Merge branch 'bundle_update_2023' of github.com:sigven/pcgr into bund…

…le_update_2023

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.4.1.9011
+current_version = 1.4.1.9013
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<dev>\d+))?

.github/workflows/build_conda_recipes.yaml

@@ -10,7 +10,7 @@ env:
   recipe_path: conda/recipe
   env_yml_path: conda/env/yml
   env_lock_path: conda/env/lock
-  VERSION: '1.4.1.9011' # versioned by bump2version
+  VERSION: '1.4.1.9013' # versioned by bump2version
 jobs:
   build_pcgrr_conda_pkg:
     # When merging to one of the branches above and the commit message matches

Dockerfile

@@ -23,6 +23,10 @@ RUN mamba create -n pcgr --file ${PCGR_CONDA_ENV_DIR}/pcgr-linux-64.lock
 RUN mamba create -n pcgrr --file ${PCGR_CONDA_ENV_DIR}/pcgrr-linux-64.lock
 RUN mamba clean --all --force-pkgs-dirs --yes
 
+FROM quay.io/bioconda/base-glibc-busybox-bash:3.1
+
+COPY --from=0 /opt/mambaforge/envs/ /opt/mambaforge/envs/
+
 ARG PCGR_ENV_NAME="pcgr"
 # pcgr env is activated by default
 ENV PATH="/opt/mambaforge/envs/${PCGR_ENV_NAME}/bin:${PATH}"

conda/env/lock/pcgr-osx-64.lock

@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: osx-64
-# input_hash: fc804ae26192be0eed33e530a6374893240ebea9dda6be796e65ca98ccb7bb28
+# input_hash: 72a8d5fb1d6bdb42fa3a15e108f108eb30a7bd3cbccd6f25e3d210ea17b3b062
 @EXPLICIT
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@@ -51,7 +51,7 @@ https://conda.anaconda.org/conda-forge/noarch/perl-extutils-makemaker-7.70-pl532
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-https://conda.anaconda.org/bioconda/noarch/perl-getopt-long-2.54-pl5321hdfd78af_0.tar.bz2#3c301587f1b58f90ecd06aeee46f7cc3
+https://conda.anaconda.org/bioconda/noarch/perl-getopt-long-2.58-pl5321hdfd78af_0.tar.bz2#10469a3defbd6dbab17d3d10dd6fd828
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@@ -212,7 +212,7 @@ https://conda.anaconda.org/bioconda/noarch/perl-libwww-perl-6.67-pl5321hdfd78af_
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-https://conda.anaconda.org/pcgr/noarch/pcgr-1.4.1.9011-py_0.tar.bz2#5284e4cd5f0c43faf8d8f835fd361923
+https://conda.anaconda.org/pcgr/noarch/pcgr-1.4.1.9013-py_0.tar.bz2#d29af9fb0700366626e1691b2211e78d
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conda/env/lock/pcgrr-linux-64.lock

