From 7dbd1258fe18774d5f15bac13a47c28a33dbdef0 Mon Sep 17 00:00:00 2001 From: hopedisastro <40783500+hopedisastro@users.noreply.github.com> Date: Mon, 11 Sep 2023 08:57:17 +1000 Subject: [PATCH 01/13] add files --- images.toml | 1 + images/eh-expansion-evaluator/Dockerfile | 16 ++++++++++++++++ 2 files changed, 17 insertions(+) create mode 100644 images/eh-expansion-evaluator/Dockerfile diff --git a/images.toml b/images.toml index ebe25511..3349e84c 100644 --- a/images.toml +++ b/images.toml @@ -4,6 +4,7 @@ bedtools = '2.30.0' bwa = '0.7.17' cellregmap = '0.0.3' dragmap = '1.3.0-tokenizer-next-fix' +eh-expansion-evaluator = 'eb982ae41f83aaf44d4a8142980f7a41ac33e979' expansionhunter = '5.0.0' expansionhunter_bw2 = 'b85cba004fba4e0223e632fae576bc7fad0da804' fastp = '0.23.4' diff --git a/images/eh-expansion-evaluator/Dockerfile b/images/eh-expansion-evaluator/Dockerfile new file mode 100644 index 00000000..4c330285 --- /dev/null +++ b/images/eh-expansion-evaluator/Dockerfile @@ -0,0 +1,16 @@ +FROM ubuntu:20.04 +ARG DEBIAN_FRONTEND=noninteractive + +ARG VERSION=${VERSION:-eb982ae41f83aaf44d4a8142980f7a41ac33e979} + +# Install Git to clone the repository +RUN apt-get update && \ + apt-get install -y \ + git \ + && \ + apt-get clean -y + +# Clone the repository, jump into it +RUN git clone https://github.com/oscarlr/EH-expansion-evaluator && \ + cd EH-expansion-evaluator + \ No newline at end of file From 8f4a8177dfbdde5f7bfee2d35ab973d5b2e2c1be Mon Sep 17 00:00:00 2001 From: hopedisastro <40783500+hopedisastro@users.noreply.github.com> Date: Mon, 11 Sep 2023 08:59:53 +1000 Subject: [PATCH 02/13] lint --- images/eh-expansion-evaluator/Dockerfile | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/images/eh-expansion-evaluator/Dockerfile b/images/eh-expansion-evaluator/Dockerfile index 4c330285..8462497c 100644 --- a/images/eh-expansion-evaluator/Dockerfile +++ b/images/eh-expansion-evaluator/Dockerfile @@ -12,5 +12,4 @@ RUN apt-get update && \ # Clone the repository, jump into it RUN git clone https://github.com/oscarlr/EH-expansion-evaluator && \ - cd EH-expansion-evaluator - \ No newline at end of file + cd EH-expansion-evaluator \ No newline at end of file From b9dbca3bc64ce4c59232449aa97852ffdcd17466 Mon Sep 17 00:00:00 2001 From: hopedisastro <40783500+hopedisastro@users.noreply.github.com> Date: Mon, 11 Sep 2023 09:02:37 +1000 Subject: [PATCH 03/13] lint --- images/eh-expansion-evaluator/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/images/eh-expansion-evaluator/Dockerfile b/images/eh-expansion-evaluator/Dockerfile index 8462497c..0d8e9395 100644 --- a/images/eh-expansion-evaluator/Dockerfile +++ b/images/eh-expansion-evaluator/Dockerfile @@ -12,4 +12,4 @@ RUN apt-get update && \ # Clone the repository, jump into it RUN git clone https://github.com/oscarlr/EH-expansion-evaluator && \ - cd EH-expansion-evaluator \ No newline at end of file + cd EH-expansion-evaluator From 767c8ea659e6961aceea757362efb25ae3a43b15 Mon Sep 17 00:00:00 2001 From: Hope Tanudisastro <40783500+hopedisastro@users.noreply.github.com> Date: Mon, 11 Sep 2023 09:27:41 +1000 Subject: [PATCH 04/13] Update images/eh-expansion-evaluator/Dockerfile Co-authored-by: Matt Welland --- images/eh-expansion-evaluator/Dockerfile | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/images/eh-expansion-evaluator/Dockerfile b/images/eh-expansion-evaluator/Dockerfile index 0d8e9395..d838d687 100644 --- a/images/eh-expansion-evaluator/Dockerfile +++ b/images/eh-expansion-evaluator/Dockerfile @@ -10,6 +10,8 @@ RUN apt-get update && \ && \ apt-get clean -y -# Clone the repository, jump into it -RUN git clone https://github.com/oscarlr/EH-expansion-evaluator && \ - cd EH-expansion-evaluator +# Clone the repository +RUN git clone https://github.com/oscarlr/EH-expansion-evaluator + +# Container should start in git repository +WORKDIR EH-expansion-evaluator From 859f843c148c09c250b0940d56040011bc376f54 Mon Sep 17 00:00:00 2001 From: hopedisastro <40783500+hopedisastro@users.noreply.github.com> Date: Mon, 11 Sep 2023 09:32:36 +1000 Subject: [PATCH 05/13] linting --- images/eh-expansion-evaluator/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/images/eh-expansion-evaluator/Dockerfile b/images/eh-expansion-evaluator/Dockerfile index d838d687..b8f6d94a 100644 --- a/images/eh-expansion-evaluator/Dockerfile +++ b/images/eh-expansion-evaluator/Dockerfile @@ -14,4 +14,4 @@ RUN apt-get update && \ RUN git clone https://github.com/oscarlr/EH-expansion-evaluator # Container should start in git repository -WORKDIR EH-expansion-evaluator +WORKDIR /EH-expansion-evaluator From c19271dee4a6f64f77d828450de651f2fc0cf7e4 Mon Sep 17 00:00:00 2001 From: Hope Tanudisastro <40783500+hopedisastro@users.noreply.github.com> Date: Mon, 11 Sep 2023 10:04:30 +1000 Subject: [PATCH 06/13] Update images/eh-expansion-evaluator/Dockerfile Co-authored-by: John Marshall --- images/eh-expansion-evaluator/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/images/eh-expansion-evaluator/Dockerfile b/images/eh-expansion-evaluator/Dockerfile index b8f6d94a..655cb40b 100644 --- a/images/eh-expansion-evaluator/Dockerfile +++ b/images/eh-expansion-evaluator/Dockerfile @@ -1,4 +1,4 @@ -FROM ubuntu:20.04 +FROM ubuntu:22.04 ARG DEBIAN_FRONTEND=noninteractive ARG VERSION=${VERSION:-eb982ae41f83aaf44d4a8142980f7a41ac33e979} From 37fbc75e71afa3c16e5a29d4c6e6f78f6c187bdf Mon Sep 17 00:00:00 2001 From: Hope Tanudisastro <40783500+hopedisastro@users.noreply.github.com> Date: Mon, 11 Sep 2023 10:05:01 +1000 Subject: [PATCH 07/13] Update images/eh-expansion-evaluator/Dockerfile Co-authored-by: John Marshall --- images/eh-expansion-evaluator/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/images/eh-expansion-evaluator/Dockerfile b/images/eh-expansion-evaluator/Dockerfile index 655cb40b..c49b15b2 100644 --- a/images/eh-expansion-evaluator/Dockerfile +++ b/images/eh-expansion-evaluator/Dockerfile @@ -11,7 +11,7 @@ RUN apt-get update && \ apt-get clean -y # Clone the repository -RUN git clone https://github.com/oscarlr/EH-expansion-evaluator +RUN git clone https://github.com/oscarlr/EH-expansion-evaluator && cd EH-expansion-evaluator && git checkout $VERSION # Container should start in git repository WORKDIR /EH-expansion-evaluator From f993453e6b3664718a5b7faabf3a1794033b2721 Mon Sep 17 00:00:00 2001 From: Hope Tanudisastro <40783500+hopedisastro@users.noreply.github.com> Date: Mon, 11 Sep 2023 10:05:23 +1000 Subject: [PATCH 08/13] Update images/eh-expansion-evaluator/Dockerfile Co-authored-by: Matt Welland --- images/eh-expansion-evaluator/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/images/eh-expansion-evaluator/Dockerfile b/images/eh-expansion-evaluator/Dockerfile index c49b15b2..fb7abdfe 100644 --- a/images/eh-expansion-evaluator/Dockerfile +++ b/images/eh-expansion-evaluator/Dockerfile @@ -5,7 +5,7 @@ ARG VERSION=${VERSION:-eb982ae41f83aaf44d4a8142980f7a41ac33e979} # Install Git to clone the repository RUN apt-get update && \ - apt-get install -y \ + apt-get install -y --no-install-recommends \ git \ && \ apt-get clean -y From d607d88d6d81cc5e169b22b2d4d08fd295ae50f1 Mon Sep 17 00:00:00 2001 From: Hope Tanudisastro <40783500+hopedisastro@users.noreply.github.com> Date: Mon, 11 Sep 2023 10:05:36 +1000 Subject: [PATCH 09/13] Update images/eh-expansion-evaluator/Dockerfile Co-authored-by: Matt Welland --- images/eh-expansion-evaluator/Dockerfile | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/images/eh-expansion-evaluator/Dockerfile b/images/eh-expansion-evaluator/Dockerfile index fb7abdfe..b0d2a2f2 100644 --- a/images/eh-expansion-evaluator/Dockerfile +++ b/images/eh-expansion-evaluator/Dockerfile @@ -8,7 +8,8 @@ RUN apt-get update && \ apt-get install -y --no-install-recommends \ git \ && \ - apt-get clean -y + apt-get clean -y \ + && rm -rf /var/lib/apt/lists/* # Clone the repository RUN git clone https://github.com/oscarlr/EH-expansion-evaluator && cd EH-expansion-evaluator && git checkout $VERSION From d9f45ad97e1f754828a3a54ac8ee7788fdf3a786 Mon Sep 17 00:00:00 