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

…le_update_2023
sigven · Jun 19, 2024 · 2ca3293 · 2ca3293
2 parents b8fdbfe + 3921fe2
commit 2ca3293
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.4.1.9015
+current_version = 1.4.1.9016
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\.(?P<dev>\d+))?

diff --git a/.github/workflows/build_conda_recipes.yaml b/.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: '1.4.1.9015' # versioned by bump2version
+  VERSION: '1.4.1.9016' # versioned by bump2version
 jobs:
   build_pcgrr_conda_pkg:
     # When merging to one of the branches above and the commit message matches

diff --git a/conda/env/lock/pcgr-linux-64.lock b/conda/env/lock/pcgr-linux-64.lock
@@ -1,11 +1,11 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 604b826168acef5afd9f41254638db0eb40189de724d845bfaf3d472e8e9868b
+# input_hash: df6430571fbb82456261636d686c3f4ba3929721b191f9a52ff5744b86e20f32
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
 https://conda.anaconda.org/bioconda/linux-64/blast-legacy-2.2.26-h9ee0642_3.tar.bz2#b7fe67ef984501e8089a142f1f58ab2f
 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.6.2-hbcca054_0.conda#847c3c2905cc467cea52c24f9cfa8080
-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_6.conda#deae631c9a587b4cfd33aa082491329b
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74
 https://conda.anaconda.org/conda-forge/linux-64/libgfortran-3.0.0-1.tar.bz2#d7c7e92a8ccc518709474dd3eda896b9
 https://conda.anaconda.org/conda-forge/linux-64/pandoc-3.2-ha770c72_0.conda#8c924f0b7f3e064b1c954a08e7c32fba
 https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-4_cp312.conda#dccc2d142812964fcc6abdc97b672dff
@@ -201,7 +201,7 @@ https://conda.anaconda.org/bioconda/linux-64/pybedtools-0.10.0-py312ha1f7cf2_1.t
 https://conda.anaconda.org/conda-forge/linux-64/scipy-1.13.1-py312hc2bc53b_0.conda#864b2399a9c998e17d1a9a4e0c601285
 https://conda.anaconda.org/bioconda/noarch/vcf2maf-umccr-1.6.21.20230511-hdfd78af_0.tar.bz2#ec3a03df0bce17c35b2a2d1436c718ea
 https://conda.anaconda.org/bioconda/linux-64/blast-2.15.0-pl5321h6f7f691_1.tar.bz2#f7e6a87317b5d00469d39a2d1ef2698f
-https://conda.anaconda.org/pcgr/noarch/pcgr-1.4.1.9015-py_0.tar.bz2#716bbfbd7c230f4b15c10ced27f129f6
+https://conda.anaconda.org/pcgr/noarch/pcgr-1.4.1.9016-py_0.tar.bz2#082878c9f25e30fa6f820267654a1798
 https://conda.anaconda.org/bioconda/noarch/perl-http-message-6.36-pl5321hdfd78af_0.tar.bz2#a213d1308ffa8e0789996ae6ecda98ae
 https://conda.anaconda.org/bioconda/noarch/perl-net-http-6.22-pl5321hdfd78af_0.tar.bz2#f3b44f2b9932c3def346e6ad9aabe43d
 https://conda.anaconda.org/bioconda/noarch/perl-www-robotrules-6.02-pl5321hdfd78af_4.tar.bz2#8305f4ed6306b1125a8c8caf2f05aec8

