From 2cd326678775360387bac3fe93d2ff715db13f19 Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Sun, 15 Dec 2024 18:53:59 +1100
Subject: [PATCH 01/12] Dockerfile refactor

---
 Dockerfile                    |   55 +-
 conda/env/lock/conda-lock.yml | 5405 ---------------------------------
 2 files changed, 32 insertions(+), 5428 deletions(-)
 delete mode 100644 conda/env/lock/conda-lock.yml

diff --git a/Dockerfile b/Dockerfile
index c58ab07..8d6304e 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,32 +1,41 @@
 FROM ubuntu:20.04
-LABEL maintainer="https://github.com/pdiakumis"
+LABEL org.opencontainers.image.authors="peterdiakumis@gmail.com" \
+      org.opencontainers.image.description="Wrappers for somatic mutation signature analysis tools" \
+      org.opencontainers.image.source="https://github.com/umccr/sigrap" \
+      org.opencontainers.image.url="https://github.com/umccr/sigrap" \
+      org.opencontainers.image.documentation="https://umccr.github.io/sigrap" \
+      org.opencontainers.image.licenses="MIT"
 
-ARG MINI_VERSION=4.12.0-0
-ARG MINI_URL=https://github.com/conda-forge/miniforge/releases/download/${MINI_VERSION}/Mambaforge-${MINI_VERSION}-Linux-x86_64.sh
-ARG MAMBA_PREFIX="/opt/mambaforge"
+ARG MINIF="miniforge"
+ARG MINIF_VERSION="24.11.0-1"
+ARG MINIF_URL="https://github.com/conda-forge/${MINIF}/releases/download/${MINIF_VERSION}/Miniforge3-${MINIF_VERSION}-Linux-x86_64.sh"
 
-# install core pkgs, mambaforge
-RUN apt-get update -qq && \
-    apt-get install --yes --no-install-recommends -qq \
-    git bash bzip2 curl ca-certificates && \
+# install core pkgs, miniforge
+RUN apt-get update && \
+    apt-get install --yes --no-install-recommends \
+    bash bzip2 curl less wget zip ca-certificates && \
     apt-get clean && \
-    rm -r /var/lib/apt/lists/* && \
-    rm -r /var/cache/apt/* && \
-    curl --silent -L "${MINI_URL}" -o "mambaforge.sh" && \
-    /bin/bash mambaforge.sh -b -p "${MAMBA_PREFIX}" && \
-    rm mambaforge.sh
+    curl --silent -L "${MINIF_URL}" -o "${MINIF}.sh" && \
+    /bin/bash "${MINIF}.sh" -b -p "/opt/${MINIF}/" && \
+    rm "${MINIF}.sh"
 
 # create conda env
-ENV PATH="${MAMBA_PREFIX}/bin:$PATH"
-ARG ENV_DIR=/home/sigrap_conda_env
-ARG ENV_NAME="sigrap_env"
-COPY ./conda/env/lock ${ENV_DIR}
-RUN conda config --set always_yes yes && \
-    mamba install -c conda-forge conda-lock==1.0.5
-RUN conda-lock install --name ${ENV_NAME} ${ENV_DIR}/conda-lock.yml && \
-    mamba clean --all --force-pkgs-dirs
+ENV PATH="/opt/${MINIF}/bin:$PATH"
+ARG CONDA_ENV_DIR="/home/conda_envs"
+ARG PKG_LOCK="sigrap-linux-64.lock"
+COPY "./conda/env/lock/${PKG_LOCK}" "${CONDA_ENV_DIR}/"
+RUN conda create -n "sigrap_env" --file "${CONDA_ENV_DIR}/${PKG_LOCK}"
+RUN conda clean --all --force-pkgs-dirs --yes
 
-ENV PATH="${MAMBA_PREFIX}/envs/${ENV_NAME}/bin:${PATH}"
-ENV CONDA_PREFIX="${MAMBA_PREFIX}/envs/${ENV_NAME}"
+# Now copy env to smaller image
+FROM quay.io/bioconda/base-glibc-debian-bash:3.1
+
+COPY --from=0 "/opt/miniforge/envs/" "/opt/miniforge/envs/"
+
+# env is activated by default
+ARG MINIF="miniforge"
+ARG CONDA_ENV_NAME="sigrap_env"
+ENV PATH="/opt/${MINIF}/envs/${CONDA_ENV_NAME}/bin:${PATH}"
+ENV CONDA_PREFIX="/opt/${MINIF}/envs/${CONDA_ENV_NAME}"
 
