From 54d2f1600d5501e18c8666fdc971c2b21c0c4d12 Mon Sep 17 00:00:00 2001
From: Tobias Marschall <tobias.marschall@0ohm.net>
Date: Wed, 4 Jul 2018 09:15:48 +0200
Subject: [PATCH] Add note on how the conda environment was created to readme.

---
 README.md | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/README.md b/README.md
index a1180af..56b494f 100755
--- a/README.md
+++ b/README.md
@@ -200,3 +200,14 @@ infrastructure. Here is an example command:
         "NA12878" : "path/to/snp/calls.vcf.gz"
     },
   ```
+
+## Note on how Conda environment was created
+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 env export > conda-environment.yml
+  ```
+
+This avoids some annoying version downgrades that sometimes happen when creating an environment incrementally.
-- 
GitLab