diff --git a/conda/env/lock/pcgr-osx-64.lock b/conda/env/lock/pcgr-osx-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: osx-64
-# input_hash: 868d8049e9e96218f56045cf578efae06049cf13291a7b5d4c5534394e2bd9ab
+# input_hash: 08008428608a5260b88f62558e2503ae382a060819418ecc0280e3fcd7741505
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/osx-64/argtable2-2.13-h10d778d_1004.conda#7ebcbc431363dfbf9ae25e6a7205d414
 https://conda.anaconda.org/conda-forge/osx-64/bzip2-1.0.8-h10d778d_5.conda#6097a6ca9ada32699b5fc4312dd6ef18
@@ -212,7 +212,7 @@ https://conda.anaconda.org/bioconda/noarch/perl-libwww-perl-6.67-pl5321hdfd78af_
 https://conda.anaconda.org/bioconda/osx-64/pybedtools-0.10.0-py310h0b3aad1_1.tar.bz2#ade72e96268dba2ca0ba1f728dfe4c43
 https://conda.anaconda.org/conda-forge/osx-64/scipy-1.13.1-py310h35d8cac_0.conda#97b362043d6a1dd28e7da5fbf277594d
 https://conda.anaconda.org/conda-forge/osx-64/compiler-rt-12.0.1-he01351e_0.tar.bz2#aa2cb3794dae4a09f19c3b7169b5df1f
-https://conda.anaconda.org/pcgr/noarch/pcgr-1.4.1.9015-py_0.tar.bz2#716bbfbd7c230f4b15c10ced27f129f6
+https://conda.anaconda.org/pcgr/noarch/pcgr-1.4.1.9016-py_0.tar.bz2#082878c9f25e30fa6f820267654a1798
 https://conda.anaconda.org/bioconda/noarch/perl-xml-dom-1.46-pl5321hdfd78af_1.tar.bz2#45b7ce435727456727f45b3e2121b23b
 https://conda.anaconda.org/bioconda/osx-64/t-coffee-12.00.7fb08c2-h26a2512_0.tar.bz2#fe6f3532da0e9d3868b58ecd07f33744
 https://conda.anaconda.org/bioconda/noarch/vcf2tsvpy-0.6.1-pyhda70652_0.tar.bz2#cb9612a58cefb7e2a144c759027c0a94