 CMD [ "sigrap.R" ]
diff --git a/conda/env/lock/conda-lock.yml b/conda/env/lock/conda-lock.yml
deleted file mode 100644
index 9081092..0000000
--- a/conda/env/lock/conda-lock.yml
+++ /dev/null
@@ -1,5405 +0,0 @@
-# This lock file was generated by conda-lock (https://github.com/conda/conda-lock). DO NOT EDIT!
-#
-# A "lock file" contains a concrete list of package versions (with checksums) to be installed. Unlike
-# e.g. `conda env create`, the resulting environment will not change as new package versions become
-# available, unless you explicitly update the lock file.
-#
-# Install this environment as "YOURENV" with:
-#     conda-lock install -n YOURENV --file conda-lock.yml
-# To update a single package to the latest version compatible with the version constraints in the source:
-#     conda-lock lock  --lockfile conda-lock.yml --update PACKAGE
-# To re-solve the entire environment, e.g. after changing a version constraint in the source file:
-#     conda-lock -f conda/env/yaml/sigrap.yaml --lockfile conda-lock.yml
-version: 1
-metadata:
-  content_hash:
-    linux-64: c8e203055ec081785e467e176fb5148fb5932a7c7b9b4cf6b871d7a36fc569f2
-  channels:
-  - url: umccr
-    used_env_vars: []
-  - url: conda-forge
-    used_env_vars: []
-  - url: bioconda
-    used_env_vars: []
-  platforms:
-  - linux-64
-  sources:
-  - conda/env/yaml/sigrap.yaml
-package:
-- name: _libgcc_mutex
-  version: '0.1'
-  manager: conda
-  platform: linux-64
-  dependencies: {}
-  url: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
-  hash:
-    md5: d7c89558ba9fa0495403155b64376d81
-    sha256: fe51de6107f9edc7aa4f786a70f4a883943bc9d39b3bb7307c04c41410990726
-  category: main
-  optional: false
-- name: _r-mutex
-  version: 1.0.1
-  manager: conda
-  platform: linux-64
-  dependencies: {}
-  url: https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2
-  hash:
-    md5: 19f9db5f4f1b7f5ef5f6d67207f25f38
-    sha256: e58f9eeb416b92b550e824bcb1b9fb1958dee69abfe3089dfd1a9173e3a0528a
-  category: main
-  optional: false
-- name: ca-certificates
-  version: 2023.5.7
-  manager: conda
-  platform: linux-64
-  dependencies: {}
-  url: https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.5.7-hbcca054_0.conda
-  hash:
-    md5: f5c65075fc34438d5b456c7f3f5ab695
-    sha256: 0cf1bb3d0bfc5519b60af2c360fa4888fb838e1476b1e0f65b9dbc48b45c7345
-  category: main
-  optional: false
-- name: font-ttf-dejavu-sans-mono
-  version: '2.37'
-  manager: conda
-  platform: linux-64
-  dependencies: {}
-  url: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
-  hash:
-    md5: 0c96522c6bdaed4b1566d11387caaf45
-    sha256: 58d7f40d2940dd0a8aa28651239adbf5613254df0f75789919c4e6762054403b
-  category: main
-  optional: false
-- name: font-ttf-inconsolata
-  version: '3.000'
-  manager: conda
-  platform: linux-64
-  dependencies: {}
-  url: https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
-  hash:
-    md5: 34893075a5c9e55cdafac56607368fc6
-    sha256: c52a29fdac682c20d252facc50f01e7c2e7ceac52aa9817aaf0bb83f7559ec5c
-  category: main
-  optional: false
-- name: font-ttf-source-code-pro
-  version: '2.038'
-  manager: conda
-  platform: linux-64
-  dependencies: {}
-  url: https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2
-  hash:
-    md5: 4d59c254e01d9cde7957100457e2d5fb
-    sha256: 00925c8c055a2275614b4d983e1df637245e19058d79fc7dd1a93b8d9fb4b139
-  category: main
-  optional: false
-- name: font-ttf-ubuntu
-  version: '0.83'
-  manager: conda
-  platform: linux-64
-  dependencies: {}
-  url: https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-hab24e00_0.tar.bz2
-  hash:
-    md5: 19410c3df09dfb12d1206132a1d357c5
-    sha256: 470d5db54102bd51dbb0c5990324a2f4a0bc976faa493b22193338adb9882e2e
-  category: main
-  optional: false
-- name: kernel-headers_linux-64
-  version: 2.6.32
-  manager: conda
-  platform: linux-64
-  dependencies: {}
-  url: https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-2.6.32-he073ed8_15.tar.bz2
-  hash:
-    md5: 5dd5127afd710f91f6a75821bac0a4f0
-    sha256: c9f33acc0f1095bd4e7a2b577dfa41fc3fef3713b3975e8467a0fbed188fe6f4
-  category: main
-  optional: false
-- name: ld_impl_linux-64
-  version: '2.40'
-  manager: conda
-  platform: linux-64
-  dependencies: {}
-  url: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda
-  hash:
-    md5: 7aca3059a1729aa76c597603f10b0dd3
-    sha256: f6cc89d887555912d6c61b295d398cff9ec982a3417d38025c45d5dd9b9e79cd
-  category: main
-  optional: false
-- name: libgcc-devel_linux-64
-  version: 13.1.0
-  manager: conda
-  platform: linux-64
-  dependencies: {}
-  url: https://conda.anaconda.org/conda-forge/linux-64/libgcc-devel_linux-64-13.1.0-he3cc6c4_0.conda
-  hash:
-    md5: 5ec50dcd74ba7461709c4ac9c4cc4190
-    sha256: 749dabbfe7b571affa19ef3ddb23e22e2eed12d5a699a9830a0f7fba2f296e02
-  category: main
-  optional: false
-- name: libgfortran5
-  version: 13.1.0
-  manager: conda
-  platform: linux-64
-  dependencies: {}
-  url: https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.1.0-h15d22d2_0.conda
-  hash:
-    md5: afb656a334c409dd9805508af1c89c7a
-    sha256: a06235f4c4b85b463d9b8a73c9e10c1b5b4105f8a0ea8ac1f2f5f64edac3dfe7
-  category: main
-  optional: false
-- name: libstdcxx-devel_linux-64
-  version: 13.1.0
-  manager: conda
-  platform: linux-64
-  dependencies: {}
-  url: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-devel_linux-64-13.1.0-he3cc6c4_0.conda
-  hash:
-    md5: e703914ad2288ab24cf5ac94d812fc11
-    sha256: 21b95f21a80462c832caa348ece5413e10ba69d922dca01826706fe7b6f3a764
-  category: main
-  optional: false
-- name: libstdcxx-ng
-  version: 13.1.0
-  manager: conda
-  platform: linux-64
-  dependencies: {}
-  url: https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.1.0-hfd8a6a1_0.conda
-  hash:
-    md5: 067bcc23164642f4c226da631f2a2e1d
-    sha256: 6f9eb2d7a96687938c0001166a3b308460a8eb02b10e9d0dd9e251f0219ea05c
-  category: main
-  optional: false
-- name: python_abi
-  version: '3.11'
-  manager: conda
-  platform: linux-64
-  dependencies: {}
-  url: https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.11-3_cp311.conda
-  hash:
-    md5: c2e2630ddb68cf52eec74dc7dfab20b5
-    sha256: 2966a87dcb0b11fad28f9fe8216bfa4071115776b47ffc7547492fed176e1a1f
-  category: main
-  optional: false
-- name: tzdata
-  version: 2023c
-  manager: conda
-  platform: linux-64
-  dependencies: {}
-  url: https://conda.anaconda.org/conda-forge/noarch/tzdata-2023c-h71feb2d_0.conda
-  hash:
-    md5: 939e3e74d8be4dac89ce83b20de2492a
-    sha256: 0449138224adfa125b220154408419ec37c06b0b49f63c5954724325903ecf55
-  category: main
-  optional: false
-- name: fonts-conda-forge
-  version: '1'
-  manager: conda
-  platform: linux-64
-  dependencies:
-    font-ttf-dejavu-sans-mono: ''
-    font-ttf-inconsolata: ''
-    font-ttf-source-code-pro: ''
-    font-ttf-ubuntu: ''
-  url: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2
-  hash:
-    md5: f766549260d6815b0c52253f1fb1bb29
-    sha256: 53f23a3319466053818540bcdf2091f253cbdbab1e0e9ae7b9e509dcaa2a5e38
-  category: main
-  optional: false
-- name: libgfortran-ng
-  version: 13.1.0
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgfortran5: 13.1.0
-  url: https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.1.0-h69a702a_0.conda
-  hash:
-    md5: 506dc07710dd5b0ba63cbf134897fc10
-    sha256: 429e1d8a3e70b632df5b876e3fc322a56f769756693daa07114c46fa5098684e
-  category: main
-  optional: false
-- name: libgomp
-  version: 13.1.0
-  manager: conda
-  platform: linux-64
-  dependencies:
-    _libgcc_mutex: '0.1'
-  url: https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.1.0-he5830b7_0.conda
-  hash:
-    md5: 56ca14d57ac29a75d23a39eb3ee0ddeb
-    sha256: 5d441d80b57f857ad305a65169a6b915d4fd6735cdc9e9bded35d493c91ef16d
-  category: main
-  optional: false
-- name: sysroot_linux-64
-  version: '2.12'
-  manager: conda
-  platform: linux-64
-  dependencies:
-    kernel-headers_linux-64: 2.6.32
-  url: https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.12-he073ed8_15.tar.bz2
-  hash:
-    md5: 66c192522eacf5bb763568b4e415d133
-    sha256: 8498c73b60a7ea6faedf36204ec5a339c78d430fa838860f2b9d5d3a1c354eff
-  category: main
-  optional: false
-- name: _openmp_mutex
-  version: '4.5'
-  manager: conda
-  platform: linux-64
-  dependencies:
-    _libgcc_mutex: '0.1'
-    libgomp: '>=7.5.0'
-  url: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
-  hash:
-    md5: 73aaf86a425cc6e73fcf236a5a46396d
-    sha256: fbe2c5e56a653bebb982eda4876a9178aedfc2b545f25d0ce9c4c0b508253d22
-  category: main
-  optional: false
-- name: binutils_impl_linux-64
-  version: '2.40'
-  manager: conda
-  platform: linux-64
-  dependencies:
-    ld_impl_linux-64: '2.40'
-    sysroot_linux-64: ''
-  url: https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.40-hf600244_0.conda
-  hash:
-    md5: 33084421a8c0af6aef1b439707f7662a
-    sha256: a7e0ea2b71a5b03d82e5a58fb6b612ab1c44d72ce161f9aa441f7ba467cd4c8d
-  category: main
-  optional: false
-- name: fonts-conda-ecosystem
-  version: '1'
-  manager: conda
-  platform: linux-64
-  dependencies:
-    fonts-conda-forge: ''
-  url: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2
-  hash:
-    md5: fee5683a3f04bd15cbd8318b096a27ab
-    sha256: a997f2f1921bb9c9d76e6fa2f6b408b7fa549edd349a77639c9fe7a23ea93e61
-  category: main
-  optional: false
-- name: libgcc-ng
-  version: 13.1.0
-  manager: conda
-  platform: linux-64
-  dependencies:
-    _libgcc_mutex: '0.1'
-    _openmp_mutex: '>=4.5'
-  url: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.1.0-he5830b7_0.conda
-  hash:
-    md5: cd93f779ff018dd85c7544c015c9db3c
-    sha256: fba897a02f35b2b5e6edc43a746d1fa6970a77b422f258246316110af8966911
-  category: main
-  optional: false
-- name: bzip2
-  version: 1.0.8
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=9.3.0'
-  url: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2
-  hash:
-    md5: a1fd65c7ccbf10880423d82bca54eb54
-    sha256: cb521319804640ff2ad6a9f118d972ed76d86bea44e5626c09a13d38f562e1fa
-  category: main
-  optional: false
-- name: c-ares
-  version: 1.19.1
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=12'
-  url: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.19.1-hd590300_0.conda
-  hash:
-    md5: e8c18d865be43e2fb3f7a145b6adf1f5
-    sha256: c4276b1a0e8f18ab08018b1881666656742b325e0fcf2354f714e924d28683b6
-  category: main
-  optional: false
-- name: fribidi
-  version: 1.0.10
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=7.5.0'
-  url: https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.10-h36c2ea0_0.tar.bz2
-  hash:
-    md5: ac7bc6a654f8f41b352b38f4051135f8
-    sha256: 5d7b6c0ee7743ba41399e9e05a58ccc1cfc903942e49ff6f677f6e423ea7a627
-  category: main
-  optional: false
-- name: gettext
-  version: 0.21.1
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=12'
-  url: https://conda.anaconda.org/conda-forge/linux-64/gettext-0.21.1-h27087fc_0.tar.bz2
-  hash:
-    md5: 14947d8770185e5153fdd04d4673ed37
-    sha256: 4fcfedc44e4c9a053f0416f9fc6ab6ed50644fca3a761126dbd00d09db1f546a
-  category: main
-  optional: false
-- name: gmp
-  version: 6.2.1
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=7.5.0'
-    libstdcxx-ng: '>=7.5.0'
-  url: https://conda.anaconda.org/conda-forge/linux-64/gmp-6.2.1-h58526e2_0.tar.bz2
-  hash:
-    md5: b94cf2db16066b242ebd26db2facbd56
-    sha256: 07a5319e1ac54fe5d38f50c60f7485af7f830b036da56957d0bfb7558a886198
-  category: main
-  optional: false
-- name: graphite2
-  version: 1.3.13
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=7.5.0'
-    libstdcxx-ng: '>=7.5.0'
-  url: https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h58526e2_1001.tar.bz2
-  hash:
-    md5: 8c54672728e8ec6aa6db90cf2806d220
-    sha256: 65da967f3101b737b08222de6a6a14e20e480e7d523a5d1e19ace7b960b5d6b1
-  category: main
-  optional: false
-- name: icu
-  version: '72.1'
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=12'
-    libstdcxx-ng: '>=12'
-  url: https://conda.anaconda.org/conda-forge/linux-64/icu-72.1-hcb278e6_0.conda
-  hash:
-    md5: 7c8d20d847bb45f56bd941578fcfa146
-    sha256: e44cc00eec068e7f7a6dd117ba17bf5d57658729b7b841945546f82505138292
-  category: main
-  optional: false
-- name: keyutils
-  version: 1.6.1
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=10.3.0'
-  url: https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2
-  hash:
-    md5: 30186d27e2c9fa62b45fb1476b7200e3
-    sha256: 150c05a6e538610ca7c43beb3a40d65c90537497a4f6a5f4d15ec0451b6f5ebb
-  category: main
-  optional: false
-- name: lerc
-  version: 4.0.0
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=12'
-    libstdcxx-ng: '>=12'
-  url: https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2
-  hash:
-    md5: 76bbff344f0134279f225174e9064c8f
-    sha256: cb55f36dcd898203927133280ae1dc643368af041a48bcf7c026acb7c47b0c12
-  category: main
-  optional: false
-- name: libdeflate
-  version: '1.18'
-  manager: conda
-  platform: linux-64
-  dependencies:
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-  url: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.18-h0b41bf4_0.conda
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-  optional: false
-- name: libev
-  version: '4.33'
-  manager: conda
-  platform: linux-64
-  dependencies:
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-  url: https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-h516909a_1.tar.bz2
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-    sha256: 8c9635aa0ea28922877dc96358f9547f6a55fc7e2eb75a556b05f1725496baf9
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-  optional: false
-- name: libexpat
-  version: 2.5.0
-  manager: conda
-  platform: linux-64
-  dependencies:
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-  url: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.5.0-hcb278e6_1.conda
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-- name: libffi
-  version: 3.4.2
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=9.4.0'
-  url: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2
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-  optional: false
-- name: libiconv
-  version: '1.17'
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=10.3.0'
-  url: https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-h166bdaf_0.tar.bz2
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-  category: main
-  optional: false
-- name: libjpeg-turbo
-  version: 2.1.5.1
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=12'
-  url: https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-2.1.5.1-h0b41bf4_0.conda
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-  category: main
-  optional: false
-- name: libnsl
-  version: 2.0.0
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=9.4.0'
-  url: https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2
-  hash:
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-  category: main
-  optional: false
-- name: libopenblas
-  version: 0.3.23
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=12'
-    libgfortran-ng: ''
-    libgfortran5: '>=11.3.0'
-  url: https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.23-pthreads_h80387f5_0.conda
-  hash:
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-  optional: false
-- name: libsanitizer
-  version: 13.1.0
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=13.1.0'
-  url: https://conda.anaconda.org/conda-forge/linux-64/libsanitizer-13.1.0-hfd8a6a1_0.conda
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-  optional: false
-- name: libuuid
-  version: 2.38.1
-  manager: conda
-  platform: linux-64
-  dependencies:
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-  url: https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda
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-  optional: false
-- name: libwebp-base
-  version: 1.3.1
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=12'
-  url: https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.3.1-hd590300_0.conda
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-  optional: false
-- name: libzlib
-  version: 1.2.13
-  manager: conda
-  platform: linux-64
-  dependencies:
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-  url: https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda
-  hash:
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-  optional: false
-- name: make
-  version: '4.3'
-  manager: conda
-  platform: linux-64
-  dependencies:
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-  url: https://conda.anaconda.org/conda-forge/linux-64/make-4.3-hd18ef5c_1.tar.bz2
-  hash:
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-  optional: false
-- name: ncurses
-  version: '6.4'
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=12'
-  url: https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4-hcb278e6_0.conda
-  hash:
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-  category: main
-  optional: false
-- name: oniguruma
-  version: 6.9.8
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=12'
-  url: https://conda.anaconda.org/conda-forge/linux-64/oniguruma-6.9.8-h166bdaf_0.tar.bz2
-  hash:
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-  category: main
-  optional: false
-- name: openssl
-  version: 3.1.1
-  manager: conda
-  platform: linux-64
-  dependencies:
-    ca-certificates: ''
-    libgcc-ng: '>=12'
-  url: https://conda.anaconda.org/conda-forge/linux-64/openssl-3.1.1-hd590300_1.conda
-  hash:
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-    sha256: 407d655643389bdb49266842a816815c981ae98f3513a6a2059b908b3abb380a
-  category: main
-  optional: false
-- name: pixman
-  version: 0.40.0
-  manager: conda
-  platform: linux-64
-  dependencies:
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-  url: https://conda.anaconda.org/conda-forge/linux-64/pixman-0.40.0-h36c2ea0_0.tar.bz2
-  hash:
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-  category: main
-  optional: false
-- name: pthread-stubs
-  version: '0.4'
-  manager: conda
-  platform: linux-64
-  dependencies:
