From de4f76d01ffb2c2dc3307b533f6a61885c25d814 Mon Sep 17 00:00:00 2001 From: Thomas Cokelaer Date: Wed, 20 Dec 2023 23:01:09 +0100 Subject: [PATCH] update environments --- environment.yml | 19 +++++++++++++++++++ sequana_pipelines/quality_control/tools.txt | 2 -- 2 files changed, 19 insertions(+), 2 deletions(-) create mode 100644 environment.yml diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..700182a --- /dev/null +++ b/environment.yml @@ -0,0 +1,19 @@ +name: mapper + +channels: + - conda-forge + - bioconda + - defaults + +dependencies: + - bwa + - samtools + - pigz + - fastqc + - sambamba + - pip: + - sequana + - cutadapt + - atropos + + diff --git a/sequana_pipelines/quality_control/tools.txt b/sequana_pipelines/quality_control/tools.txt index 6bb5a0d..3ed1011 100644 --- a/sequana_pipelines/quality_control/tools.txt +++ b/sequana_pipelines/quality_control/tools.txt @@ -1,8 +1,6 @@ - bwa - sambamba - samtools -- kraken2 -- ktImportText - fastqc - pigz - cutadapt