diff --git a/CHANGELOG.md b/CHANGELOG.md index dc43547fa0..50736fa5b1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,7 @@ * Drop [nf-core/rnaseq](https://github.com/nf-core/rnaseq]) from `blacklist.json` to make template sync available * Fix bugs in `nf-core download` * The _latest_ release is now fetched by default if not specified - * Downloaded pipeline files are now properly executable + * Downloaded pipeline files are now properly executable. ## [v1.5](https://github.com/nf-core/tools/releases/tag/1.5) - 2019-03-13 Iron Shark diff --git a/Dockerfile b/Dockerfile index 6594e7bd0b..a63e25af58 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,5 +3,5 @@ LABEL authors="phil.ewels@scilifelab.se,alexander.peltzer@qbic.uni-tuebingen.de" description="Docker image containing base requirements for the nfcore pipelines" # Install procps so that Nextflow can poll CPU usage -RUN apt-get update && apt-get install -y procps && apt-get clean -y +RUN apt-get update && apt-get install -y procps && apt-get clean -y RUN conda install conda=4.6.7 diff --git a/README.md b/README.md index a593218564..23c8a17021 100644 --- a/README.md +++ b/README.md @@ -9,13 +9,17 @@ A python package with helper tools for the nf-core community. ## Table of contents -* [Installation](#installation) -* [Listing pipelines](#listing-pipelines) (`nf-core list`) -* [Downloading pipelines for offline use](#downloading-pipelines-for-offline-use) (`nf-core download`) -* [Listing software licences](#pipeline-software-licences): List software licences for a given workflow (`nf-core licences`) -* [Creating a new workflow](#creating-a-new-workflow) (`nf-core create`) -* [Checking a pipeline against nf-core guidelines](#linting-a-workflow) (`nf-core lint`) -* [Bumping a pipeline version number](#bumping-a-pipeline-version-number) (`nf-core bump-version`) +* [`nf-core` tools installation](#installation) +* [`nf-core list` - List available pipelines](#listing-pipelines) +* [`nf-core download` - Download pipeline for offline use](#downloading-pipelines-for-offline-use) +* [`nf-core licences` - List software licences in a pipeline](#pipeline-software-licences) +* [`nf-core create` - Create a new workflow from the nf-core template](#creating-a-new-workflow) +* [`nf-core lint` - Check pipeline code against nf-core guidelines](#linting-a-workflow) +* [`nf-core bump-version` - Change a pipeline version number](#bumping-a-pipeline-version-number) + + +The nf-core tools package is written in Python and can be imported and used within other packages. +For documentation of the internal Python functions, please refer to the [Tools Python API docs](https://nf-co.re/tools-docs/). ## Installation @@ -25,6 +29,12 @@ You can install `nf-core/tools` from [PyPI](https://pypi.python.org/pypi/nf-core pip install nf-core ``` +Alternatively, it can be installed using [bioconda](https://bioconda.github.io/recipes/nf-core/README.html): + +```bash +conda install -c bioconda nf-core +``` + If you would like the development version instead, the command is: ```bash