Merge pull request #242 from sigven/locale

Set locale to avoid apptainer warnings on HPC
sigven · Jun 20, 2024 · b141441 · b141441
2 parents 2ca3293 + 1486740
commit b141441
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.4.1.9016
+current_version = 1.4.1.9019
 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
@@ -5,12 +5,13 @@ on:
     branches:
       - master
       - bundle_update_2023
+      - locale
 env:
   atoken: ${{ secrets.ANACONDA_UPLOAD_TOKEN }}
   recipe_path: conda/recipe
   env_yml_path: conda/env/yml
   env_lock_path: conda/env/lock
-  VERSION: '1.4.1.9016' # versioned by bump2version
+  VERSION: '1.4.1.9019' # versioned by bump2version
 jobs:
   build_pcgrr_conda_pkg:
     # When merging to one of the branches above and the commit message matches
@@ -85,6 +86,7 @@ jobs:
           git commit -m "${MSG}"
           git push
       - name: 🌐 Website publish
+        if: github.ref_name == 'master'
         run: |
           micromamba env create -n pkgdownenv -f ${env_yml_path}/pkgdown.yml
           micromamba activate pkgdownenv
@@ -125,8 +127,8 @@ jobs:
               sha: the_sha
             })
 
-     #- name: 🗑 Free Disk Space
-     #  uses: jlumbroso/free-disk-space@main
+      - name: 🗑 Free Disk Space
+        uses: jlumbroso/free-disk-space@main
       # work with tag from above
       - name: Code checkout
         uses: actions/checkout@v4
@@ -152,9 +154,10 @@ jobs:
             sigven/pcgr:${{ env.VERSION }}
           outputs: type=docker,dest=pcgr_${{ env.VERSION }}.tar
 
+      # Apptainer
       - name: Apptainer setup
         uses: eWaterCycle/setup-apptainer@v2
-      - name: ⚫ Apptainer build
+      - name: 🕹️ Apptainer build
         run: |
           ls -lSha
           df -h

diff --git a/Dockerfile b/Dockerfile
@@ -26,7 +26,7 @@ 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
+FROM quay.io/bioconda/base-glibc-debian-bash:3.1
 