diff --git a/conda/env/lock/pcgrr-linux-64.lock b/conda/env/lock/pcgrr-linux-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: eec851db1d851d8a92140ca2fd5e55a7667dd89ac9aecdfd8ed3d26586e713ef
+# input_hash: a01aaf6b50f52e080b7dbfd938e3de505ffea44c78b046868dd807bfa5d09245
 @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
@@ -12,7 +12,7 @@ https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed3
 https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb
 https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_2.conda#cbbe59391138ea5ad3658c76912e147f
 https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-2.6.32-he073ed8_17.conda#d731b543793afc0433c4fd593e693fce
-https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_6.conda#deae631c9a587b4cfd33aa082491329b
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-hf3520f5_7.conda#b80f2f396ca2c28b8c14c437a4ed1e74
 https://conda.anaconda.org/conda-forge/linux-64/pandoc-3.1.11.1-ha770c72_0.conda#0e2f14aff42adf4675bcd5335d644a5f
 https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.12-4_cp312.conda#dccc2d142812964fcc6abdc97b672dff
 https://conda.anaconda.org/conda-forge/noarch/tzdata-2024a-h0c530f3_0.conda#161081fc7cec0bfda0d86d7cb595f8d8
@@ -22,7 +22,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_10.conda
 https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-13.2.0-hdb50d1a_110.conda#122bd91ac51b5c71fb3aec797f1b96b3
 https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.12-he073ed8_17.conda#595db67e32b276298ff3d94d07d47fbf
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.40-ha1999f0_6.conda#2eb1a413a24f40a263832e4623bc11d2
+https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.40-ha1999f0_7.conda#3f840c7ed70a96b5ebde8044b2f36f32
 https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab
 https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_10.conda#bbb96c5e7a11ef8ca2b666fe9fe3d199
 https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
@@ -89,7 +89,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libglib-2.80.2-h8a4344b_1.conda#
 https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.27-pthreads_h413a1c8_0.conda#a356024784da6dfd4683dc5ecf45b155
 https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-h1dd3fc0_3.conda#66f03896ffbe1a110ffda05c7a856504
 https://conda.anaconda.org/conda-forge/linux-64/libxml2-2.12.7-hc051c1a_1.conda#340278ded8b0dc3a73f3660bbb0adbc6
-https://conda.anaconda.org/conda-forge/linux-64/python-3.12.3-hab00c5b_0_cpython.conda#2540b74d304f71d3e89c81209db4db84
+https://conda.anaconda.org/conda-forge/linux-64/python-3.12.4-h194c7f8_0_cpython.conda#d73490214f536cccb5819e9873048c92
 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
 https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.9-h8ee46fc_0.conda#077b6e8ad6a3ddb741fce2496dd01bec
@@ -194,7 +194,7 @@ https://conda.anaconda.org/conda-forge/noarch/r-timedate-4032.109-r43hc72bb7e_0.
 https://conda.anaconda.org/conda-forge/linux-64/r-utf8-1.2.4-r43h57805ef_0.conda#d228498392dce22d3fe6266554498493
 https://conda.anaconda.org/conda-forge/noarch/r-viridislite-0.4.2-r43hc72bb7e_1.conda#307f6c8262afed91d2999568e2268ed6
 https://conda.anaconda.org/conda-forge/noarch/r-withr-3.0.0-r43hc72bb7e_0.conda#7380a50d9daae38b40777f7630b8c3ba
-https://conda.anaconda.org/conda-forge/linux-64/r-xfun-0.44-r43ha18555a_0.conda#8fbbfbc83f3f8572c8d5bb066a1eb8a4
+https://conda.anaconda.org/conda-forge/linux-64/r-xfun-0.45-r43ha18555a_0.conda#cced29e73709a7c9b2495a4f5d695d66
 https://conda.anaconda.org/conda-forge/linux-64/r-xml-3.99_0.16.1-r43hc6530ce_0.conda#928dbf6d1fad85646b6b08f54bf65ed5
 https://conda.anaconda.org/conda-forge/noarch/r-xtable-1.8_4-r43hc72bb7e_5.conda#5feaea09b5105200b972101ed5c6ba44
 https://conda.anaconda.org/conda-forge/linux-64/r-yaml-2.3.8-r43h57805ef_0.conda#41db1ee9d0073339e681379b92e7dfb6
@@ -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-1.4.1.9015-r43_0.tar.bz2#31fa9b83fd18e0b6ee571849c08243c6
+https://conda.anaconda.org/pcgr/noarch/r-pcgrr-1.4.1.9016-r43_0.tar.bz2#bcca7fbef7165257a5b45165cae1b950
 https://conda.anaconda.org/pcgr/noarch/r-cpsr-1.0.1.9014-r43_0.tar.bz2#984c10b7420207efd790c6d1ea44df45
diff --git a/conda/env/lock/pcgrr-osx-64.lock b/conda/env/lock/pcgrr-osx-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: osx-64
-# input_hash: 867fad51d68b2d19f3954ec1bdf97a3eddb238f8bfda5c59bc6106c4c891cc6e
+# input_hash: db5ac7aa6c400890ddebdcc56eb3f7e2ca577a9e48aedb4c0172f0d57658c66a
 @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
@@ -71,7 +71,7 @@ https://conda.anaconda.org/conda-forge/osx-64/libglib-2.80.2-h736d271_1.conda#af
 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
+https://conda.anaconda.org/conda-forge/osx-64/python-3.12.4-h37a9e06_0_cpython.conda#94e2b77992f580ac6b7a4fc9b53018b3
 https://conda.anaconda.org/conda-forge/osx-64/quarto-1.4.550-h694c41f_1.conda#451204adcf15c8411d12ba240e7e979a
 https://conda.anaconda.org/conda-forge/osx-64/tktable-2.10-ha166976_5.conda#602295ab8aad142337605f1f9ef77640
 https://conda.anaconda.org/conda-forge/noarch/argcomplete-3.4.0-pyhd8ed1ab_0.conda#9f736cae0da3365a4dbbfbadfac9f3a2
@@ -188,7 +188,7 @@ https://conda.anaconda.org/conda-forge/noarch/r-timedate-4032.109-r43hc72bb7e_0.
 https://conda.anaconda.org/conda-forge/osx-64/r-utf8-1.2.4-r43hb2c329c_0.conda#5c3dba20201cf43a963c116621a63a58
 https://conda.anaconda.org/conda-forge/noarch/r-viridislite-0.4.2-r43hc72bb7e_1.conda#307f6c8262afed91d2999568e2268ed6
 https://conda.anaconda.org/conda-forge/noarch/r-withr-3.0.0-r43hc72bb7e_0.conda#7380a50d9daae38b40777f7630b8c3ba
-https://conda.anaconda.org/conda-forge/osx-64/r-xfun-0.44-r43h25d921d_0.conda#4b2528e83a5dead3f921ef4d83469366
+https://conda.anaconda.org/conda-forge/osx-64/r-xfun-0.45-r43h25d921d_0.conda#e82a5b1f7a9b78eeeb4f1b63a7cf7d7a
 https://conda.anaconda.org/conda-forge/osx-64/r-xml-3.99_0.16.1-r43hceedce5_0.conda#f2725b363c143a17307f7362c7e188e1
 https://conda.anaconda.org/conda-forge/noarch/r-xtable-1.8_4-r43hc72bb7e_5.conda#5feaea09b5105200b972101ed5c6ba44
 https://conda.anaconda.org/conda-forge/osx-64/r-yaml-2.3.8-r43hb2c329c_0.conda#7f14ad8117de577e992b2b09cbe43663
@@ -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-1.4.1.9015-r43_0.tar.bz2#31fa9b83fd18e0b6ee571849c08243c6
+https://conda.anaconda.org/pcgr/noarch/r-pcgrr-1.4.1.9016-r43_0.tar.bz2#bcca7fbef7165257a5b45165cae1b950
 https://conda.anaconda.org/pcgr/noarch/r-cpsr-1.0.1.9014-r43_0.tar.bz2#984c10b7420207efd790c6d1ea44df45
diff --git a/conda/env/yml/pcgr.yml b/conda/env/yml/pcgr.yml
@@ -6,7 +6,7 @@ channels:
   - conda-forge
 
