diff --git a/README.md b/README.md index 8be7d6717e287672666b0101992a9944ca2532c2..b808846dc6169e9ae6e4ab6d3cdeb46e3a1af70f 100644 --- a/README.md +++ b/README.md @@ -30,6 +30,21 @@ On MacOS X: ```bash conda create -n paqr_kapac -c bioconda -c ostrokach --file requirements_py3.txt ``` +**Important Update**: Please not that we experienced some difficulties with some anaconda-packages which have been removed from anaconda cloud. In order to create the python3 environment please follow these steps: + ```bash + conda create -n paqr_kapac -c bioconda -c ostrokach -c r -c defaults --file requirements_py3_UPDATED.txt + ``` +This will result in an environment without the R package "optparse". In order to install this package please run: + ```bash + conda activate paqr_kapac + R + ``` +Now, you should find your console to be in an active R session. Here, execute: + ```R + install.packages("optparse") + q() + ``` + If you already have a conda version with python2 installed, create the new python 3 environment like this: ```bash conda create -n paqr_kapac -c bioconda -c ostrokach --file requirements_py3.txt python=3 diff --git a/requirements_py3_UPDATED.txt b/requirements_py3_UPDATED.txt new file mode 100644 index 0000000000000000000000000000000000000000..9e46dac96606db53910446731146fcd5891730a1 --- /dev/null +++ b/requirements_py3_UPDATED.txt @@ -0,0 +1,11 @@ +# This file may be used to create an environment using: +# $ conda create --name tutorial --file <this file> +python=3.5.4 +snakemake=3.13.0 +graphviz=2.38.0 +star=2.5.2a +samtools=1.3.1 +bedtools=2.26.0 +gzip=1.7 +r-base=3.5.1 +sra-tools=2.8.2