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-  url: https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2
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-  optional: false
-- name: sed
-  version: '4.8'
-  manager: conda
-  platform: linux-64
-  dependencies:
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-  url: https://conda.anaconda.org/conda-forge/linux-64/sed-4.8-he412f7d_0.tar.bz2
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-  optional: false
-- name: xorg-kbproto
-  version: 1.0.7
-  manager: conda
-  platform: linux-64
-  dependencies:
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-  url: https://conda.anaconda.org/conda-forge/linux-64/xorg-kbproto-1.0.7-h7f98852_1002.tar.bz2
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-- name: xorg-libice
-  version: 1.0.10
-  manager: conda
-  platform: linux-64
-  dependencies:
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-  url: https://conda.anaconda.org/conda-forge/linux-64/xorg-libice-1.0.10-h7f98852_0.tar.bz2
-  hash:
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-  optional: false
-- name: xorg-libxau
-  version: 1.0.11
-  manager: conda
-  platform: linux-64
-  dependencies:
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-  url: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.11-hd590300_0.conda
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-  optional: false
-- name: xorg-libxdmcp
-  version: 1.1.3
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=9.3.0'
-  url: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.3-h7f98852_0.tar.bz2
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-  optional: false
-- name: xorg-renderproto
-  version: 0.11.1
-  manager: conda
-  platform: linux-64
-  dependencies:
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-  url: https://conda.anaconda.org/conda-forge/linux-64/xorg-renderproto-0.11.1-h7f98852_1002.tar.bz2
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-  optional: false
-- name: xorg-xextproto
-  version: 7.3.0
-  manager: conda
-  platform: linux-64
-  dependencies:
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-  url: https://conda.anaconda.org/conda-forge/linux-64/xorg-xextproto-7.3.0-h0b41bf4_1003.conda
-  hash:
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-- name: xorg-xproto
-  version: 7.0.31
-  manager: conda
-  platform: linux-64
-  dependencies:
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-  url: https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h7f98852_1007.tar.bz2
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-  optional: false
-- name: xz
-  version: 5.2.6
-  manager: conda
-  platform: linux-64
-  dependencies:
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-  url: https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2
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-- name: yaml
-  version: 0.2.5
-  manager: conda
-  platform: linux-64
-  dependencies:
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-  url: https://conda.anaconda.org/conda-forge/linux-64/yaml-0.2.5-h7f98852_2.tar.bz2
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-- name: expat
-  version: 2.5.0
-  manager: conda
-  platform: linux-64
-  dependencies:
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-    libgcc-ng: '>=12'
-  url: https://conda.anaconda.org/conda-forge/linux-64/expat-2.5.0-hcb278e6_1.conda
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-  category: main
-  optional: false
-- name: gcc_impl_linux-64
-  version: 13.1.0
-  manager: conda
-  platform: linux-64
-  dependencies:
-    binutils_impl_linux-64: '>=2.39'
-    libgcc-devel_linux-64: 13.1.0
-    libgcc-ng: '>=13.1.0'
-    libgomp: '>=13.1.0'
-    libsanitizer: 13.1.0
-    libstdcxx-ng: '>=13.1.0'
-    sysroot_linux-64: ''
-  url: https://conda.anaconda.org/conda-forge/linux-64/gcc_impl_linux-64-13.1.0-hc4be1a9_0.conda
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-  category: main
-  optional: false
-- name: jq
-  version: '1.6'
-  manager: conda
-  platform: linux-64
-  dependencies:
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-    oniguruma: '>=6.9.3,<6.10.0a0'
-  url: https://conda.anaconda.org/conda-forge/linux-64/jq-1.6-h36c2ea0_1000.tar.bz2
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-- name: libblas
-  version: 3.9.0
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libopenblas: '>=0.3.23,<1.0a0'
-  url: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-17_linux64_openblas.conda
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-- name: libedit
-  version: 3.1.20191231
-  manager: conda
-  platform: linux-64
-  dependencies:
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-    ncurses: '>=6.2,<7.0.0a0'
-  url: https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2
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-- name: libnghttp2
-  version: 1.52.0
-  manager: conda
-  platform: linux-64
-  dependencies:
-    c-ares: '>=1.18.1,<2.0a0'
-    libev: '>=4.33,<4.34.0a0'
-    libgcc-ng: '>=12'
-    libstdcxx-ng: '>=12'
-    libzlib: '>=1.2.13,<1.3.0a0'
-    openssl: '>=3.0.8,<4.0a0'
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-- name: libpng
-  version: 1.6.39
-  manager: conda
-  platform: linux-64
-  dependencies:
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-    libzlib: '>=1.2.13,<1.3.0a0'
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-- name: libsqlite
-  version: 3.42.0
-  manager: conda
-  platform: linux-64
-  dependencies:
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-    libzlib: '>=1.2.13,<1.3.0a0'
-  url: https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.42.0-h2797004_0.conda
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-- name: libssh2
-  version: 1.11.0
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=12'
-    libzlib: '>=1.2.13,<1.3.0a0'
-    openssl: '>=3.1.1,<4.0a0'
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-  category: main
-  optional: false
-- name: libxcb
-  version: '1.15'
-  manager: conda
-  platform: linux-64
-  dependencies:
-    libgcc-ng: '>=12'
-    pthread-stubs: ''
-    xorg-libxau: ''
-    xorg-libxdmcp: ''
-  url: https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.15-h0b41bf4_0.conda
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-  category: main
-  optional: false
-- name: libxml2
-  version: 2.11.4
-  manager: conda
-  platform: linux-64
-  dependencies:
-    icu: '>=72.1,<73.0a0'
-    libgcc-ng: '>=12'
-    libiconv: '>=1.17,<2.0a0'
-    libzlib: '>=1.2.13,<1.3.0a0'
-    xz: '>=5.2.6,<6.0a0'
-  url: https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.11.4-h0d562d8_0.conda
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-  dependencies:
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-- name: readline
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-  manager: conda
-  platform: linux-64
-  dependencies:
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-    ncurses: '>=6.3,<7.0a0'
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-- name: tk
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-  platform: linux-64
-  dependencies:
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-- name: xorg-libsm
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-  dependencies:
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-- name: zlib
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-  dependencies:
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-- name: zstd
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-  manager: conda
-  platform: linux-64
-  dependencies:
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-    libstdcxx-ng: '>=12'
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-- name: bwidget
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-  platform: linux-64
-  dependencies:
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-- name: freetype
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-  manager: conda
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-- name: gfortran_impl_linux-64
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-- name: gxx_impl_linux-64
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-  platform: linux-64
-  dependencies:
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-- name: krb5
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-- name: libcblas
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-  dependencies:
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-  url: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-17_linux64_openblas.conda
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-- name: libgit2
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-  manager: conda
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-  dependencies:
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-- name: libglib
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-- name: liblapack
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-- name: libtiff
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-  dependencies:
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-- name: python
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-  dependencies:
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-    readline: '>=8.2,<9.0a0'
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-    xz: '>=5.2.6,<6.0a0'
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-- name: tktable
-  version: '2.10'
-  manager: conda
-  platform: linux-64
-  dependencies:
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-    tk: '>=8.6.10,<8.7.0a0'
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-- name: xorg-libx11
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-  platform: linux-64
-  dependencies:
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-    libxcb: '>=1.15,<1.16.0a0'
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-- name: argcomplete
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-  manager: conda
-  platform: linux-64
-  dependencies:
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-- name: fontconfig
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-  manager: conda
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-  dependencies:
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-- name: gsl
-  version: '2.7'
-  manager: conda
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-  dependencies:
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-- name: libcurl
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-  manager: conda
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-  dependencies:
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-- name: libv8
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-  manager: conda
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-  dependencies:
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-    libgcc-ng: '>=12'
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-- name: pyyaml
-  version: '6.0'
-  manager: conda
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-  dependencies:
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-    python: '>=3.11,<3.12.0a0'
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-- name: setuptools
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-  manager: conda
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-  dependencies:
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-- name: toml
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-- name: tomlkit
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-  platform: linux-64
-  dependencies:
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-  url: https://conda.anaconda.org/conda-forge/noarch/tomlkit-0.11.8-pyha770c72_0.conda
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-- name: xmltodict
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-  dependencies:
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-- name: xorg-libxext
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-  platform: linux-64
-  dependencies:
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-  url: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxext-1.3.4-h0b41bf4_2.conda
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-- name: xorg-libxrender
-  version: 0.9.11
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-  platform: linux-64
-  dependencies:
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-    xorg-libx11: '>=1.8.6,<2.0a0'
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-  url: https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.11-hd590300_0.conda
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-- name: xorg-libxt
-  version: 1.3.0
-  manager: conda
-  platform: linux-64
-  dependencies:
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-    xorg-kbproto: ''
-    xorg-libice: 1.0.*
-    xorg-libsm: 1.2.*
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-- name: r-cluster
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-- name: r-codetools
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-- name: r-commonmark
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-- name: r-curl
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-- name: r-jsonlite
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-- name: r-lattice
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-- name: r-lazyeval
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-- name: r-lpsolve
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-- name: r-matrixstats
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-- name: r-mime
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-- name: r-r.methodss3
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-    bioconductor-rtracklayer: '>=1.58.0,<1.59.0'
-    bioconductor-s4vectors: '>=0.36.0,<0.37.0'
-    bioconductor-summarizedexperiment: '>=1.28.0,<1.29.0'
-    bioconductor-xvector: '>=0.38.0,<0.39.0'
-    bioconductor-zlibbioc: '>=1.44.0,<1.45.0'
-    libblas: '>=3.9.0,<4.0a0'
-    libgcc-ng: '>=12'
-    liblapack: '>=3.9.0,<4.0a0'
-    r-base: '>=4.2,<4.3.0a0'
-    r-dbi: ''
-  url: https://conda.anaconda.org/bioconda/linux-64/bioconductor-variantannotation-1.44.0-r42ha9d7317_1.tar.bz2
-  hash:
-    md5: 2f6fc699c11d18fbef3ac2e820d0132b
-    sha256: 0c757af3274cfc6dabc7c0cbb1d4cf11ed650c5cba49248d3a6a066e1f91e9fb
-  category: main
-  optional: false
-- name: bioconductor-mutationalpatterns
-  version: 3.8.0
-  manager: conda
-  platform: linux-64
-  dependencies:
-    bioconductor-biocgenerics: '>=0.44.0,<0.45.0'
-    bioconductor-biostrings: '>=2.66.0,<2.67.0'
-    bioconductor-bsgenome: '>=1.66.0,<1.67.0'
-    bioconductor-genomeinfodb: '>=1.34.0,<1.35.0'
-    bioconductor-genomicranges: '>=1.50.0,<1.51.0'
-    bioconductor-iranges: '>=2.32.0,<2.33.0'
-    bioconductor-s4vectors: '>=0.36.0,<0.37.0'
-    bioconductor-variantannotation: '>=1.44.0,<1.45.0'
-    r-base: '>=4.2,<4.3.0a0'
-    r-cowplot: '>=0.9.2'
-    r-dplyr: '>=0.8.3'
-    r-ggalluvial: '>=0.12.2'
-    r-ggdendro: '>=0.1-20'
-    r-ggplot2: '>=2.1.0'
-    r-magrittr: '>=1.5'
-    r-nmf: '>=0.20.6'
-    r-pracma: '>=1.8.8'
-    r-purrr: '>=0.3.2'
-    r-rcolorbrewer: ''
-    r-stringr: '>=1.4.0'
-    r-tibble: '>=2.1.3'
-    r-tidyr: '>=1.0.0'
-  url: https://conda.anaconda.org/bioconda/noarch/bioconductor-mutationalpatterns-3.8.0-r42hdfd78af_0.tar.bz2
-  hash:
-    md5: 21b627724582050880db8bd258c4e9c9
-    sha256: 4c7abdc48f1a91fce08c01eb09680473c5cdac6cf5f25ca1b375386a47edfdc7
-  category: main
-  optional: false
-- name: bioconductor-structuralvariantannotation
-  version: 1.13.0
-  manager: conda
-  platform: linux-64
-  dependencies:
-    bioconductor-biocgenerics: '>=0.44.0,<0.45.0'
-    bioconductor-biostrings: '>=2.66.0,<2.67.0'
-    bioconductor-genomeinfodb: '>=1.34.0,<1.35.0'
-    bioconductor-genomicfeatures: '>=1.50.0,<1.51.0'
-    bioconductor-genomicranges: '>=1.50.0,<1.51.0'
-    bioconductor-iranges: '>=2.32.0,<2.33.0'
-    bioconductor-rtracklayer: '>=1.58.0,<1.59.0'
-    bioconductor-s4vectors: '>=0.36.0,<0.37.0'
-    bioconductor-summarizedexperiment: '>=1.28.0,<1.29.0'
-    bioconductor-variantannotation: '>=1.44.0,<1.45.0'
-    r-assertthat: ''
-    r-base: '>=4.2,<4.3.0a0'
-    r-dplyr: ''
-    r-rlang: ''
-    r-stringr: ''
-  url: https://conda.anaconda.org/bioconda/noarch/bioconductor-structuralvariantannotation-1.13.0-r42hdfd78af_0.tar.bz2
-  hash:
-    md5: 9c6900e1481eab63082fa2c913304fdd
-    sha256: f32ce7780e132ddd9b16cbe3de605f3c330452f9ca0e82bf2953a3ce06b279e5
-  category: main
-  optional: false
-- name: r-signature.tools.lib
-  version: 2.1.2
-  manager: conda
-  platform: linux-64
-  dependencies:
-    bioconductor-biocgenerics: ''
-    bioconductor-bsgenome: ''
-    bioconductor-genomeinfodb: ''
-    bioconductor-genomicranges: ''
-    bioconductor-iranges: ''
-    bioconductor-summarizedexperiment: ''
-    bioconductor-variantannotation: ''
-    r-base: '>=4.2,<4.3.0a0'
-    r-cluster: ''
-    r-combinat: ''
-    r-doparallel: ''
-    r-dorng: ''
-    r-foreach: ''
-    r-gensa: ''
-    r-ggplot2: ''
-    r-gmp: ''
-    r-limsolve: ''
-    r-lpsolve: ''
-    r-nmf: ''
-    r-nnlm: ''
-    r-nnls: ''
-    r-plyr: ''
-    r-rcircos: ''
-    r-readr: ''
-    r-scales: ''
-  url: https://conda.anaconda.org/umccr/noarch/r-signature.tools.lib-2.1.2-r42_0.tar.bz2
-  hash:
-    md5: 92b33f162f30c3ba60806c3c4e151afe
-    sha256: 443a9afb9f73d83a5411f2722658c55f4444dc648a80c9cfb07bd8e8e6601eac
-  category: main
-  optional: false
-- name: r-sigrap
-  version: 0.1.1
-  manager: conda
-  platform: linux-64
-  dependencies:
-    r-dt: ''
-    r-gpgr: ''
-    r-ggplot2: ''
-    r-readr: ''
-    r-dplyr: ''
-    r-tidyr: ''
-    r-cli: ''
-    r-bedr: ''
-    r-assertthat: ''
-    r-signature.tools.lib: ''
-    bioconductor-variantannotation: ''
-    r-chord: ''
-    bioconductor-mutationalpatterns: ''
-    bioconductor-structuralvariantannotation: ''
-    r-base: '>=4.2,<4.3.0a0'
-  url: https://conda.anaconda.org/umccr/noarch/r-sigrap-0.1.1-r42_0.tar.bz2
-  hash:
-    md5: 63a05ed0b6eb68641a9c530dbb9254c4
-    sha256: 0f9b428ef811561a92abda90f013e1b6bdd4a4966074d9caf7c6b3484d13b800
-  category: main
-  optional: false

