From 4c78fdea59159bfa73a856e6d7bbb3589442815c Mon Sep 17 00:00:00 2001
From: Marcel Martin <marcel.martin@scilifelab.se>
Date: Tue, 30 Jun 2020 13:06:57 +0200
Subject: [PATCH] Pin Bowtie2 to a working version

Bowtie2 2.4.1, which we get otherwise at the moment, is packaged incorrectly
in Bioconda, see <https://github.com/bioconda/bioconda-recipes/issues/22836>.
---
 environment.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 235a804..dd33585 100644
--- a/environment.yml
+++ b/environment.yml
@@ -7,7 +7,8 @@ dependencies:
   - snakemake-minimal
   - samtools
   - cutadapt
-  - bowtie2
+  # The package for Bowtie2 2.4.1 creates VN: tag without value in SAM header
+  - bowtie2 =2.3.5.1
   - je-suite
   - igvtools
   - deeptools