 dependencies:
-  - pcgr::pcgr ==1.4.1.9015 # versioned by bump2version
+  - pcgr::pcgr ==1.4.1.9016 # versioned by bump2version
   - bedtools
   - bcftools
   - cyvcf2

diff --git a/conda/env/yml/pcgrr.yml b/conda/env/yml/pcgrr.yml
@@ -7,7 +7,7 @@ channels:
 
 dependencies:
   - python
-  - pcgr::r-pcgrr ==1.4.1.9015 # versioned by bump2version
+  - pcgr::r-pcgrr ==1.4.1.9016 # versioned by bump2version
   - pcgr::r-cpsr
   - r-argparse
   - bioconductor-bsgenome.hsapiens.ucsc.hg38

diff --git a/conda/env/yml/pkgdown.yml b/conda/env/yml/pkgdown.yml
@@ -4,7 +4,7 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - pcgr::r-pcgrr ==1.4.1.9015 # versioned by bump2version
+  - pcgr::r-pcgrr ==1.4.1.9016 # versioned by bump2version
   - r-pkgdown
   - r-readr
   - r-glue

diff --git a/conda/recipe/pcgr/meta.yaml b/conda/recipe/pcgr/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: pcgr
-  version: 1.4.1.9015 # versioned by bump2version
+  version: 1.4.1.9016 # versioned by bump2version
 
 source:
   path: ../../..

diff --git a/conda/recipe/pcgrr/build.sh b/conda/recipe/pcgrr/build.sh
@@ -1,6 +1,4 @@
 #!/bin/bash
 
 export DISABLE_AUTOBREW=1
-${R} -e "install.packages('remotes', repos = 'https://cloud.r-project.org/', lib = '${PREFIX}/lib/R/library')"
-${R} -e "remotes::install_github(repo = 'caravagnalab/CNAqc', ref = '274cde9', lib = '${PREFIX}/lib/R/library')"
 ${R} CMD INSTALL --build . ${R_ARGS}
diff --git a/conda/recipe/pcgrr/meta.yaml b/conda/recipe/pcgrr/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: r-pcgrr
-  version: 1.4.1.9015 # versioned by bump2version
+  version: 1.4.1.9016 # versioned by bump2version
 
 source:
   path: ../../../pcgrr

diff --git a/pcgr/_version.py b/pcgr/_version.py
@@ -1,2 +1,2 @@
 # versioned by bump2version
-__version__ = '1.4.1.9015'
+__version__ = '1.4.1.9016'
diff --git a/pcgrr/DESCRIPTION b/pcgrr/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: pcgrr
 Type: Package
 Title: Personal Cancer Genome ReporteR
-Version: 1.4.1.9015
+Version: 1.4.1.9016
 Authors@R:
     c(person(given = "Sigve",
              family = "Nakken",

diff --git a/pcgrr/vignettes/installation.Rmd b/pcgrr/vignettes/installation.Rmd
@@ -15,7 +15,7 @@ require(glue, include.only = "glue")
 
 ```{r vars, echo=FALSE}
 Sys.setenv(VEP_VERSION = "112")
-Sys.setenv(PCGR_VERSION = "1.4.1.9015")
+Sys.setenv(PCGR_VERSION = "1.4.1.9016")
 Sys.setenv(BUNDLE_VERSION = "20240612")
 VEP_VERSION <- Sys.getenv("VEP_VERSION")
 PCGR_VERSION <- Sys.getenv("PCGR_VERSION")

diff --git a/pyproject.toml b/pyproject.toml
@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "pcgr"
-version = "1.4.1.9015" # versioned by bump2version
+version = "1.4.1.9016" # versioned by bump2version
 description = "Personal Cancer Genome Reporter (PCGR) - variant interpretation for precision cancer medicine"
 authors = [
     {name = "Sigve Nakken", email = "[email protected]"},