From c70435483705a35fbdac148646530f7b7552ab69 Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Sun, 15 Dec 2024 21:20:30 +1100
Subject: [PATCH 02/12] add argparse dep

---
 DESCRIPTION            | 1 +
 R/utils.R              | 6 ++++++
 conda/recipe/meta.yaml | 2 ++
 3 files changed, 9 insertions(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index 6c99e33..4bff187 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -33,6 +33,7 @@ Imports:
     tidyr,
     VariantAnnotation
 Suggests:
+    argparse,
     BSgenome.Hsapiens.UCSC.hg19,
     BSgenome.Hsapiens.UCSC.hg38,
     BSgenome.Hsapiens.1000genomes.hs37d5,
diff --git a/R/utils.R b/R/utils.R
index 8640066..8dfe592 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -35,3 +35,9 @@ pkg_exists <- function(p) {
   assertthat::assert_that(is.character(p))
   nzchar(system.file(package = p))
 }
+
+#' @noRd
+dummy1 <- function() {
+  # Solves R CMD check: Namespaces in Imports field not imported from
+  argparse::ArgumentParser
+}
diff --git a/conda/recipe/meta.yaml b/conda/recipe/meta.yaml
index 7a47c8c..2b455bc 100644
--- a/conda/recipe/meta.yaml
+++ b/conda/recipe/meta.yaml
@@ -17,6 +17,7 @@ requirements:
     - git
   host:
     - r-base ==4.3
+    - r-argparse
     - r-assertthat
     - r-bedr
     - r-chord
@@ -38,6 +39,7 @@ requirements:
     - bioconductor-genomicfeatures
   run:
     - r-base ==4.3
+    - r-argparse
     - r-assertthat
     - r-bedr
     - r-chord

From 004cb52296c6efe9a11b29958e10bb1e8d810b2a Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Sun, 15 Dec 2024 22:00:28 +1100
Subject: [PATCH 03/12] use dplyr::where

---
 R/chord.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/chord.R b/R/chord.R
index dcfeb61..c81b7f3 100644
--- a/R/chord.R
+++ b/R/chord.R
@@ -51,7 +51,7 @@ chord_run <- function(vcf.snv = NULL, vcf.sv = NULL, df.sv = NULL,
       do.bootstrap = TRUE, verbose = FALSE
     ) |>
     dplyr::mutate(
-      dplyr::across(tidyselect::vars_select_helpers$where(is.numeric), round, 3)
+      dplyr::across(dplyr::where(is.numeric), \(x) round(x, 3))
     )
 
   # custom order of prediction cols

From 58faee4cf2607c702777bbdebb122e3c0c459d2e Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Sun, 15 Dec 2024 22:04:32 +1100
Subject: [PATCH 04/12] chord cli: bsgenome required beforehand

---
 .github/workflows/deploy.yaml | 2 +-
 inst/cli/chord.R              | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
index a21aaaa..3706e0f 100644
--- a/.github/workflows/deploy.yaml
+++ b/.github/workflows/deploy.yaml
@@ -4,7 +4,7 @@ on:
   push:
     branches:
       - main
-      - gha-test
+      - docker_update
 env:
   atoken: ${{ secrets.ANACONDA_UPLOAD_TOKEN }}
   recipe_path: conda/recipe
diff --git a/inst/cli/chord.R b/inst/cli/chord.R
index e59e187..3d39e68 100644
--- a/inst/cli/chord.R
+++ b/inst/cli/chord.R
@@ -8,6 +8,8 @@ chord_add_args <- function(subp) {
 
 chord_parse_args <- function(args) {
   cli::cli_h1("Started running CHORD!")
+  # CHORD requires this to be loaded...
+  suppressPackageStartupMessages(library("BSgenome.Hsapiens.UCSC.hg38"))
   res <- sigrap::chord_run(
     vcf.snv = args$snv, vcf.sv = args$sv,
     sample.name = args$sample, outpath = args$out

From 4d421afc81be3867a381a42818bb6339c4881159 Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Mon, 16 Dec 2024 14:05:31 +1100
Subject: [PATCH 05/12] conda recipe: explicitly pull from umccr

