From 8745d077e1bf0a679414bb597649b3c2f5ab57da Mon Sep 17 00:00:00 2001 From: vipints Date: Thu, 12 Dec 2024 14:10:02 +0100 Subject: [PATCH 01/12] recipe for scROSHI based on CRAN --- recipes/r-scroshi/build.sh | 22 +++++++++ recipes/r-scroshi/meta.yaml | 93 +++++++++++++++++++++++++++++++++++++ 2 files changed, 115 insertions(+) create mode 100644 recipes/r-scroshi/build.sh create mode 100644 recipes/r-scroshi/meta.yaml diff --git a/recipes/r-scroshi/build.sh b/recipes/r-scroshi/build.sh new file mode 100644 index 0000000000000..df943f40e3e3d --- /dev/null +++ b/recipes/r-scroshi/build.sh @@ -0,0 +1,22 @@ +#!/bin/bash + +# 'Autobrew' is being used by more and more packages these days +# to grab static libraries from Homebrew bottles. These bottles +# are fetched via Homebrew's --force-bottle option which grabs +# a bottle for the build machine which may not be macOS 10.9. +# Also, we want to use conda packages (and shared libraries) for +# these 'system' dependencies. See: +# https://github.com/jeroen/autobrew/issues/3 +export DISABLE_AUTOBREW=1 + +# R refuses to build packages that mark themselves as Priority: Recommended +mv DESCRIPTION DESCRIPTION.old +grep -va '^Priority: ' DESCRIPTION.old > DESCRIPTION +# shellcheck disable=SC2086 +${R} CMD INSTALL --build . ${R_ARGS} + +# Add more build steps here, if they are necessary. + +# See +# https://docs.conda.io/projects/conda-build +# for a list of environment variables that are set during the build process. diff --git a/recipes/r-scroshi/meta.yaml b/recipes/r-scroshi/meta.yaml new file mode 100644 index 0000000000000..0d75125b693f3 --- /dev/null +++ b/recipes/r-scroshi/meta.yaml @@ -0,0 +1,93 @@ +{% set version = '1.0.0.0' %} + +package: + name: r-scroshi + version: {{ version|replace("-", "_") }} + +source: + url: + - {{ cran_mirror }}/src/contrib/scROSHI_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/scROSHI/scROSHI_{{ version }}.tar.gz + sha256: 332ed379c27d4becfae31f164e6267850cd927dbb357c3a77de1f320d65baf96 + +build: + # If this is a new build for the same version, increment the build number. + number: 0 + # no skip + + # This is required to make R link correctly on Linux. + rpaths: + - lib/R/lib/ + - lib/ + +requirements: + host: + - r-base + - r-s4vectors + - r-singlecellexperiment + - r-summarizedexperiment + - r-limma + - r-uwot + + run: + - r-base + - r-s4vectors + - r-singlecellexperiment + - r-summarizedexperiment + - r-limma + - r-uwot + +test: + commands: + # You can put additional test commands to be run here. + - $R -e "library('scROSHI')" # [not win] + - "\"%R%\" -e \"library('scROSHI')\"" # [win] + + # You can also put a file called run_test.r, run_test.py, run_test.sh, + # or run_test.bat in the recipe that will be run at test time. + + # requires: + # Put any additional test requirements here. + +about: + home: https://CRAN.R-project.org/package=scROSHI + license: MIT + summary: 'Identifying cell types based on expression profiles is a pillar of single cell analysis. + ''scROSHI'' identifies cell types based on expression profiles of single cell analysis + by utilizing previously obtained cell type specific gene sets. It takes into account + the hierarchical nature of cell type relationship and does not require training + or annotated data. A detailed description of the method can be found at: Prummer, + Bertolini, Bosshard, Barkmann, Yates, Boeva, The Tumor Profiler Consortium, Stekhoven, + and Singer (2022) .' + license_family: MIT + license_file: + - '{{ environ["PREFIX"] }}/lib/R/share/licenses/MIT' + - LICENSE +extra: + identifiers: + - doi:10.1093/nargab/lqad058 +# The original CRAN metadata for this package was: + +# Package: scROSHI +# Title: Robust Supervised Hierarchical Identification of Single Cells +# Version: 1.0.0.0 +# Authors@R: c(person(given = "Lars", family = "Bosshard", role = c("aut", "cre"), email = "bosshard@nexus.ethz.ch", comment = c(ORCID = "0000-0002-4550-4777")), person(given = "Michael", family = "Prummer", role = c("aut"), email = "prummer@nexus.ethz.ch", comment = c(ORCID = "0000-0001-9896-3929"))) +# Maintainer: Lars Bosshard +# Description: Identifying cell types based on expression profiles is a pillar of single cell analysis. 'scROSHI' identifies cell types based on expression profiles of single cell analysis by utilizing previously obtained cell type specific gene sets. It takes into account the hierarchical nature of cell type relationship and does not require training or annotated data. A detailed description of the method can be found at: Prummer, Bertolini, Bosshard, Barkmann, Yates, Boeva, The Tumor Profiler Consortium, Stekhoven, and Singer (2022) . +# License: MIT + file LICENSE +# Encoding: UTF-8 +# LazyData: true +# RoxygenNote: 7.2.1 +# Imports: limma, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, utils, uwot +# Depends: R (>= 3.60) +# biocViews: +# LazyDataCompression: xz +# NeedsCompilation: no +# Packaged: 2023-01-09 09:38:17 UTC; bolars +# Author: Lars Bosshard [aut, cre] (), Michael Prummer [aut] () +# Repository: CRAN +# Date/Publication: 2023-01-10 13:50:02 UTC + +# See +# https://docs.conda.io/projects/conda-build for +# more information about meta.yaml From 5c47e354303c44bdb2ac0a26f2e800a70f5d6c8b Mon Sep 17 00:00:00 2001 From: vipints Date: Thu, 12 Dec 2024 14:52:20 +0100 Subject: [PATCH 02/12] short summary for scroshi program --- recipes/r-scroshi/meta.yaml | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/recipes/r-scroshi/meta.yaml b/recipes/r-scroshi/meta.yaml index 0d75125b693f3..30ff3ac6c4016 100644 --- a/recipes/r-scroshi/meta.yaml +++ b/recipes/r-scroshi/meta.yaml @@ -52,13 +52,8 @@ test: about: home: https://CRAN.R-project.org/package=scROSHI license: MIT - summary: 'Identifying cell types based on expression profiles is a pillar of single cell analysis. - ''scROSHI'' identifies cell types based on expression profiles of single cell analysis - by utilizing previously obtained cell type specific gene sets. It takes into account - the hierarchical nature of cell type relationship and does not require training - or annotated data. A detailed description of the method can be found at: Prummer, - Bertolini, Bosshard, Barkmann, Yates, Boeva, The Tumor Profiler Consortium, Stekhoven, - and Singer (2022) .' + summary: 'scROSHI identifies cell types based on expression profiles of single cell analysis + by utilizing previously obtained cell type specific gene sets.' license_family: MIT license_file: - '{{ environ["PREFIX"] }}/lib/R/share/licenses/MIT' From 2188ba4cf4c201f767168df89493c19677a1d9df Mon Sep 17 00:00:00 2001 From: vipints Date: Thu, 12 Dec 2024 15:03:26 +0100 Subject: [PATCH 03/12] adjusted the newline character --- recipes/r-scroshi/meta.