From 04800070e1917e5fabf5dd9f8a47ee08645fbdd9 Mon Sep 17 00:00:00 2001 From: Darryl Nousome Date: Thu, 30 May 2024 12:09:43 -0400 Subject: [PATCH 1/4] fix: typo in docker --- docker/logan_base/Dockerfile | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/docker/logan_base/Dockerfile b/docker/logan_base/Dockerfile index 7da9e7b..7dc16f9 100644 --- a/docker/logan_base/Dockerfile +++ b/docker/logan_base/Dockerfile @@ -20,8 +20,8 @@ WORKDIR /opt2 RUN apt-get update \ && apt-get -y upgrade \ && DEBIAN_FRONTEND=noninteractive apt-get install -y \ - bc \ - openjdk-17-jdk + bc + #openjdk-17-jdk # Common bioinformatics tools # bwa/0.7.17-4 bowtie/1.2.3 bowtie2/2.3.5.1 @@ -205,15 +205,15 @@ RUN wget -O muse_2.0.4.tar.gz https://github.com/wwylab/MuSE/archive/refs/tags/v ENV PATH="/opt2/MuSE:$PATH" # HMFtools for PURPLE/COBALT/AMBER -RUN wget https://github.com/hartwigmedical/hmftools/releases/download/amber-v4.0/amber-4.0.jar \ +RUN wget https://github.com/hartwigmedical/hmftools/releases/download/amber-v4.0/amber_v4.0.jar \ && wget https://github.com/hartwigmedical/hmftools/releases/download/cobalt-v1.16/cobalt_v1.16.jar \ - && wget https://github.com/hartwigmedical/hmftools/releases/download/purple-v4.0/purple_v4.0.jar \ - && wget https://github.com/hartwigmedical/hmftools/releases/download/sage-v3.4/sage_v3.4.jar \ + && wget https://github.com/hartwigmedical/hmftools/releases/download/purple-v4.0.2/purple_v4.0.2.jar \ + && wget https://github.com/hartwigmedical/hmftools/releases/download/sage-v3.4.3/sage_v3.4.3.jar \ && mkdir hmftools \ - && mv amber-4.0.jar hmftools/amber.jar \ + && mv amber_v4.0.jar hmftools/amber.jar \ && mv cobalt_v1.16.jar hmftools/cobalt.jar \ - && mv purple_v4.0.jar hmftools/purple.jar \ - && mv sage.v3.4.jar hmftools/sage.jar \ + && mv purple_v4.0.2.jar hmftools/purple.jar \ + && mv sage_v3.4.3.jar hmftools/sage.jar \ && chmod a+x hmftools/amber.jar ENV PATH="/opt2/hmftools:$PATH" From 67e36db09771638cd78c661711a737e7b3758d54 Mon Sep 17 00:00:00 2001 From: Darryl Nousome Date: Thu, 30 May 2024 12:11:27 -0400 Subject: [PATCH 2/4] fix: requires jdk17 --- docker/logan_base/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docker/logan_base/Dockerfile b/docker/logan_base/Dockerfile index 7dc16f9..2afd70f 100644 --- a/docker/logan_base/Dockerfile +++ b/docker/logan_base/Dockerfile @@ -20,8 +20,8 @@ WORKDIR /opt2 RUN apt-get update \ && apt-get -y upgrade \ && DEBIAN_FRONTEND=noninteractive apt-get install -y \ - bc - #openjdk-17-jdk + bc \ + openjdk-17-jdk # Common bioinformatics tools # bwa/0.7.17-4 bowtie/1.2.3 bowtie2/2.3.5.1 From b10ecf3dfb2a814cfd05f9ccef137efa1cd34b70 Mon Sep 17 00:00:00 2001 From: Darryl Nousome Date: Thu, 30 May 2024 12:09:43 -0400 Subject: [PATCH 3/4] fix: typo in docker --- docker/logan_base/Dockerfile | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/docker/logan_base/Dockerfile b/docker/logan_base/Dockerfile index 7da9e7b..7dc16f9 100644 --- a/docker/logan_base/Dockerfile +++ b/docker/logan_base/Dockerfile @@ -20,8 +20,8 @@ WORKDIR /opt2 RUN apt-get update \ && apt-get -y upgrade \ && DEBIAN_FRONTEND=noninteractive apt-get install -y \ - bc \ - openjdk-17-jdk + bc + #openjdk-17-jdk # Common bioinformatics tools # bwa/0.7.17-4 bowtie/1.2.3 bowtie2/2.3.5.1 @@ -205,15 +205,15 @@ RUN wget -O muse_2.0.4.tar.gz https://github.com/wwylab/MuSE/archive/refs/tags/v ENV PATH="/opt2/MuSE:$PATH" # HMFtools for PURPLE/COBALT/AMBER -RUN wget https://github.com/hartwigmedical/hmftools/releases/download/amber-v4.0/amber-4.0.jar \ +RUN wget https://github.com/hartwigmedical/hmftools/releases/download/amber-v4.0/amber_v4.0.jar \ && wget https://github.com/hartwigmedical/hmftools/releases/download/cobalt-v1.16/cobalt_v1.16.jar \ - && wget https://github.com/hartwigmedical/hmftools/releases/download/purple-v4.0/purple_v4.0.jar \ - && wget https://github.com/hartwigmedical/hmftools/releases/download/sage-v3.4/sage_v3.4.jar \ + && wget https://github.com/hartwigmedical/hmftools/releases/download/purple-v4.0.2/purple_v4.0.2.jar \ + && wget https://github.com/hartwigmedical/hmftools/releases/download/sage-v3.4.3/sage_v3.4.3.jar \ && mkdir hmftools \ - && mv amber-4.0.jar hmftools/amber.jar \ + && mv amber_v4.0.jar hmftools/amber.jar \ && mv cobalt_v1.16.jar hmftools/cobalt.jar \ - && mv purple_v4.0.jar hmftools/purple.jar \ - && mv sage.v3.4.jar hmftools/sage.jar \ + && mv purple_v4.0.2.jar hmftools/purple.jar \ + && mv sage_v3.4.3.jar hmftools/sage.jar \ && chmod a+x hmftools/amber.jar ENV PATH="/opt2/hmftools:$PATH" From f3d337be2a594aa984c5c535ffc1535912f5ea1c Mon Sep 17 00:00:00 2001 From: Darryl Nousome Date: Thu, 30 May 2024 12:11:27 -0400 Subject: [PATCH 4/4] fix: requires jdk17 --- docker/logan_base/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docker/logan_base/Dockerfile b/docker/logan_base/Dockerfile index 7dc16f9..2afd70f 100644 --- a/docker/logan_base/Dockerfile +++ b/docker/logan_base/Dockerfile @@ -20,8 +20,8 @@ WORKDIR /opt2 RUN apt-get update \ && apt-get -y upgrade \ && DEBIAN_FRONTEND=noninteractive apt-get install -y \ - bc - #openjdk-17-jdk + bc \ + openjdk-17-jdk # Common bioinformatics tools # bwa/0.7.17-4 bowtie/1.2.3 bowtie2/2.3.5.1