.1=py36h470a237_0
+  - ncurses=5.9=10
+  - numpy=1.14.5=py36_blas_openblashd3ea46f_200
+  - openblas=0.2.20=8
+  - openssl=1.0.2o=0
+  - pandas=0.23.1=py36_0
+  - pango=1.40.14=0
+  - paramiko=2.1.2=py36_0
+  - pcre=8.39=0
+  - pip=9.0.3=py36_0
+  - pixman=0.34.0=2
+  - psutil=5.4.6=py36_0
+  - pyasn1=0.4.3=py_0
+  - pycparser=2.18=py36_0
+  - python=3.6.5=1
+  - python-dateutil=2.7.3=py_0
+  - pytz=2018.5=py_0
+  - pyyaml=3.12=py36_1
+  - r-assertthat=0.2.0=r3.4.1_0
+  - r-base=3.4.1=4
+  - r-bh=1.66.0_1=r3.4.1_0
+  - r-bindr=0.1.1=r3.4.1_0
+  - r-bindrcpp=0.2=r3.4.1_0
+  - r-bitops=1.0_6=r3.4.1_0
+  - r-cli=1.0.0=r3.4.1_0
+  - r-colorspace=1.3_2=r3.4.1_0
+  - r-cowplot=0.9.2=r3.4.1_0
+  - r-crayon=1.3.4=r3.4.1_0
+  - r-curl=3.2=r3.4.1_0
+  - r-devtools=1.13.5=r3.4.1_0
+  - r-dichromat=2.0_0=r3.4.1_0
+  - r-digest=0.6.15=r3.4.1_0
+  - r-dplyr=0.7.4=r3.4.1_0
+  - r-futile.logger=1.4.3=r3.4.1_0
+  - r-futile.options=1.0.0=r3.4.1_0
+  - r-ggplot2=2.2.1=r3.4.1_0
+  - r-git2r=0.21.0=r341h0c37787_0
+  - r-glue=1.2.0=r3.4.1_0
+  - r-gridextra=2.3=r3.4.1_0
+  - r-gtable=0.2.0=r3.4.1_0
+  - r-hexbin=1.27.2=r3.4.1_0
+  - r-httr=1.3.1=r3.4.1_0
+  - r-jsonlite=1.5=r3.4.1_0
+  - r-labeling=0.3=r3.4.1_0
+  - r-lambda.r=1.2=r3.4.1_0
+  - r-lattice=0.20_34=r3.4.1_0
+  - r-lazyeval=0.2.1=r3.4.1_0
+  - r-magrittr=1.5=r3.4.1_0
+  - r-mass=7.3_48=r3.4.1_0
+  - r-matrix=1.2_14=r3.4.1_0
+  - r-matrixstats=0.53.1=r341_0
+  - r-memoise=1.1.0=r3.4.1_0
+  - r-mime=0.5=r3.4.1_0
+  - r-munsell=0.5.0=r341_0
+  - r-openssl=1.0.1=r3.4.1_0
+  - r-pillar=1.2.2=r341h6115d3f_1
+  - r-pkgconfig=2.0.1=r3.4.1_0
+  - r-plogr=0.1_1=r3.4.1_0
+  - r-plyr=1.8.4=r3.4.1_0
+  - r-r6=2.2.2=r3.4.1_0
+  - r-rcolorbrewer=1.1_2=r3.4.1_0
+  - r-rcpp=0.12.15=r3.4.1_0
+  - r-rcurl=1.95_4.8=r3.4.1_0
+  - r-reshape2=1.4.3=r3.4.1_0
+  - r-rlang=0.2.1=r341_0
+  - r-rstudioapi=0.7=r3.4.1_0
+  - r-scales=0.5.0=r3.4.1_0
+  - r-snow=0.4_2=r3.4.1_0
+  - r-stringi=1.1.7=r3.4.1_1
+  - r-stringr=1.3.0=r3.4.1_0
+  - r-tibble=1.4.2=r3.4.1_0
+  - r-utf8=1.1.3=r3.4.1_0
+  - r-viridislite=0.3.0=r3.4.1_0
+  - r-whisker=0.3_2=r3.4.1_0
+  - r-withr=2.1.1=r3.4.1_0
+  - r-xml=3.98_1.6=r3.4.1_0
+  - ratelimiter=1.2.0=py36_0
+  - readline=7.0=0
+  - requests=2.13.0=py36_0
+  - rhash=1.3.4=0
+  - scipy=1.1.0=py36_blas_openblas_200
+  - setuptools=39.2.0=py36_0
+  - six=1.11.0=py36_1
+  - sqlite=3.20.1=2
+  - tk=8.6.7=0
+  - wheel=0.31.0=py36_0
+  - wrapt=1.10.11=py36_0
+  - xz=5.2.3=0
+  - yaml=0.1.7=0
+  - yarl=1.2.6=py36h470a237_0
+  - zlib=1.2.11=h470a237_3
+  - bcrypt=3.1.4=py36h621fe67_0
+  - bz2file=0.98=py36_0
+  - intel-openmp=2018.0.3=0
+  - libgcc=7.2.0=h69d50b8_2
+  - libgcc-ng=7.2.0=hdf63c60_3
+  - libgfortran=3.0.0=1
+  - libgfortran-ng=7.2.0=hdf63c60_3
+  - libstdcxx-ng=7.2.0=hdf63c60_3
+  - mkl=2018.0.3=1
+  - wget=1.19.5=h1ad7b7a_0