From 96ac3e839a23b645851a28ade13025a51437050b Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 4 May 2023 10:58:28 +0200 Subject: [PATCH 01/10] Bump mafft version to v7.520 We were using v7.475 (~2.5y old) which had serious bug occasionally requesting excessive memory See https://mafft.cbrc.jp/alignment/software/changelog.html --- Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 19bd695f..793d4c83 100644 --- a/Dockerfile +++ b/Dockerfile @@ -89,8 +89,9 @@ RUN curl -fsSL https://github.com/vcftools/vcftools/releases/download/v0.1.16/vc # NOTE: Running this program requires support for emulation on the Docker host # if the processor architecture is not amd64. # TODO: Build from source to avoid emulation. Instructions: https://mafft.cbrc.jp/alignment/software/installation_without_root.html +# Last update: 2023-05-03 to v7.520 from v7.475 (~end of 2020) WORKDIR /download/mafft -RUN curl -fsSL https://mafft.cbrc.jp/alignment/software/mafft-7.475-linux.tgz \ +RUN curl -fsSL https://mafft.cbrc.jp/alignment/software/mafft-7.520-linux.tgz \ | tar xzvpf - --no-same-owner --strip-components=2 mafft-linux64/mafftdir/ \ && cp -p bin/* /final/bin \ && cp -p libexec/* /final/libexec From 3a480478269e1166f3f73090643202fbbd35a160 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 4 May 2023 11:02:15 +0200 Subject: [PATCH 02/10] Update IQtree to v2.2.2.4 --- Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 793d4c83..101b61bd 100644 --- a/Dockerfile +++ b/Dockerfile @@ -100,8 +100,9 @@ RUN curl -fsSL https://mafft.cbrc.jp/alignment/software/mafft-7.520-linux.tgz \ # NOTE: Running this program requires support for emulation on the Docker host # if the processor architecture is not amd64. # TODO: Build from source to avoid emulation. Instructions: http://www.iqtree.org/doc/Compilation-Guide +# Last update: 2023-05-03 to v2.2.2.4 from v2.1.2 (2020-10-22) WORKDIR /download/IQ-TREE -RUN curl -fsSL https://github.com/iqtree/iqtree2/releases/download/v2.1.2/iqtree-2.1.2-Linux.tar.gz \ +RUN curl -fsSL https://github.com/iqtree/iqtree2/releases/download/v2.2.2.4/iqtree-2.2.2.4-Linux.tar.gz \ | tar xzvpf - --no-same-owner --strip-components=1 \ && mv bin/iqtree2 /final/bin/iqtree From 5c1b62d5e2900ceef64278e7bf20fcdaff08adc3 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 4 May 2023 11:06:09 +0200 Subject: [PATCH 03/10] Update csvtk to v0.25.0 --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 101b61bd..7adaeb89 100644 --- a/Dockerfile +++ b/Dockerfile @@ -127,7 +127,7 @@ RUN curl -L -o tsv-utils.tar.gz https://github.com/eBay/tsv-utils/releases/downl && rm -f tsv-utils.tar.gz # Download csvtk -RUN curl -L https://github.com/shenwei356/csvtk/releases/download/v0.24.0/csvtk_${TARGETOS}_${TARGETARCH}.tar.gz | tar xz --no-same-owner -C /final/bin +RUN curl -L https://github.com/shenwei356/csvtk/releases/download/v0.25.0/csvtk_${TARGETOS}_${TARGETARCH}.tar.gz | tar xz --no-same-owner -C /final/bin # Download seqkit RUN curl -L https://github.com/shenwei356/seqkit/releases/download/v2.2.0/seqkit_${TARGETOS}_${TARGETARCH}.tar.gz | tar xz --no-same-owner -C /final/bin From ccad81dce4d482f9996dc14055be34bd6751c922 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 4 May 2023 11:06:21 +0200 Subject: [PATCH 04/10] Update seqkit to v2.4.0 --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 7adaeb89..98e0976d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -130,7 +130,7 @@ RUN curl -L -o tsv-utils.tar.gz https://github.com/eBay/tsv-utils/releases/downl RUN curl -L https://github.com/shenwei356/csvtk/releases/download/v0.25.0/csvtk_${TARGETOS}_${TARGETARCH}.tar.gz | tar xz --no-same-owner -C /final/bin # Download seqkit -RUN curl -L https://github.com/shenwei356/seqkit/releases/download/v2.2.0/seqkit_${TARGETOS}_${TARGETARCH}.tar.gz | tar xz --no-same-owner -C /final/bin +RUN curl -L https://github.com/shenwei356/seqkit/releases/download/v2.4.0/seqkit_${TARGETOS}_${TARGETARCH}.tar.gz | tar xz --no-same-owner -C /final/bin # Download gofasta (for ncov/Pangolin) # NOTE: Running this program requires support for emulation on the Docker host From 67fde48d69b2213136ab70f4cdbd8be0fbef6e5a Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 4 May 2023 11:09:27 +0200 Subject: [PATCH 05/10] Update gofasta to v1.2.0 --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 98e0976d..4c620e2d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -136,7 +136,7 @@ RUN curl -L https://github.com/shenwei356/seqkit/releases/download/v2.4.0/seqkit # NOTE: Running this program requires support for emulation on the Docker host # if the processor architecture is not amd64. # TODO: Build from source to avoid emulation. Instructions: https://github.com/virus-evolution/gofasta/tree/v0.0.6#installation -RUN curl -fsSL https://github.com/virus-evolution/gofasta/releases/download/v0.0.6/gofasta-linux-amd64 \ +RUN curl -fsSL https://github.com/virus-evolution/gofasta/releases/download/v1.2.0/gofasta-linux-amd64 \ -o /final/bin/gofasta # Download minimap2 (for ncov/Pangolin) From 9bb76df40826f0a8f9c22770c2b73cef2377c494 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 4 May 2023 11:10:27 +0200 Subject: [PATCH 06/10] Update minimamp2 to v2.26 --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 4c620e2d..89f3531a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -143,8 +143,8 @@ RUN curl -fsSL https://github.com/virus-evolution/gofasta/releases/download/v1.2 # NOTE: Running this program requires support for emulation on the Docker host # if the processor architecture is not amd64. # TODO: Build from source to avoid emulation. Instructions: https://github.com/lh3/minimap2/tree/v2.24#install -RUN curl -fsSL https://github.com/lh3/minimap2/releases/download/v2.24/minimap2-2.24_x64-linux.tar.bz2 \ - | tar xjvpf - --no-same-owner --strip-components=1 -C /final/bin minimap2-2.24_x64-linux/minimap2 +RUN curl -fsSL https://github.com/lh3/minimap2/releases/download/v2.26/minimap2-2.26_x64-linux.tar.bz2 \ + | tar xjvpf - --no-same-owner --strip-components=1 -C /final/bin minimap2-2.26_x64-linux/minimap2 # 3. Install programs via pip From ad77c3ac0728a16124518295cb525908bc225088 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 4 May 2023 11:14:20 +0200 Subject: [PATCH 07/10] Update awscli to v1.27.126 --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 89f3531a..c2cce3d7 100644 --- a/Dockerfile +++ b/Dockerfile @@ -183,7 +183,7 @@ RUN if [[ "$TARGETPLATFORM" == linux/arm64 ]]; then \ RUN pip3 install envdir==1.0.1 # Install tooling for our AWS Batch builds, which use `aws s3`. -RUN pip3 install awscli==1.18.195 +RUN pip3 install awscli==1.27.126 # Install Snakemake and related optional dependencies. # Pinned to 7.24.1 for stability (2023-03-13) From 21f70b8b8122d8bd2cdb9a35c49b8127c19817b6 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 4 May 2023 11:15:22 +0200 Subject: [PATCH 08/10] Update google-cloud-storage to v2.8.0 --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index c2cce3d7..e8158c7a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -190,7 +190,7 @@ RUN pip3 install awscli==1.27.126 RUN pip3 install snakemake==7.24.1 # Google Cloud Storage package is required for Snakemake to fetch remote files # from Google Storage URIs. -RUN pip3 install google-cloud-storage==2.7.0 +RUN pip3 install google-cloud-storage==2.8.0 # Install epiweeks (for ncov) RUN pip3 install epiweeks==2.1.2 From 59e6ed2483b61ab5ff72597bcddc09c5275c85e5 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 4 May 2023 11:16:20 +0200 Subject: [PATCH 09/10] Update epiweeks to v2.2.0 --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index e8158c7a..37445db3 100644 --- a/Dockerfile +++ b/Dockerfile @@ -193,7 +193,7 @@ RUN pip3 install snakemake==7.24.1 RUN pip3 install google-cloud-storage==2.8.0 # Install epiweeks (for ncov) -RUN pip3 install epiweeks==2.1.2 +RUN pip3 install epiweeks==2.2.0 # Install Pangolin and PangoLEARN + deps (for ncov) # The cov-lineages projects aren't available on PyPI, so install via git URLs. From 23c3c7211f30c6dcfed363a82869dbfd8ae788cb Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Thu, 4 May 2023 11:22:55 +0200 Subject: [PATCH 10/10] Update snakemake to v7.25.2 --- Dockerfile | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 37445db3..e51c4c95 100644 --- a/Dockerfile +++ b/Dockerfile @@ -186,8 +186,7 @@ RUN pip3 install envdir==1.0.1 RUN pip3 install awscli==1.27.126 # Install Snakemake and related optional dependencies. -# Pinned to 7.24.1 for stability (2023-03-13) -RUN pip3 install snakemake==7.24.1 +RUN pip3 install snakemake==7.25.2 # Google Cloud Storage package is required for Snakemake to fetch remote files # from Google Storage URIs. RUN pip3 install google-cloud-storage==2.8.0