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/recipes/r-scroshi/meta.yaml b/recipes/r-scroshi/meta.yaml index 30ff3ac6c4016..042f922dd5bca 100644 --- a/recipes/r-scroshi/meta.yaml +++ b/recipes/r-scroshi/meta.yaml @@ -52,8 +52,7 @@ test: about: home: https://CRAN.R-project.org/package=scROSHI license: MIT - summary: 'scROSHI identifies cell types based on expression profiles of single cell analysis - by utilizing previously obtained cell type specific gene sets.' + summary: 'scROSHI identifies cell types based on expression profiles of single cell analysis by utilizing previously obtained cell type specific gene sets.' license_family: MIT license_file: - '{{ environ["PREFIX"] }}/lib/R/share/licenses/MIT' From 6f7e511f7a1d0f897f9afddb69587ebb70375d13 Mon Sep 17 00:00:00 2001 From: vipints Date: Thu, 12 Dec 2024 15:08:27 +0100 Subject: [PATCH 04/12] additional-platforms tag added in extra field --- recipes/r-scroshi/meta.yaml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/recipes/r-scroshi/meta.yaml b/recipes/r-scroshi/meta.yaml index 042f922dd5bca..79fd302f9af7f 100644 --- a/recipes/r-scroshi/meta.yaml +++ b/recipes/r-scroshi/meta.yaml @@ -13,8 +13,6 @@ source: build: # If this is a new build for the same version, increment the build number. number: 0 - # no skip - # This is required to make R link correctly on Linux. rpaths: - lib/R/lib/ @@ -44,8 +42,6 @@ test: - "\"%R%\" -e \"library('scROSHI')\"" # [win] # You can also put a file called run_test.r, run_test.py, run_test.sh, - # or run_test.bat in the recipe that will be run at test time. - # requires: # Put any additional test requirements here. @@ -58,6 +54,8 @@ about: - '{{ environ["PREFIX"] }}/lib/R/share/licenses/MIT' - LICENSE extra: + additional-platforms: + - linux-aarch64 identifiers: - doi:10.1093/nargab/lqad058 # The original CRAN metadata for this package was: From 82d0eb1a93d2069e81211f763433f9a38840edc0 Mon Sep 17 00:00:00 2001 From: vipints Date: Thu, 12 Dec 2024 15:12:19 +0100 Subject: [PATCH 05/12] run_exports added to the build section --- recipes/r-scroshi/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/r-scroshi/meta.yaml b/recipes/r-scroshi/meta.yaml index 79fd302f9af7f..9411e5c8e4334 100644 --- a/recipes/r-scroshi/meta.yaml +++ b/recipes/r-scroshi/meta.yaml @@ -14,6 +14,8 @@ build: # If this is a new build for the same version, increment the build number. number: 0 # This is required to make R link correctly on Linux. + run_exports: + - {{ pin_subpackage("r-scroshi", max_pin="x") }} rpaths: - lib/R/lib/ - lib/ From 6c4e62ebbb35de0fb3511c8248d7abd6f32dcd6f Mon Sep 17 00:00:00 2001 From: vipints Date: Thu, 12 Dec 2024 15:20:38 +0100 Subject: [PATCH 06/12] title summary changed --- recipes/r-scroshi/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/r-scroshi/meta.yaml b/recipes/r-scroshi/meta.yaml index 9411e5c8e4334..30e73a6e43939 100644 --- a/recipes/r-scroshi/meta.yaml +++ b/recipes/r-scroshi/meta.yaml @@ -50,7 +50,7 @@ test: about: home: https://CRAN.R-project.org/package=scROSHI license: MIT - summary: 'scROSHI identifies cell types based on expression profiles of single cell analysis by utilizing previously obtained cell type specific gene sets.' + summary: 'scROSHI: robust supervised hierarchical identification of single cells' license_family: MIT license_file: - '{{ environ["PREFIX"] }}/lib/R/share/licenses/MIT' From b1e6d9c894dd7d1247c423c425be0b983ce89a91 Mon Sep 17 00:00:00 2001 From: vipints Date: Thu, 12 Dec 2024 15:24:40 +0100 Subject: [PATCH 07/12] the recipe should be build as noarch --- recipes/r-scroshi/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/r-scroshi/meta.yaml b/recipes/r-scroshi/meta.yaml index 30e73a6e43939..f3a1330343777 100644 --- a/recipes/r-scroshi/meta.yaml +++ b/recipes/r-scroshi/meta.yaml @@ -21,6 +21,8 @@ build: - lib/ requirements: + build: + noarch: generic host: - r-base - r-s4vectors From 6832c58524bbd91151774dfcc6015ce42ab75f89 Mon Sep 17 00:00:00 2001 From: vipints Date: Thu, 12 Dec 2024 15:28:07 +0100 Subject: [PATCH 08/12] fixed the build section --- recipes/r-scroshi/meta.