 COPY --from=0 /opt/mambaforge/envs/ /opt/mambaforge/envs/
 

diff --git a/conda/env/lock/pcgr-linux-64.lock b/conda/env/lock/pcgr-linux-64.lock
@@ -1,6 +1,6 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: df6430571fbb82456261636d686c3f4ba3929721b191f9a52ff5744b86e20f32
+# input_hash: c67e863b6b1bcd492711b5f53604da4f89462c6bc44b751d8390cb0e604636d3
 @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
@@ -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-1.4.1.9016-py_0.tar.bz2#082878c9f25e30fa6f820267654a1798
+https://conda.anaconda.org/pcgr/noarch/pcgr-1.4.1.9019-py_0.tar.bz2#c0e551dd45f5802f226f654f50e78c53
 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: 08008428608a5260b88f62558e2503ae382a060819418ecc0280e3fcd7741505
+# input_hash: 7985ef7bc19181daf269f76028a4367ccd9143de1434c49432cdc042b9cdd00a
 @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-1.4.1.9016-py_0.tar.bz2#082878c9f25e30fa6f820267654a1798
+https://conda.anaconda.org/pcgr/noarch/pcgr-1.4.1.9019-py_0.tar.bz2#c0e551dd45f5802f226f654f50e78c53
 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: a01aaf6b50f52e080b7dbfd938e3de505ffea44c78b046868dd807bfa5d09245
+# input_hash: 81825ef68192e5d9623a94cf6de817ee84fea2dae9a939d7ff51e25ebe43ec9f
 @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
@@ -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-1.4.1.9016-r43_0.tar.bz2#bcca7fbef7165257a5b45165cae1b950
-https://conda.anaconda.org/pcgr/noarch/r-cpsr-1.0.1.9014-r43_0.tar.bz2#984c10b7420207efd790c6d1ea44df45
+https://conda.anaconda.org/pcgr/noarch/r-pcgrr-1.4.1.9019-r43_0.tar.bz2#eb6b341753cea5e076bab5cf5f501a32
+https://conda.anaconda.org/pcgr/noarch/r-cpsr-1.0.1.9015-r43_0.tar.bz2#911bb3e2fdbbb91ae3c8d74006141fe3
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: db5ac7aa6c400890ddebdcc56eb3f7e2ca577a9e48aedb4c0172f0d57658c66a
+# input_hash: 00e59c15a1ce1fa31f11804a602a83c58daa9256c8c0d8cb0e8138c7f1d4fa27
 @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
@@ -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-1.4.1.9016-r43_0.tar.bz2#bcca7fbef7165257a5b45165cae1b950
-https://conda.anaconda.org/pcgr/noarch/r-cpsr-1.0.1.9014-r43_0.tar.bz2#984c10b7420207efd790c6d1ea44df45
+https://conda.anaconda.org/pcgr/noarch/r-pcgrr-1.4.1.9019-r43_0.tar.bz2#eb6b341753cea5e076bab5cf5f501a32
+https://conda.anaconda.org/pcgr/noarch/r-cpsr-1.0.1.9015-r43_0.tar.bz2#911bb3e2fdbbb91ae3c8d74006141fe3
diff --git a/conda/env/yml/pcgr.yml b/conda/env/yml/pcgr.yml
@@ -6,7 +6,7 @@ channels:
   - conda-forge
 
 dependencies:
-  - pcgr::pcgr ==1.4.1.9016 # versioned by bump2version
+  - pcgr::pcgr ==1.4.1.9019 # 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 ==1.4.1.9016 # versioned by bump2version
+  - pcgr::r-pcgrr ==1.4.1.9019 # 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 ==1.4.1.9016 # versioned by bump2version
+  - pcgr::r-pcgrr ==1.4.1.9019 # 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: 1.4.1.9016 # versioned by bump2version
+  version: 1.4.1.9019 # versioned by bump2version
 
 source:
   path: ../../..

diff --git a/conda/recipe/pcgrr/meta.yaml b/conda/recipe/pcgrr/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: r-pcgrr
-  version: 1.4.1.9016 # versioned by bump2version
+  version: 1.4.1.9019 # versioned by bump2version
 
 source:
   path: ../../../pcgrr

diff --git a/pcgr/_version.py b/pcgr/_version.py
@@ -1,2 +1,2 @@
 # versioned by bump2version
-__version__ = '1.4.1.9016'
+__version__ = '1.4.1.9019'
diff --git a/pcgr/main.py b/pcgr/main.py
@@ -109,7 +109,6 @@ def cli():
     optional_cna.add_argument("--input_cna", dest="input_cna", help="Somatic copy number alteration segments (tab-separated values)")
     optional_cna.add_argument("--n_copy_gain", type=int, default=6, dest="n_copy_gain", help="Minimum number of total copy number for segments considered as gains/amplifications (default: %(default)s)")
     optional_cna.add_argument("--cna_overlap_pct", type=float, default=50, dest="cna_overlap_pct", help="Mean percent overlap between copy number segment and gene transcripts for reporting of gains/losses in tumor suppressor genes/oncogenes, (default: %(default)s)")
-
     #optional_rna.add_argument("--input_rna_fusion", dest = "input_rna_fusion", help = "File with RNA fusion transcripts detected in tumor (tab-separated values)")
     optional_rna.add_argument("--input_rna_expression", dest = "input_rna_exp", help = "File with bulk RNA expression counts (TPM) of transcripts in tumor (tab-separated values)")
     optional_rna.add_argument('--expression_sim', action='store_true', help="Compare expression profile of tumor sample to known expression profiles (default: %(default)s)")

diff --git a/pcgr/utils.py b/pcgr/utils.py
@@ -36,9 +36,9 @@ def warn_message(message, logger):
     logger.warning("")
     logger.warning(message)
     logger.warning("")
- 
+
 def random_id_generator(size = 10, chars = string.ascii_lowercase + string.digits):
-    return ''.join(random.choice(chars) for _ in range(size))   
+    return ''.join(random.choice(chars) for _ in range(size))
 
