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connor-lab / ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
GNU Affero General Public License v3.0
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ivar 1.2.3 conda dependency conflict #65

Closed jts closed 4 years ago

jts commented 4 years ago

Just a head's up when you update ivar, when we changed our local version to ivar 1.2.3 conda fails to solve the environment. @mlaszloffy fixed this by changing the samtools and pysam versions:

--- a/environments/illumina/environment.yml
+++ b/environments/illumina/environment.yml
@@ -8,7 +8,7 @@ dependencies:
   - biopython=1.74
   - pandas=0.23.0=py36_1
   - bwa=0.7.17=pl5.22.0_2
-  - samtools=1.9
+  - samtools=1.10
   - trim-galore=0.6.5
   - ivar=1.2.3
-  - pysam=0.15.2
+  - pysam=0.16.0.1
m-bull commented 4 years ago

Cheers @jts and @mlaszloffy - ivar at 1.2.3 in https://github.com/connor-lab/ncov2019-artic-nf/commit/bc9884de54445eeeb5a73cb2f50fc2f10c9f3b4a.