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/recipes/r-scroshi/meta.yaml b/recipes/r-scroshi/meta.yaml index f3a1330343777..09178ff0f25b4 100644 --- a/recipes/r-scroshi/meta.yaml +++ b/recipes/r-scroshi/meta.yaml @@ -19,10 +19,9 @@ build: rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: - build: - noarch: generic host: - r-base - r-s4vectors From cdb241a4f14369e0625c0d8ecc70219c99b6c67b Mon Sep 17 00:00:00 2001 From: vipints Date: Thu, 12 Dec 2024 15:52:47 +0100 Subject: [PATCH 09/12] bioconda channel to fetch the modules --- recipes/r-scroshi/meta.yaml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/recipes/r-scroshi/meta.yaml b/recipes/r-scroshi/meta.yaml index 09178ff0f25b4..f4503d5507e3b 100644 --- a/recipes/r-scroshi/meta.yaml +++ b/recipes/r-scroshi/meta.yaml @@ -24,18 +24,18 @@ build: requirements: host: - r-base - - r-s4vectors - - r-singlecellexperiment - - r-summarizedexperiment - - r-limma + - bioconductor-s4vectors + - bioconductor-singlecellexperiment + - bioconductor-summarizedexperiment + - bioconductor-limma - r-uwot run: - r-base - - r-s4vectors - - r-singlecellexperiment - - r-summarizedexperiment - - r-limma + - bioconductor-s4vectors + - bioconductor-singlecellexperiment + - bioconductor-summarizedexperiment + - bioconductor-limma - r-uwot test: From 1223aa0a4d7a5687098597e143433bf0954cee66 Mon Sep 17 00:00:00 2001 From: vipints Date: Thu, 12 Dec 2024 21:43:19 +0100 Subject: [PATCH 10/12] additional platform info deleted --- recipes/r-scroshi/meta.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/recipes/r-scroshi/meta.yaml b/recipes/r-scroshi/meta.yaml index f4503d5507e3b..3286eaccb763e 100644 --- a/recipes/r-scroshi/meta.yaml +++ b/recipes/r-scroshi/meta.yaml @@ -57,8 +57,6 @@ about: - '{{ environ["PREFIX"] }}/lib/R/share/licenses/MIT' - LICENSE extra: - additional-platforms: - - linux-aarch64 identifiers: - doi:10.1093/nargab/lqad058 # The original CRAN metadata for this package was: From e7ca9309cd03e5829e1598b2e46bf4d871422432 Mon Sep 17 00:00:00 2001 From: vipints Date: Fri, 13 Dec 2024 10:33:43 +0100 Subject: [PATCH 11/12] added exact version of required packages --- recipes/r-scroshi/meta.yaml | 56 ++++++++----------------------------- 1 file changed, 12 insertions(+), 44 deletions(-) diff --git a/recipes/r-scroshi/meta.yaml b/recipes/r-scroshi/meta.yaml index 3286eaccb763e..8dae775d703f1 100644 --- a/recipes/r-scroshi/meta.yaml +++ b/recipes/r-scroshi/meta.yaml @@ -11,9 +11,7 @@ source: sha256: 332ed379c27d4becfae31f164e6267850cd927dbb357c3a77de1f320d65baf96 build: - # If this is a new build for the same version, increment the build number. number: 0 - # This is required to make R link correctly on Linux. run_exports: - {{ pin_subpackage("r-scroshi", max_pin="x") }} rpaths: @@ -23,31 +21,26 @@ build: requirements: host: - - r-base - - bioconductor-s4vectors - - bioconductor-singlecellexperiment - - bioconductor-summarizedexperiment - - bioconductor-limma - - r-uwot + - r-base==4.3.2 + - bioconductor-s4vectors==0.40.2 + - bioconductor-singlecellexperiment==1.24.0 + - bioconductor-summarizedexperiment==1.32.0 + - bioconductor-limma==3.58.1 + - r-uwot==0.1.16 run: - - r-base - - bioconductor-s4vectors - - bioconductor-singlecellexperiment - - bioconductor-summarizedexperiment - - bioconductor-limma - - r-uwot + - r-base==4.3.2 + - bioconductor-s4vectors==0.40.2 + - bioconductor-singlecellexperiment==1.24.0 + - bioconductor-summarizedexperiment==1.32.0 + - bioconductor-limma==3.58.1 + - r-uwot==0.1.16 test: commands: - # You can put additional test commands to be run here. - $R -e "library('scROSHI')" # [not win] - "\"%R%\" -e \"library('scROSHI')\"" # [win] - # You can also put a file called run_test.r, run_test.py, run_test.sh, - # requires: - # Put any additional test requirements here. - about: home: https://CRAN.R-project.org/package=scROSHI license: MIT @@ -59,28 +52,3 @@ about: extra: identifiers: - doi:10.1093/nargab/lqad058 -# The original CRAN metadata for this package was: - -# Package: scROSHI -# Title: Robust Supervised Hierarchical Identification of Single Cells -# Version: 1.0.0.0 -# Authors@R: c(person(given = "Lars", family = "Bosshard", role = c("aut", "cre"), email = "bosshard@nexus.ethz.ch", comment = c(ORCID = "0000-0002-4550-4777")), person(given = "Michael", family = "Prummer", role = c("aut"), email = "prummer@nexus.ethz.ch", comment = c(ORCID = "0000-0001-9896-3929"))) -# Maintainer: Lars Bosshard -# Description: Identifying cell types based on expression profiles is a pillar of single cell analysis. 'scROSHI' identifies cell types based on expression profiles of single cell analysis by utilizing previously obtained cell type specific gene sets. It takes into account the hierarchical nature of cell type relationship and does not require training or annotated data. A detailed description of the method can be found at: Prummer, Bertolini, Bosshard, Barkmann, Yates, Boeva, The Tumor Profiler Consortium, Stekhoven, and Singer (2022) . -# License: MIT + file LICENSE -# Encoding: UTF-8 -# LazyData: true -# RoxygenNote: 7.2.1 -# Imports: limma, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, utils, uwot -# Depends: R (>= 3.60) -# biocViews: -# LazyDataCompression: xz -# NeedsCompilation: no -# Packaged: 2023-01-09 09:38:17 UTC; bolars -# Author: Lars Bosshard [aut, cre] (), Michael Prummer [aut] () -# Repository: CRAN -# Date/Publication: 2023-01-10 13:50:02 UTC - -# See -# https://docs.conda.io/projects/conda-build for -# more information about meta.yaml From 68b69fe3fef92179a2433c9eb397962ddde6dfda Mon Sep 17 00:00:00 2001 From: vipints Date: Fri, 13 Dec 2024 10:42:34 +0100 Subject: [PATCH 12/12] fixed spacing between package and version number --- recipes/r-scroshi/meta.yaml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/recipes/r-scroshi/meta.yaml b/recipes/r-scroshi/meta.yaml index 8dae775d703f1..1de49ef5c034b 100644 --- a/recipes/r-scroshi/meta.yaml +++ b/recipes/r-scroshi/meta.yaml @@ -21,20 +21,20 @@ build: requirements: host: - - r-base==4.3.2 - - bioconductor-s4vectors==0.40.2 - - bioconductor-singlecellexperiment==1.24.0 - - bioconductor-summarizedexperiment==1.32.0 - - bioconductor-limma==3.58.1 - - r-uwot==0.1.16 + - r-base ==4.3.2 + - bioconductor-s4vectors ==0.40.2 + - bioconductor-singlecellexperiment ==1.24.0 + - bioconductor-summarizedexperiment ==1.32.0 + - bioconductor-limma ==3.58.1 + - r-uwot ==0.1.16 run: - - r-base==4.3.2 - - bioconductor-s4vectors==0.40.2 - - bioconductor-singlecellexperiment==1.24.0 - - bioconductor-summarizedexperiment==1.32.0 - - bioconductor-limma==3.58.1 - - r-uwot==0.1.16 + - r-base ==4.3.2 + - bioconductor-s4vectors ==0.40.2 + - bioconductor-singlecellexperiment ==1.24.0 + - bioconductor-summarizedexperiment ==1.32.0 + - bioconductor-limma ==3.58.1 + - r-uwot ==0.1.16 test: commands: