From 39c1aa6611620d5494f072609996d007d77eaf91 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Tue, 18 Oct 2016 16:10:31 +0200 Subject: [PATCH] Started results docs. Made a skeleton start on the results documentation. Added SciLifeLab logo for main readme. Added note about setting NextFlow environment variables for UPPMAX. --- README.md | 16 ++++++++++++++-- docs/README.md | 3 +++ docs/images/SciLifeLab_logo.png | Bin 0 -> 3732 bytes 3 files changed, 17 insertions(+), 2 deletions(-) create mode 100644 docs/README.md create mode 100644 docs/images/SciLifeLab_logo.png diff --git a/README.md b/README.md index 153c6e2..1067e0e 100644 --- a/README.md +++ b/README.md @@ -8,6 +8,10 @@ This pipeline is currently under active development and has very little in the w There's a pretty good chance that it won't run. Any help debugging is very welcome! Please fork, make changes and submit a pull request. +## Pipeline Results +See the [pipeline documentation](docs/README.md) for explanations of +the results files. + ## Installation ### NextFlow installation To use this pipeline, you need to have a working version of NextFlow installed. You can find more @@ -18,11 +22,19 @@ of NextFlow looks like this: curl -fsSL get.nextflow.io | bash mv ./nextflow ~/bin ``` -Note that if you're running on a Swedish UPPMAX cluster you can load NextFlow as an environment module: + +#### UPPMAX +If you're running on a Swedish UPPMAX cluster you can load NextFlow as an environment module instead: ``` module load nextflow ``` +The first time you load this you will get a warning about setting environment variables. To automatically set these at login, you can add the following lines to your `~/.bashrc` file: +```bash +export NXF_LAUNCHBASE=$SNIC_TMP +export NXF_TEMP=$SNIC_TMP +``` + ### NextFlow configuration Next, you need to set up a config file so that NextFlow knows how to run and where to find reference indexes. You can find an example configuration file for UPPMAX (milou) with this repository: @@ -111,4 +123,4 @@ These scripts were written for use at the [National Genomics Infrastructure](htt at [SciLifeLab](http://www.scilifelab.se/) in Stockholm, Sweden. Written by Phil Ewels (@ewels) and Rickard Hammarén (@Hammarn). -

+

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