---
 conda/recipe/meta.yaml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/conda/recipe/meta.yaml b/conda/recipe/meta.yaml
index 2b455bc..6b42ff7 100644
--- a/conda/recipe/meta.yaml
+++ b/conda/recipe/meta.yaml
@@ -20,7 +20,7 @@ requirements:
     - r-argparse
     - r-assertthat
     - r-bedr
-    - r-chord
+    - umccr::r-chord
     - r-cli
     - r-dplyr
     - r-dt
@@ -29,7 +29,7 @@ requirements:
     - r-jsonlite
     - bioconductor-mutationalpatterns
     - r-readr
-    - r-signature.tools.lib
+    - umccr::r-signature.tools.lib
     - bioconductor-structuralvariantannotation
     - r-tidyr
     - bioconductor-variantannotation
@@ -42,7 +42,7 @@ requirements:
     - r-argparse
     - r-assertthat
     - r-bedr
-    - r-chord
+    - umccr::r-chord
     - r-cli
     - r-dplyr
     - r-dt
@@ -51,7 +51,7 @@ requirements:
     - r-jsonlite
     - bioconductor-mutationalpatterns
     - r-readr
-    - r-signature.tools.lib
+    - umccr::r-signature.tools.lib
     - bioconductor-structuralvariantannotation
     - r-tidyr
     - bioconductor-variantannotation

From afcb79264e4d81d6ba39453dbe28a90a1a927902 Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Mon, 16 Dec 2024 14:05:50 +1100
Subject: [PATCH 06/12] =?UTF-8?q?Bump=20version:=200.1.2.5=20=E2=86=92=200?=
 =?UTF-8?q?.1.2.6?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .bumpversion.toml             | 2 +-
 .github/workflows/deploy.yaml | 2 +-
 DESCRIPTION                   | 2 +-
 conda/env/yaml/sigrap.yaml    | 2 +-
 conda/recipe/meta.yaml        | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.bumpversion.toml b/.bumpversion.toml
index e8855ae..967b135 100644
--- a/.bumpversion.toml
+++ b/.bumpversion.toml
@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "0.1.2.5"
+current_version = "0.1.2.6"
 search = "{current_version}"
 replace = "{new_version}"
 message = "Bump version: {current_version} → {new_version}"
diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
index 3706e0f..82528a2 100644
--- a/.github/workflows/deploy.yaml
+++ b/.github/workflows/deploy.yaml
@@ -10,7 +10,7 @@ env:
   recipe_path: conda/recipe
   env_yaml_path: conda/env/yaml
   env_lock_path: conda/env/lock
-  VERSION: '0.1.2.5' # versioned by bump2version
+  VERSION: '0.1.2.6' # versioned by bump2version
   GDRIVE_CREDENTIALS_DATA: ${{ secrets.GDRIVE_CREDENTIALS_DATA }}
 
 jobs:
diff --git a/DESCRIPTION b/DESCRIPTION
index 4bff187..848b1cc 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: sigrap
 Title: Wrappers for somatic mutation signature analysis tools
-Version: 0.1.2.5
+Version: 0.1.2.6
 Description: Wraps functionality from somatic signature analysis tools.
 Authors@R:
     person(given = "Peter",
diff --git a/conda/env/yaml/sigrap.yaml b/conda/env/yaml/sigrap.yaml
index fe67896..0c5c1c8 100644
--- a/conda/env/yaml/sigrap.yaml
+++ b/conda/env/yaml/sigrap.yaml
@@ -6,4 +6,4 @@ channels:
   - bioconda
 
 dependencies:
-  - r-sigrap ==0.1.2.5 # bump
+  - r-sigrap ==0.1.2.6 # bump
diff --git a/conda/recipe/meta.yaml b/conda/recipe/meta.yaml
index 6b42ff7..593afcf 100644
--- a/conda/recipe/meta.yaml
+++ b/conda/recipe/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: r-sigrap
-  version: 0.1.2.5 # bump2version
+  version: 0.1.2.6 # bump2version
 
 source:
   path: ../..

From 1c2f44b27c354171ed4ea51f97be58f8b04833cb Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Mon, 16 Dec 2024 03:14:33 +0000
Subject: [PATCH 07/12] [bot] Updating conda-lock files (v0.1.2.6)

