From 702cf96e8235150a1fb4fbae1c40182eb72c4228 Mon Sep 17 00:00:00 2001 From: Matthieu Muffato Date: Wed, 27 Sep 2023 05:45:50 +0000 Subject: [PATCH] Updated the test instructions, as the GitHub path is hardcoded in the test data too --- docs/usage.md | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 60306b84..5c0e969d 100755 --- a/docs/usage.md +++ b/docs/usage.md @@ -30,17 +30,13 @@ First, choose a download location `${TREEVAL_TEST_DATA}` and run this command: ``` cd ${TREEVAL_TEST_DATA} curl https://tolit.cog.sanger.ac.uk/test-data/resources/treeval/TreeValTinyData.tar.gz | tar xzf - +sed -i "s|/home/runner/work/treeval/treeval|${TREEVAL_TEST_DATA}|" TreeValTinyData/gene_alignment_data/fungi/csv_data/LaetiporusSulphureus.gfLaeSulp1-data.csv ``` -Then, modify the configuration file to point at that download location: +Then, modify the configuration file to point at that download location and off you go: ``` sed -i "s|/home/runner/work/treeval/treeval|${TREEVAL_TEST_DATA}|" assets/github_testing/TreeValTinyTest.yaml -``` - -And off you go: - -``` nextflow run . -profile test_github,singularity ```