From b7db496eaf391b750ccc23a912fb4d3b9d759a99 Mon Sep 17 00:00:00 2001 From: ppenev-eligo Date: Fri, 4 Jul 2025 13:42:21 +0200 Subject: [PATCH 1/2] add minipolish In the cases where minipolish3 fails it breaks miniasm, while still claiming its installed ok. --- pipelines/Dockerfile_by_Ryan_Wick/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipelines/Dockerfile_by_Ryan_Wick/Dockerfile b/pipelines/Dockerfile_by_Ryan_Wick/Dockerfile index d977f3e..6956c38 100644 --- a/pipelines/Dockerfile_by_Ryan_Wick/Dockerfile +++ b/pipelines/Dockerfile_by_Ryan_Wick/Dockerfile @@ -2,7 +2,7 @@ FROM mambaorg/micromamba:latest # Create an "autocycler" environment with long-read assemblers. RUN micromamba create -y -n autocycler python=3.12 -c conda-forge -c bioconda curl && \ - for tool in canu flye lja metamdbg miniasm minimap2 minipolish3 necat nextdenovo nextpolish racon raven-assembler wtdbg; do \ + for tool in canu flye lja metamdbg miniasm minimap2 minipolish3 minipolish necat nextdenovo nextpolish racon raven-assembler wtdbg; do \ if micromamba install -y -n autocycler -c conda-forge -c bioconda "$tool"; then \ printf " $tool" >> /tmp/installed_tools.txt; \ else \ From 0c2fa5639d63db14998bc64ca5efb7a5312929d2 Mon Sep 17 00:00:00 2001 From: Ryan Wick Date: Mon, 7 Jul 2025 12:31:05 +1000 Subject: [PATCH 2/2] Update Dockerfile Remove minipolish3 --- pipelines/Dockerfile_by_Ryan_Wick/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipelines/Dockerfile_by_Ryan_Wick/Dockerfile b/pipelines/Dockerfile_by_Ryan_Wick/Dockerfile index 6956c38..4051cc5 100644 --- a/pipelines/Dockerfile_by_Ryan_Wick/Dockerfile +++ b/pipelines/Dockerfile_by_Ryan_Wick/Dockerfile @@ -2,7 +2,7 @@ FROM mambaorg/micromamba:latest # Create an "autocycler" environment with long-read assemblers. RUN micromamba create -y -n autocycler python=3.12 -c conda-forge -c bioconda curl && \ - for tool in canu flye lja metamdbg miniasm minimap2 minipolish3 minipolish necat nextdenovo nextpolish racon raven-assembler wtdbg; do \ + for tool in canu flye lja metamdbg miniasm minimap2 minipolish necat nextdenovo nextpolish racon raven-assembler wtdbg; do \ if micromamba install -y -n autocycler -c conda-forge -c bioconda "$tool"; then \ printf " $tool" >> /tmp/installed_tools.txt; \ else \