@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 1d20d9756d339e2d9c6ee29475b0f2714d9c2e9503dbe58c363e7bcc02910226
+# input_hash: 1865f68da5c458ecf0985c98f4c6fbac8fd9a7e0f970dd22d81c876dd171eb22
 @EXPLICIT
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@@ -13,45 +13,40 @@ https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77
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-https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-13.2.0-hceb6213_107.conda#2b409e9645fb3d69115d04496d1219cc
-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-hc0a3c3a_7.conda#53ebd4c833fa01cb2c6353e99f905406
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 https://conda.anaconda.org/conda-forge/linux-64/quarto-1.4.550-ha770c72_1.conda#b7b89be76bcdab239f7956e5fc2727ab
 https://conda.anaconda.org/conda-forge/linux-64/tktable-2.10-h0c5db8f_5.conda#9464044754ea25557a9c93f0327d90a6
@@ -324,5 +324,5 @@ https://conda.anaconda.org/bioconda/noarch/bioconductor-bsgenome.hsapiens.ucsc.h
 https://conda.anaconda.org/bioconda/noarch/bioconductor-genomicfeatures-1.54.1-r43hdfd78af_0.tar.bz2#445ea419486180673fffc192b5fe8edb
 https://conda.anaconda.org/bioconda/linux-64/bioconductor-variantannotation-1.48.1-r43ha9d7317_1.tar.bz2#01c0b8e76583c3f8872e3181dd06ffbd
 https://conda.anaconda.org/bioconda/noarch/bioconductor-mutationalpatterns-3.12.0-r43hdfd78af_0.tar.bz2#d22030798f7d464ddb092e4651625210
-https://conda.anaconda.org/pcgr/noarch/r-pcgrr-1.4.1.9011-r43_0.tar.bz2#fe788957e77c93f5e3a905ccbde73088
-https://conda.anaconda.org/pcgr/noarch/r-cpsr-1.0.1.9009-r43_0.tar.bz2#47d1b24261396022fe4d383eb79fd868
+https://conda.anaconda.org/pcgr/noarch/r-pcgrr-1.4.1.9013-r43_0.tar.bz2#8337bbc9d94d0268b9a3dab4be5eec74
+https://conda.anaconda.org/pcgr/noarch/r-cpsr-1.0.1.9012-r43_0.tar.bz2#246a894396a58bc6a09dfaa6ef297b35