2001 From: hopedisastro <40783500+hopedisastro@users.noreply.github.com> Date: Mon, 11 Sep 2023 10:37:50 +1000 Subject: [PATCH 10/13] packages install, python install --- images/eh-expansion-evaluator/Dockerfile | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/images/eh-expansion-evaluator/Dockerfile b/images/eh-expansion-evaluator/Dockerfile index b0d2a2f2..6f39e2e4 100644 --- a/images/eh-expansion-evaluator/Dockerfile +++ b/images/eh-expansion-evaluator/Dockerfile @@ -1,18 +1,22 @@ -FROM ubuntu:22.04 +FROM ubuntu:20.04 ARG DEBIAN_FRONTEND=noninteractive - ARG VERSION=${VERSION:-eb982ae41f83aaf44d4a8142980f7a41ac33e979} # Install Git to clone the repository -RUN apt-get update && \ - apt-get install -y --no-install-recommends \ +RUN apt-get update && apt-get install --no-install-recommends -qqy \ + python3-dev=3.8.2-0ubuntu2 \ + python3-pip=20.0.2-5ubuntu1.9 \ + python3.6\ git \ && \ apt-get clean -y \ && rm -rf /var/lib/apt/lists/* +# Install Python packages +RUN pip3 install numpy pandas scikit-learn + # Clone the repository RUN git clone https://github.com/oscarlr/EH-expansion-evaluator && cd EH-expansion-evaluator && git checkout $VERSION # Container should start in git repository -WORKDIR /EH-expansion-evaluator +WORKDIR EH-expansion-evaluator From e32aee99b41c91ad6e27feb87ef05a11e566daca Mon Sep 17 00:00:00 2001 From: hopedisastro <40783500+hopedisastro@users.noreply.github.com> Date: Mon, 11 Sep 2023 10:46:00 +1000 Subject: [PATCH 11/13] added package versions --- images/eh-expansion-evaluator/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/images/eh-expansion-evaluator/Dockerfile b/images/eh-expansion-evaluator/Dockerfile index 6f39e2e4..82744eb4 100644 --- a/images/eh-expansion-evaluator/Dockerfile +++ b/images/eh-expansion-evaluator/Dockerfile @@ -13,7 +13,7 @@ RUN apt-get update && apt-get install --no-install-recommends -qqy \ && rm -rf /var/lib/apt/lists/* # Install Python packages -RUN pip3 install numpy pandas scikit-learn +RUN pip3 install numpy==1.24.4 pandas==2.0.3 scikit-learn==1.3.0 # Clone the repository RUN git clone https://github.com/oscarlr/EH-expansion-evaluator && cd EH-expansion-evaluator && git checkout $VERSION From c5e4d48279548ab619663e1e9bd6941627d0a16a Mon Sep 17 00:00:00 2001 From: hopedisastro <40783500+hopedisastro@users.noreply.github.com> Date: Mon, 11 Sep 2023 11:02:52 +1000 Subject: [PATCH 12/13] lint --- images/eh-expansion-evaluator/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/images/eh-expansion-evaluator/Dockerfile b/images/eh-expansion-evaluator/Dockerfile index 82744eb4..50d36651 100644 --- a/images/eh-expansion-evaluator/Dockerfile +++ b/images/eh-expansion-evaluator/Dockerfile @@ -13,7 +13,7 @@ RUN apt-get update && apt-get install --no-install-recommends -qqy \ && rm -rf /var/lib/apt/lists/* # Install Python packages -RUN pip3 install numpy==1.24.4 pandas==2.0.3 scikit-learn==1.3.0 +RUN pip3 install --no-cache-dir numpy==1.24.4 pandas==2.0.3 scikit-learn==1.3.0 # Clone the repository RUN git clone https://github.com/oscarlr/EH-expansion-evaluator && cd EH-expansion-evaluator && git checkout $VERSION From 7d6cdca79527f7ce5cd4f9d7604a8511e2567d6c Mon Sep 17 00:00:00 2001 From: Hope Tanudisastro <40783500+hopedisastro@users.noreply.github.com> Date: Mon, 11 Sep 2023 17:37:20 +1000 Subject: [PATCH 13/13] Update images/eh-expansion-evaluator/Dockerfile Co-authored-by: Matt Welland --- images/eh-expansion-evaluator/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/images/eh-expansion-evaluator/Dockerfile b/images/eh-expansion-evaluator/Dockerfile index 50d36651..44e8d3b0 100644 --- a/images/eh-expansion-evaluator/Dockerfile +++ b/images/eh-expansion-evaluator/Dockerfile @@ -19,4 +19,4 @@ RUN pip3 install --no-cache-dir numpy==1.24.4 pandas==2.0.3 scikit-learn==1.3.0 RUN git clone https://github.com/oscarlr/EH-expansion-evaluator && cd EH-expansion-evaluator && git checkout $VERSION # Container should start in git repository -WORKDIR EH-expansion-evaluator +WORKDIR /EH-expansion-evaluator