 #def random_string(length):
 #    letters = string.ascii_lowercase
@@ -166,7 +166,7 @@ def safe_makedir(dname):
     return dname
 
 def sort_bed(unsorted_bed_fname: str, sorted_bed_fname: str, debug = False, logger = None):
-    
+
     ## Sort regions in target BED
     if os.path.exists(unsorted_bed_fname) and os.stat(unsorted_bed_fname).st_size != 0:
         cmd_sort_custom_bed1 = 'egrep \'^[0-9]\' ' + str(unsorted_bed_fname) + \
@@ -197,7 +197,6 @@ def check_file_exists(fname: str, strict = True, logger = None) -> bool:
             return(False)
         else:
             error_message(msg, logger)
-
     return(True)
 
 def check_tabix_file(fname: str, logger = None) -> bool:
@@ -210,3 +209,4 @@ def check_tabix_file(fname: str, logger = None) -> bool:
         ## check file size is more than zero
         check_file_exists(tabix_file)
     return(True)
+
diff --git a/pcgrr/DESCRIPTION b/pcgrr/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: pcgrr
 Type: Package
 Title: Personal Cancer Genome ReporteR
-Version: 1.4.1.9016
+Version: 1.4.1.9019
 Authors@R:
     c(person(given = "Sigve",
              family = "Nakken",

diff --git a/pcgrr/R/main.R b/pcgrr/R/main.R
@@ -907,15 +907,15 @@ write_report_quarto_html <- function(report = NULL){
       if(file.exists(quarto_input)){
 
         ## make temporary directory for quarto report rendering
-        tmp_quarto_dir <- file.path(
+        tmp_quarto_dir1 <- file.path(
           output_dir,
           paste0('quarto_', stringi::stri_rand_strings(1, 15))
         )
-        pcgrr::mkdir(tmp_quarto_dir)
+        pcgrr::mkdir(tmp_quarto_dir1)
         # files get copied under tmp/templates/
-        file.copy(pcgr_rep_template_path, tmp_quarto_dir, recursive = TRUE, overwrite = TRUE)
+        file.copy(pcgr_rep_template_path, tmp_quarto_dir1, recursive = TRUE, overwrite = TRUE)
         # so now overwrite the variable
-        tmp_quarto_dir <- file.path(tmp_quarto_dir, templates_dir)
+        tmp_quarto_dir <- file.path(tmp_quarto_dir1, templates_dir)
 
         quarto_main_template <-
           file.path(tmp_quarto_dir, "pcgr_quarto_report.qmd")
@@ -970,7 +970,7 @@ write_report_quarto_html <- function(report = NULL){
 
         ## remove temporary quarto directory (if debugging is switched off)
         if(!(settings$conf$debug)){
-          unlink(tmp_quarto_dir, force = TRUE, recursive = TRUE)
+          unlink(c(tmp_quarto_dir, tmp_quarto_dir1), force = TRUE, recursive = TRUE)
         }
         #pcgrr::log4r_info("------")
       }

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 = "1.4.1.9016")
+Sys.setenv(PCGR_VERSION = "1.4.1.9019")
 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 = "1.4.1.9016" # versioned by bump2version
+version = "1.4.1.9019" # versioned by bump2version
 description = "Personal Cancer Genome Reporter (PCGR) - variant interpretation for precision cancer medicine"
 authors = [
     {name = "Sigve Nakken", email = "[email protected]"},