conda/env/lock/pcgrr-osx-64.lock

@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: osx-64
-# input_hash: 68be71b1703e63f86332f69cb56e1691f3d99ae7b7995c7ddc5727818a812426
+# input_hash: 2a84fcf28c9b61aff3aa698b7910da7345554e64f576f2e8f837c05bc4b0b8d6
 @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/bzip2-1.0.8-h10d778d_5.conda#6097a6ca9ada32699b5fc4312dd6ef18
@@ -68,7 +68,7 @@ https://conda.anaconda.org/conda-forge/osx-64/freetype-2.12.1-h60636b9_2.conda#2
 https://conda.anaconda.org/conda-forge/osx-64/libcurl-8.8.0-hf9fcc65_0.conda#276894efcbca23aa674e280e90bc5673
 https://conda.anaconda.org/conda-forge/osx-64/libgfortran-5.0.0-13_2_0_h97931a8_3.conda#0b6e23a012ee7a9a5f6b244f5a92c1d5
 https://conda.anaconda.org/conda-forge/osx-64/libglib-2.80.2-h0f68cf7_0.conda#b3947a5dfc6c63b1f479268e75643090
-https://conda.anaconda.org/conda-forge/osx-64/libllvm18-18.1.7-hd5e122f_0.conda#bc138883a1fbb4d446b8a5565b1c1bc0
+https://conda.anaconda.org/conda-forge/osx-64/libllvm18-18.1.7-h9ce406d_1.conda#09c18ebe4f7061a38eae1b95d487942b
 https://conda.anaconda.org/conda-forge/osx-64/libtiff-4.6.0-h129831d_3.conda#568593071d2e6cea7b5fc1f75bfa10ca
 https://conda.anaconda.org/conda-forge/osx-64/mpfr-4.2.1-h4f6b447_1.conda#b90df08f0deb2f58631447c1462c92a7
 https://conda.anaconda.org/conda-forge/osx-64/python-3.12.3-h1411813_0_cpython.conda#df1448ec6cbf8eceb03d29003cf72ae6
@@ -80,7 +80,7 @@ https://conda.anaconda.org/conda-forge/osx-64/fontconfig-2.14.2-h5bb23bf_0.conda
 https://conda.anaconda.org/conda-forge/osx-64/ld64_osx-64-711-had5d0d3_0.conda#cb63e1d1e11a1fffad54333330486ddd
 https://conda.anaconda.org/conda-forge/osx-64/libclang-cpp18.1-18.1.7-default_h4c8afb6_0.conda#41f0f6a496dfda7a7731005f9120fc08
 https://conda.anaconda.org/conda-forge/osx-64/libopenblas-0.3.27-openmp_hfef2a42_0.conda#00237c9c7f2cb6725fe2960680a6e225
-https://conda.anaconda.org/conda-forge/osx-64/llvm-tools-18.1.7-hd5e122f_0.conda#c8f3c58497f799f4d617282903d1cab0
+https://conda.anaconda.org/conda-forge/osx-64/llvm-tools-18.1.7-h9ce406d_1.conda#e830f2650a4cabd34013b0d398ff501c
 https://conda.anaconda.org/conda-forge/osx-64/mpc-1.3.1-h81bd1dd_0.conda#c752c0eb6c250919559172c011e5f65b
 https://conda.anaconda.org/conda-forge/osx-64/pyyaml-6.0.1-py312h104f124_1.conda#260ed90aaf06061edabd7209638cf03b
 https://conda.anaconda.org/conda-forge/noarch/setuptools-70.0.0-pyhd8ed1ab_0.conda#c8ddb4f34a208df4dd42509a0f6a1c89
@@ -318,5 +318,5 @@ https://conda.anaconda.org/bioconda/noarch/bioconductor-bsgenome.hsapiens.ucsc.h
 https://conda.anaconda.org/bioconda/noarch/bioconductor-genomicfeatures-1.54.1-r43hdfd78af_0.tar.bz2#445ea419486180673fffc192b5fe8edb
 https://conda.anaconda.org/bioconda/osx-64/bioconductor-variantannotation-1.48.1-r43h4c50009_1.tar.bz2#4bc1f791804daa0570cd35a63ca0a268
 https://conda.anaconda.org/bioconda/noarch/bioconductor-mutationalpatterns-3.12.0-r43hdfd78af_0.tar.bz2#d22030798f7d464ddb092e4651625210
-https://conda.anaconda.org/pcgr/noarch/r-pcgrr-1.4.1.9011-r43_0.tar.bz2#fe788957e77c93f5e3a905ccbde73088
-https://conda.anaconda.org/pcgr/noarch/r-cpsr-1.0.1.9009-r43_0.tar.bz2#47d1b24261396022fe4d383eb79fd868
+https://conda.anaconda.org/pcgr/noarch/r-pcgrr-1.4.1.9013-r43_0.tar.bz2#8337bbc9d94d0268b9a3dab4be5eec74
+https://conda.anaconda.org/pcgr/noarch/r-cpsr-1.0.1.9012-r43_0.tar.bz2#246a894396a58bc6a09dfaa6ef297b35

conda/env/yml/pcgr.yml

@@ -6,7 +6,7 @@ channels:
   - conda-forge
 
 dependencies:
-  - pcgr::pcgr ==1.4.1.9011 # versioned by bump2version
+  - pcgr::pcgr ==1.4.1.9013 # versioned by bump2version
   - bedtools
   - bcftools
   - cyvcf2

conda/env/yml/pcgrr.yml

@@ -7,7 +7,7 @@ channels:
 
 dependencies:
   - python
-  - pcgr::r-pcgrr ==1.4.1.9011 # versioned by bump2version
+  - pcgr::r-pcgrr ==1.4.1.9013 # versioned by bump2version
   - pcgr::r-cpsr
   - r-argparse
   - bioconductor-bsgenome.hsapiens.ucsc.hg38

conda/env/yml/pkgdown.yml

@@ -4,7 +4,7 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - pcgr::r-pcgrr ==1.4.1.9011 # versioned by bump2version
+  - pcgr::r-pcgrr ==1.4.1.9013 # versioned by bump2version
   - r-pkgdown
   - r-readr
   - pandoc

conda/recipe/pcgr/meta.yaml

@@ -1,6 +1,6 @@
 package:
   name: pcgr
-  version: 1.4.1.9011 # versioned by bump2version
+  version: 1.4.1.9013 # versioned by bump2version
 
 source:
   path: ../../..