From cdb20b8008a92ea0f27d0d7b4758a9c2c5f11f11 Mon Sep 17 00:00:00 2001 From: Tobias Marschall <tobias.marschall@0ohm.net> Date: Fri, 6 Jul 2018 15:50:26 +0200 Subject: [PATCH] Add freebayes to conda environment --- README.md | 2 +- conda-environment.yml | 22 +++++++++++++++++----- 2 files changed, 18 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 56b494f..465896a 100755 --- a/README.md +++ b/README.md @@ -205,7 +205,7 @@ infrastructure. Here is an example command: The provided environment `conda-environment.yml` is the result of running: ``` - conda create -y -n strandseqnation bcftools bioconductor-biobase bioconductor-biocgenerics bioconductor-biocinstaller bioconductor-biocparallel bioconductor-biostrings bioconductor-bsgenome bioconductor-bsgenome.hsapiens.ucsc.hg38 bioconductor-delayedarray bioconductor-fastseg bioconductor-genomeinfodb bioconductor-genomeinfodbdata bioconductor-genomicalignments bioconductor-genomicranges bioconductor-iranges bioconductor-rsamtools bioconductor-rtracklayer bioconductor-s4vectors bioconductor-summarizedexperiment bioconductor-xvector bioconductor-zlibbioc filechunkio ftputil htslib pysftp r-data.table r-peer samtools snakemake urllib3 aioeasywebdav aiohttp appdirs asn1crypto async-timeout boost boost-cpp bzip2 ca-certificates cairo certifi cffi chardet cmake configargparse cryptography curl docutils dropbox expat fontconfig freetype gettext glib graphite2 gsl harfbuzz icu idna jpeg krb5 libffi libiconv libpng libssh2 libtiff libuv libxml2 multidict ncurses openssl pandas pango paramiko pcre pip pixman psutil pyasn1 pycparser pynacl python python-dateutil pytz pyyaml r-assertthat r-base r-bh r-bitops r-colorspace r-cowplot r-curl r-devtools r-dichromat r-digest r-futile.logger r-futile.options r-ggplot2 r-git2r r-gridextra r-gtable r-hexbin r-httr r-jsonlite r-labeling r-lambda.r r-lattice r-lazyeval r-magrittr r-mass r-matrix r-matrixstats r-memoise r-mime r-munsell r-openssl r-plyr r-r6 r-rcolorbrewer r-rcpp r-rcurl r-reshape2 r-rlang r-rstudioapi r-scales r-snow r-stringi r-stringr r-tibble r-viridislite r-whisker r-withr r-xml ratelimiter readline requests rhash setuptools six sqlite tk wheel wrapt xz yaml yarl zlib bcrypt intel-openmp libgcc libgcc-ng libgfortran-ng libstdcxx-ng mkl numpy wget r-dplyr scipy whatshap + conda create -y -n strandseqnation bcftools bioconductor-biobase bioconductor-biocgenerics bioconductor-biocinstaller bioconductor-biocparallel bioconductor-biostrings bioconductor-bsgenome bioconductor-bsgenome.hsapiens.ucsc.hg38 bioconductor-delayedarray bioconductor-fastseg bioconductor-genomeinfodb bioconductor-genomeinfodbdata bioconductor-genomicalignments bioconductor-genomicranges bioconductor-iranges bioconductor-rsamtools bioconductor-rtracklayer bioconductor-s4vectors bioconductor-summarizedexperiment bioconductor-xvector bioconductor-zlibbioc filechunkio ftputil htslib pysftp r-data.table r-peer samtools snakemake urllib3 aioeasywebdav aiohttp appdirs asn1crypto async-timeout boost boost-cpp bzip2 ca-certificates cairo certifi cffi chardet cmake configargparse cryptography curl docutils dropbox expat fontconfig freetype gettext glib graphite2 gsl harfbuzz icu idna jpeg krb5 libffi libiconv libpng libssh2 libtiff libuv libxml2 multidict ncurses openssl pandas pango paramiko pcre pip pixman psutil pyasn1 pycparser pynacl python python-dateutil pytz pyyaml r-assertthat r-base r-bh r-bitops r-colorspace r-cowplot r-curl r-devtools r-dichromat r-digest r-futile.logger r-futile.options r-ggplot2 r-git2r r-gridextra r-gtable r-hexbin r-httr r-jsonlite r-labeling r-lambda.r r-lattice r-lazyeval r-magrittr r-mass r-matrix r-matrixstats r-memoise r-mime r-munsell r-openssl r-plyr r-r6 r-rcolorbrewer r-rcpp r-rcurl r-reshape2 r-rlang r-rstudioapi r-scales r-snow r-stringi r-stringr r-tibble r-viridislite r-whisker r-withr r-xml ratelimiter readline requests rhash setuptools six sqlite tk wheel wrapt xz yaml yarl zlib bcrypt intel-openmp libgcc libgcc-ng libgfortran-ng libstdcxx-ng mkl numpy wget r-dplyr scipy whatshap freebayes conda env export > conda-environment.yml ``` diff --git a/conda-environment.yml b/conda-environment.yml index 1c51570..a3c9102 100644 --- a/conda-environment.yml +++ b/conda-environment.yml @@ -28,6 +28,7 @@ dependencies: - bioconductor-zlibbioc=1.24.0=r3.4.1_0 - dropbox=5.2.1=py36_0 - filechunkio=1.6=py36_0 + - freebayes=1.0.2=0 - ftputil=3.2=py36_0 - htslib=1.7=0 - libdeflate=1.0=h470a237_0 @@ -54,7 +55,7 @@ dependencies: - boost-cpp=1.67.0=h3a22d5f_0 - bzip2=1.0.6=1 - ca-certificates=2018.4.16=0 - - cairo=1.14.10=0 + - cairo=1.14.12=he56eebe_0 - certifi=2018.4.16=py36_0 - cffi=1.11.5=py36_0 - chardet=3.0.4=py36_0 @@ -64,7 +65,7 @@ dependencies: - curl=7.60.0=0 - docutils=0.14=py36_0 - expat=2.2.5=hfc679d8_1 - - fontconfig=2.12.6=0 + - fontconfig=2.13.0=1 - freetype=2.8.1=0 - gettext=0.19.8.1=0 - glib=2.55.0=0 @@ -81,15 +82,17 @@ dependencies: - libpng=1.6.34=ha92aebf_1 - libssh2=1.8.0=h5b517e9_2 - libtiff=4.0.9=he6b73bb_1 + - libuuid=1.0.3=1 - libuv=1.20.3=0 + - libxcb=1.13=h470a237_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 + - pandas=0.23.2=py36_0 + - pango=1.40.14=hd50be51_1 - paramiko=2.1.2=py36_0 - pcre=8.39=0 - pip=9.0.3=py36_0 @@ -112,7 +115,7 @@ dependencies: - 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-devtools=1.13.6=r341_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 @@ -170,6 +173,15 @@ dependencies: - tk=8.6.7=0 - wheel=0.31.0=py36_0 - wrapt=1.10.11=py36_0 + - xorg-kbproto=1.0.7=h470a237_2 + - xorg-libice=1.0.9=2 + - xorg-libsm=1.2.2=2 + - xorg-libx11=1.6.5=0 + - xorg-libxau=1.0.8=h470a237_4 + - xorg-libxdmcp=1.1.2=h470a237_4 + - xorg-libxrender=0.9.10=0 + - xorg-renderproto=0.11.1=h470a237_2 + - xorg-xproto=7.0.31=h470a237_7 - xz=5.2.3=0 - yaml=0.1.7=0 - yarl=1.2.6=py36h470a237_0 -- GitLab