---
 conda/env/lock/sigrap-linux-64.lock | 10 ++++++----
 conda/env/lock/sigrap-osx-64.lock   | 10 ++++++----
 2 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/conda/env/lock/sigrap-linux-64.lock b/conda/env/lock/sigrap-linux-64.lock
index c50f07e..1a7ffbb 100644
--- a/conda/env/lock/sigrap-linux-64.lock
+++ b/conda/env/lock/sigrap-linux-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 43c2a063684b03e24b59c8ab6b34db39228ef9703d11171e3fad00f696f5e8ff
+# input_hash: 5cc396b4dda3dacd69432eb38cc79aa2b8de30de0049f054ea7523668f18aebd
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38
@@ -139,6 +139,7 @@ https://conda.anaconda.org/conda-forge/linux-64/r-fansi-1.0.6-r43hb1dbf0f_1.cond
 https://conda.anaconda.org/conda-forge/linux-64/r-farver-2.1.2-r43ha18555a_1.conda#85a82a5b78397daf57f002120aed9e3e
 https://conda.anaconda.org/conda-forge/linux-64/r-fastmap-1.2.0-r43ha18555a_1.conda#ac100509c0d93c8dc19e53fb299a48b5
 https://conda.anaconda.org/conda-forge/linux-64/r-filelock-1.0.3-r43hb1dbf0f_1.conda#fed4578af498b0745d546c0161a85032
+https://conda.anaconda.org/conda-forge/noarch/r-findpython-1.0.9-r43hc72bb7e_0.conda#464095877eb683139b054beb4911a805
 https://conda.anaconda.org/conda-forge/noarch/r-formatr-1.14-r43hc72bb7e_2.conda#20d39b48868b55b5335a0c578fdda15b
 https://conda.anaconda.org/conda-forge/linux-64/r-fs-1.6.5-r43h93ab643_0.conda#e5b0af08e3688a1c05b7980e3ec2beae
 https://conda.anaconda.org/conda-forge/noarch/r-futile.options-1.0.1-r43hc72bb7e_1005.conda#57962626cdffa616861bb383076195a2
@@ -193,6 +194,7 @@ https://conda.anaconda.org/bioconda/noarch/bioconductor-genomeinfodbdata-1.2.11-
 https://conda.anaconda.org/bioconda/noarch/bioconductor-matrixgenerics-1.14.0-r43hdfd78af_3.tar.bz2#c79f36cc0cd464874aefd50a700d0079
 https://conda.anaconda.org/bioconda/linux-64/bioconductor-rhtslib-2.4.0-r43ha9d7317_2.tar.bz2#f54f24c26d9e1eb7d582f2806c3b6824
 https://conda.anaconda.org/bioconda/linux-64/bioconductor-s4vectors-0.40.2-r43ha9d7317_2.tar.bz2#6aa465e83dabb7ed5b853519d8a334e4
+https://conda.anaconda.org/conda-forge/noarch/r-argparse-2.2.4-r43hc72bb7e_0.conda#f71b07c64727e11c9b2605538be2b062
 https://conda.anaconda.org/conda-forge/linux-64/r-askpass-1.2.1-r43h2b5f3a1_0.conda#8ccad521ab24a75928dd54af1e42632d
 https://conda.anaconda.org/conda-forge/noarch/r-bibtex-0.5.1-r43hc72bb7e_2.conda#4514eabc038859b5ae5e119208b23f6d
 https://conda.anaconda.org/conda-forge/linux-64/r-bit64-4.5.2-r43h2b5f3a1_0.conda#f10def39b10f9c7c337a11ee94d8cb6c
@@ -294,11 +296,11 @@ https://conda.anaconda.org/bioconda/noarch/bioconductor-biomart-2.58.0-r43hdfd78
 https://conda.anaconda.org/bioconda/noarch/bioconductor-bsgenome-1.70.1-r43hdfd78af_0.tar.bz2#f512b74569fb95a2903444ce684a49f8
 https://conda.anaconda.org/bioconda/noarch/bioconductor-bsgenome.hsapiens.ucsc.hg38-1.4.5-r43hdfd78af_2.tar.bz2#3b72021dfa812d6e93f3a88d89ff788f
 https://conda.anaconda.org/bioconda/noarch/bioconductor-genomicfeatures-1.54.1-r43hdfd78af_0.tar.bz2#445ea419486180673fffc192b5fe8edb
-https://conda.anaconda.org/umccr/noarch/r-mutsigextractor-1.25-r43_0.tar.bz2#f0f801cf6db941ab8e2edf88b921f3c6
+https://conda.anaconda.org/umccr/noarch/r-mutsigextractor-1.29-r43_0.tar.bz2#fbffe55f402335e73301b46604225bcf
 https://conda.anaconda.org/bioconda/noarch/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene-3.18.0-r43hdfd78af_0.tar.bz2#ce94f05d0b311a6518e8bc9e49aac303
 https://conda.anaconda.org/bioconda/linux-64/bioconductor-variantannotation-1.48.1-r43ha9d7317_1.tar.bz2#01c0b8e76583c3f8872e3181dd06ffbd
-https://conda.anaconda.org/umccr/noarch/r-chord-2.00-r43_0.tar.bz2#72f23d2a3f89de28c3bc40d6e24c348c
+https://conda.anaconda.org/umccr/noarch/r-chord-2.03-r43_0.tar.bz2#57d33e0a17838ee6ef05d29f3c1bbf28
 https://conda.anaconda.org/bioconda/noarch/bioconductor-mutationalpatterns-3.12.0-r43hdfd78af_0.tar.bz2#d22030798f7d464ddb092e4651625210
 https://conda.anaconda.org/bioconda/noarch/bioconductor-structuralvariantannotation-1.18.0-r43hdfd78af_0.tar.bz2#5a341f13b9fd453b9a45a00550f3531d
 https://conda.anaconda.org/umccr/noarch/r-signature.tools.lib-2.1.2-r43_0.tar.bz2#b7980eb46ec349d6446772f78935cf3f
-https://conda.anaconda.org/umccr/noarch/r-sigrap-0.1.2.5-r43_0.tar.bz2#98d69308cf49d04639a8b7c8957cfc0a
+https://conda.anaconda.org/umccr/noarch/r-sigrap-0.1.2.6-r43_0.tar.bz2#af3cc92f5354b1fda7de2fb65985a1d9
diff --git a/conda/env/lock/sigrap-osx-64.lock b/conda/env/lock/sigrap-osx-64.lock
index c01ff6b..f8abaf3 100644
--- a/conda/env/lock/sigrap-osx-64.lock
+++ b/conda/env/lock/sigrap-osx-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: osx-64
-# input_hash: e598eeee24431572bc814509bcebcd99b70364420d546a24d5a58a2249479dd7
+# input_hash: 90b7e0d0d177971f4bb7a8faba7064d3f02a82d3ebf460867b6629216dc463f4
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38
 https://conda.anaconda.org/conda-forge/osx-64/ca-certificates-2024.12.14-h8857fd0_0.conda#b7b887091c99ed2e74845e75e9128410
@@ -138,6 +138,7 @@ https://conda.anaconda.org/conda-forge/osx-64/r-fansi-1.0.6-r43h6b9d099_1.conda#
 https://conda.anaconda.org/conda-forge/osx-64/r-farver-2.1.2-r43h25d921d_1.conda#bce811aa3bd9b1e69a56d788276f315e
 https://conda.anaconda.org/conda-forge/osx-64/r-fastmap-1.2.0-r43h25d921d_1.conda#a4bf96516bd9184f1bad907c812e01ad
 https://conda.anaconda.org/conda-forge/osx-64/r-filelock-1.0.3-r43h6b9d099_1.conda#73bf4c37dc4ad418a837ba6eadf52b4f
+https://conda.anaconda.org/conda-forge/noarch/r-findpython-1.0.9-r43hc72bb7e_0.conda#464095877eb683139b054beb4911a805
 https://conda.anaconda.org/conda-forge/noarch/r-formatr-1.14-r43hc72bb7e_2.conda#20d39b48868b55b5335a0c578fdda15b
 https://conda.anaconda.org/conda-forge/osx-64/r-fs-1.6.5-r43hb79fae8_0.conda#d562f43ee4edd28045255a4f943e19b1
 https://conda.anaconda.org/conda-forge/noarch/r-futile.options-1.0.1-r43hc72bb7e_1005.conda#57962626cdffa616861bb383076195a2
@@ -192,6 +193,7 @@ https://conda.anaconda.org/bioconda/noarch/bioconductor-genomeinfodbdata-1.2.11-
 https://conda.anaconda.org/bioconda/noarch/bioconductor-matrixgenerics-1.14.0-r43hdfd78af_3.tar.bz2#c79f36cc0cd464874aefd50a700d0079
 https://conda.anaconda.org/bioconda/osx-64/bioconductor-rhtslib-2.4.0-r43h4c50009_2.tar.bz2#87acafb6a63e0426c27c759ba2dc097b
 https://conda.anaconda.org/bioconda/osx-64/bioconductor-s4vectors-0.40.2-r43h4c50009_2.tar.bz2#935e0479f88ba1893d264e95ff235b27
+https://conda.anaconda.org/conda-forge/noarch/r-argparse-2.2.4-r43hc72bb7e_0.conda#f71b07c64727e11c9b2605538be2b062
 https://conda.anaconda.org/conda-forge/osx-64/r-askpass-1.2.1-r43h199b6f9_0.conda#4a4d49b04c9be27164b6320476be9a2f
 https://conda.anaconda.org/conda-forge/noarch/r-bibtex-0.5.1-r43hc72bb7e_2.conda#4514eabc038859b5ae5e119208b23f6d
 https://conda.anaconda.org/conda-forge/osx-64/r-bit64-4.5.2-r43h199b6f9_0.conda#2970c5ac606947b15875f3cca84d483a
@@ -293,11 +295,11 @@ https://conda.anaconda.org/bioconda/noarch/bioconductor-biomart-2.58.0-r43hdfd78
 https://conda.anaconda.org/bioconda/noarch/bioconductor-bsgenome-1.70.1-r43hdfd78af_0.tar.bz2#f512b74569fb95a2903444ce684a49f8
 https://conda.anaconda.org/bioconda/noarch/bioconductor-bsgenome.hsapiens.ucsc.hg38-1.4.5-r43hdfd78af_2.tar.bz2#3b72021dfa812d6e93f3a88d89ff788f
 https://conda.anaconda.org/bioconda/noarch/bioconductor-genomicfeatures-1.54.1-r43hdfd78af_0.tar.bz2#445ea419486180673fffc192b5fe8edb
-https://conda.anaconda.org/umccr/noarch/r-mutsigextractor-1.25-r43_0.tar.bz2#f0f801cf6db941ab8e2edf88b921f3c6
+https://conda.anaconda.org/umccr/noarch/r-mutsigextractor-1.29-r43_0.tar.bz2#fbffe55f402335e73301b46604225bcf
 https://conda.anaconda.org/bioconda/noarch/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene-3.18.0-r43hdfd78af_0.tar.bz2#ce94f05d0b311a6518e8bc9e49aac303
 https://conda.anaconda.org/bioconda/osx-64/bioconductor-variantannotation-1.48.1-r43h4c50009_1.tar.bz2#4bc1f791804daa0570cd35a63ca0a268
-https://conda.anaconda.org/umccr/noarch/r-chord-2.00-r43_0.tar.bz2#72f23d2a3f89de28c3bc40d6e24c348c
+https://conda.anaconda.org/umccr/noarch/r-chord-2.03-r43_0.tar.bz2#57d33e0a17838ee6ef05d29f3c1bbf28
 https://conda.anaconda.org/bioconda/noarch/bioconductor-mutationalpatterns-3.12.0-r43hdfd78af_0.tar.bz2#d22030798f7d464ddb092e4651625210
 https://conda.anaconda.org/bioconda/noarch/bioconductor-structuralvariantannotation-1.18.0-r43hdfd78af_0.tar.bz2#5a341f13b9fd453b9a45a00550f3531d
 https://conda.anaconda.org/umccr/noarch/r-signature.tools.lib-2.1.2-r43_0.tar.bz2#b7980eb46ec349d6446772f78935cf3f
-https://conda.anaconda.org/umccr/noarch/r-sigrap-0.1.2.5-r43_0.tar.bz2#98d69308cf49d04639a8b7c8957cfc0a
+https://conda.anaconda.org/umccr/noarch/r-sigrap-0.1.2.6-r43_0.tar.bz2#af3cc92f5354b1fda7de2fb65985a1d9

From c9e9e7ffdbf61f91232fbe757f64aec875d6fa23 Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Mon, 16 Dec 2024 15:01:22 +1100
Subject: [PATCH 08/12] chord cli: bsgenome load not recognised anyhow..

---
 inst/cli/chord.R | 2 --
 1 file changed, 2 deletions(-)

diff --git a/inst/cli/chord.R b/inst/cli/chord.R
index 3d39e68..e59e187 100644
--- a/inst/cli/chord.R
+++ b/inst/cli/chord.R
@@ -8,8 +8,6 @@ chord_add_args <- function(subp) {
 
 chord_parse_args <- function(args) {
   cli::cli_h1("Started running CHORD!")
-  # CHORD requires this to be loaded...
-  suppressPackageStartupMessages(library("BSgenome.Hsapiens.UCSC.hg38"))
   res <- sigrap::chord_run(
     vcf.snv = args$snv, vcf.sv = args$sv,
     sample.name = args$sample, outpath = args$out

From f2c3bd017d731e9bdeb6244b6927691852ab9999 Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Mon, 16 Dec 2024 15:01:39 +1100
Subject: [PATCH 09/12] Dockerfile: move LABEL to stage 2

---
 Dockerfile | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 8d6304e..499c01a 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,11 +1,4 @@
 FROM ubuntu:20.04
-LABEL org.opencontainers.image.authors="peterdiakumis@gmail.com" \
-      org.opencontainers.image.description="Wrappers for somatic mutation signature analysis tools" \
-      org.opencontainers.image.source="https://github.com/umccr/sigrap" \
-      org.opencontainers.image.url="https://github.com/umccr/sigrap" \
-      org.opencontainers.image.documentation="https://umccr.github.io/sigrap" \
-      org.opencontainers.image.licenses="MIT"
-
 ARG MINIF="miniforge"
 ARG MINIF_VERSION="24.11.0-1"
 ARG MINIF_URL="https://github.com/conda-forge/${MINIF}/releases/download/${MINIF_VERSION}/Miniforge3-${MINIF_VERSION}-Linux-x86_64.sh"
@@ -29,6 +22,12 @@ RUN conda clean --all --force-pkgs-dirs --yes
 
 # Now copy env to smaller image
 FROM quay.io/bioconda/base-glibc-debian-bash:3.1
+LABEL org.opencontainers.image.authors="peterdiakumis@gmail.com" \
+      org.opencontainers.image.description="Wrappers for somatic mutation signature analysis tools" \
+      org.opencontainers.image.source="https://github.com/umccr/sigrap" \
+      org.opencontainers.image.url="https://github.com/umccr/sigrap" \
+      org.opencontainers.image.documentation="https://umccr.github.io/sigrap" \
+      org.opencontainers.image.licenses="MIT"
 
 COPY --from=0 "/opt/miniforge/envs/" "/opt/miniforge/envs/"
 

From 0a240e5df7253b71dc3f128733a7e57fd884cbe4 Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Mon, 16 Dec 2024 15:01:48 +1100
Subject: [PATCH 10/12] =?UTF-8?q?Bump=20version:=200.1.2.6=20=E2=86=92=200?=
 =?UTF-8?q?.1.2.7?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .bumpversion.toml             | 2 +-
 .github/workflows/deploy.yaml | 2 +-
 DESCRIPTION                   | 2 +-
 conda/env/yaml/sigrap.yaml    | 2 +-
 conda/recipe/meta.yaml        | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.bumpversion.toml b/.bumpversion.toml
index 967b135..d9b29db 100644
--- a/.bumpversion.toml
+++ b/.bumpversion.toml
@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "0.1.2.6"
+current_version = "0.1.2.7"
 search = "{current_version}"
 replace = "{new_version}"
 message = "Bump version: {current_version} → {new_version}"
diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
index 82528a2..03a6b1f 100644
--- a/.github/workflows/deploy.yaml
+++ b/.github/workflows/deploy.yaml
@@ -10,7 +10,7 @@ env:
   recipe_path: conda/recipe
   env_yaml_path: conda/env/yaml
   env_lock_path: conda/env/lock
-  VERSION: '0.1.2.6' # versioned by bump2version
+  VERSION: '0.1.2.7' # versioned by bump2version
   GDRIVE_CREDENTIALS_DATA: ${{ secrets.GDRIVE_CREDENTIALS_DATA }}
 
 jobs:
diff --git a/DESCRIPTION b/DESCRIPTION
index 848b1cc..313c41e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: sigrap
 Title: Wrappers for somatic mutation signature analysis tools
-Version: 0.1.2.6
+Version: 0.1.2.7
 Description: Wraps functionality from somatic signature analysis tools.
 Authors@R:
     person(given = "Peter",
diff --git a/conda/env/yaml/sigrap.yaml b/conda/env/yaml/sigrap.yaml
index 0c5c1c8..1808a87 100644
--- a/conda/env/yaml/sigrap.yaml
+++ b/conda/env/yaml/sigrap.yaml
@@ -6,4 +6,4 @@ channels:
   - bioconda
 
 dependencies:
-  - r-sigrap ==0.1.2.6 # bump
+  - r-sigrap ==0.1.2.7 # bump
diff --git a/conda/recipe/meta.yaml b/conda/recipe/meta.yaml
index 593afcf..a74f84b 100644
--- a/conda/recipe/meta.yaml
+++ b/conda/recipe/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: r-sigrap
-  version: 0.1.2.6 # bump2version
+  version: 0.1.2.7 # bump2version
 
 source:
   path: ../..

From f4e69511d29097497c2b3dcc29b8c2257bd184d3 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Mon, 16 Dec 2024 04:09:35 +0000
Subject: [PATCH 11/12] [bot] Updating conda-lock files (v0.1.2.7)

---
 conda/env/lock/sigrap-linux-64.lock | 4 ++--
 conda/env/lock/sigrap-osx-64.lock   | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/conda/env/lock/sigrap-linux-64.lock b/conda/env/lock/sigrap-linux-64.lock
index 1a7ffbb..38f5828 100644
--- a/conda/env/lock/sigrap-linux-64.lock
+++ b/conda/env/lock/sigrap-linux-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 5cc396b4dda3dacd69432eb38cc79aa2b8de30de0049f054ea7523668f18aebd
+# input_hash: 2bcaf289708f6d7f2c7ad5ba519bf9956534718db38d81d50f589f07c5be4c18
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38
@@ -303,4 +303,4 @@ https://conda.anaconda.org/umccr/noarch/r-chord-2.03-r43_0.tar.bz2#57d33e0a17838
 https://conda.anaconda.org/bioconda/noarch/bioconductor-mutationalpatterns-3.12.0-r43hdfd78af_0.tar.bz2#d22030798f7d464ddb092e4651625210
 https://conda.anaconda.org/bioconda/noarch/bioconductor-structuralvariantannotation-1.18.0-r43hdfd78af_0.tar.bz2#5a341f13b9fd453b9a45a00550f3531d
 https://conda.anaconda.org/umccr/noarch/r-signature.tools.lib-2.1.2-r43_0.tar.bz2#b7980eb46ec349d6446772f78935cf3f
-https://conda.anaconda.org/umccr/noarch/r-sigrap-0.1.2.6-r43_0.tar.bz2#af3cc92f5354b1fda7de2fb65985a1d9
+https://conda.anaconda.org/umccr/noarch/r-sigrap-0.1.2.7-r43_0.tar.bz2#dd4ea149cbacb902c4d3e8c12d0de8d2
diff --git a/conda/env/lock/sigrap-osx-64.lock b/conda/env/lock/sigrap-osx-64.lock
index f8abaf3..49bab11 100644
--- a/conda/env/lock/sigrap-osx-64.lock
+++ b/conda/env/lock/sigrap-osx-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: osx-64
-# input_hash: 90b7e0d0d177971f4bb7a8faba7064d3f02a82d3ebf460867b6629216dc463f4
+# input_hash: ff62aed3ab79d16cfe597c338eb3333226f72c174a31ccbe109534b4014c8cf7
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38
 https://conda.anaconda.org/conda-forge/osx-64/ca-certificates-2024.12.14-h8857fd0_0.conda#b7b887091c99ed2e74845e75e9128410
@@ -302,4 +302,4 @@ https://conda.anaconda.org/umccr/noarch/r-chord-2.03-r43_0.tar.bz2#57d33e0a17838
 https://conda.anaconda.org/bioconda/noarch/bioconductor-mutationalpatterns-3.12.0-r43hdfd78af_0.tar.bz2#d22030798f7d464ddb092e4651625210
 https://conda.anaconda.org/bioconda/noarch/bioconductor-structuralvariantannotation-1.18.0-r43hdfd78af_0.tar.bz2#5a341f13b9fd453b9a45a00550f3531d
 https://conda.anaconda.org/umccr/noarch/r-signature.tools.lib-2.1.2-r43_0.tar.bz2#b7980eb46ec349d6446772f78935cf3f
-https://conda.anaconda.org/umccr/noarch/r-sigrap-0.1.2.6-r43_0.tar.bz2#af3cc92f5354b1fda7de2fb65985a1d9
+https://conda.anaconda.org/umccr/noarch/r-sigrap-0.1.2.7-r43_0.tar.bz2#dd4ea149cbacb902c4d3e8c12d0de8d2

From dce194309039000d773c5b5a9d216d2cd9caba70 Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Mon, 16 Dec 2024 18:29:06 +1100
Subject: [PATCH 12/12] gha: remove testing branch

---
 .github/workflows/deploy.yaml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
index 03a6b1f..1f04434 100644
--- a/.github/workflows/deploy.yaml
+++ b/.github/workflows/deploy.yaml
@@ -4,7 +4,6 @@ on:
   push:
     branches:
       - main
-      - docker_update
 env:
   atoken: ${{ secrets.ANACONDA_UPLOAD_TOKEN }}
   recipe_path: conda/recipe