From cd154e0bc92d99949af012f75f92e725e5ab8622 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?= Date: Mon, 30 Jul 2018 14:46:55 -0300 Subject: [PATCH 01/12] Add r-softimpute --- recipes/r-softimpute/build.sh | 11 +++++++ recipes/r-softimpute/meta.yaml | 52 ++++++++++++++++++++++++++++++++++ 2 files changed, 63 insertions(+) create mode 100644 recipes/r-softimpute/build.sh create mode 100644 recipes/r-softimpute/meta.yaml diff --git a/recipes/r-softimpute/build.sh b/recipes/r-softimpute/build.sh new file mode 100644 index 0000000000000..cc966cfd3aaea --- /dev/null +++ b/recipes/r-softimpute/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash + +if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then + export DISABLE_AUTOBREW=1 + mv DESCRIPTION DESCRIPTION.old + grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION + $R CMD INSTALL --build . +else + mkdir -p $PREFIX/lib/R/library/softImpute + mv * $PREFIX/lib/R/library/softImpute +fi diff --git a/recipes/r-softimpute/meta.yaml b/recipes/r-softimpute/meta.yaml new file mode 100644 index 0000000000000..f7de2b582250a --- /dev/null +++ b/recipes/r-softimpute/meta.yaml @@ -0,0 +1,52 @@ +{% set version = '1.4' %} +{% set posix = 'm2-' if win else '' %} +{% set native = 'm2w64-' if win else '' %} + +package: + name: r-softimpute + version: {{ version|replace("-", "_") }} +source: + fn: softImpute_{{ version }}.tar.gz + url: + - {{ cran_mirror }}/src/contrib/softImpute_{{ version }}.tar.gz + - {{ cran_mirror }}/src/contrib/Archive/softImpute/softImpute_{{ version }}.tar.gz + sha256: 98f5e66aefbf50a6a170421316a9f4b96651521a2196424245052340e75f9d1d +build: + merge_build_host: True # [win] + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - {{ compiler('c') }} # [not win] + - {{ compiler('fortran') }} # [not win] + - {{native}}toolchain # [win] + - {{posix}}filesystem # [win] + - {{posix}}make + - {{posix}}sed # [win] + - {{posix}}coreutils # [win] + - {{posix}}zip # [win] + host: + - r-base + - r-matrix + run: + - r-base + - {{native}}gcc-libs # [win] + - r-matrix +test: + commands: + - $R -e "library('softImpute')" # [not win] + - "\"%R%\" -e \"library('softImpute')\"" # [win] +about: + home: https://CRAN.R-project.org/package=softImpute + license: GPL-2 + summary: Iterative methods for matrix completion that use nuclear-norm regularization. There + are two main approaches.The one approach uses iterative soft-thresholded svds to + impute the missing values. The second approach uses alternating least squares. Both + have an "EM" flavor, in that at each iteration the matrix is completed with the + current estimate. For large matrices there is a special sparse-matrix class named + "Incomplete" that efficiently handles all computations. The package includes procedures + for centering and scaling rows, columns or both, and for computing low-rank SVDs + on large sparse centered matrices (i.e. principal components) + license_family: GPL2 From 88f2c2c70dcea86ceecc71046a4442a841285868 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?= Date: Mon, 30 Jul 2018 14:47:27 -0300 Subject: [PATCH 02/12] Add bioconductor-zinbwave --- recipes/bioconductor-zinbwave/build.sh | 4 +++ recipes/bioconductor-zinbwave/meta.yaml | 47 +++++++++++++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 recipes/bioconductor-zinbwave/build.sh create mode 100644 recipes/bioconductor-zinbwave/meta.yaml diff --git a/recipes/bioconductor-zinbwave/build.sh b/recipes/bioconductor-zinbwave/build.sh new file mode 100644 index 0000000000000..da43ce2168312 --- /dev/null +++ b/recipes/bioconductor-zinbwave/build.sh @@ -0,0 +1,4 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-zinbwave/meta.yaml b/recipes/bioconductor-zinbwave/meta.yaml new file mode 100644 index 0000000000000..fcdee5dfc12ee --- /dev/null +++ b/recipes/bioconductor-zinbwave/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.0" %} +{% set name = "zinbwave" %} +{% set bioc = "3.6" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + fn: '{{ name }}_{{ version }}.tar.gz' + url: + - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + sha256: 2ac640227b3adc489086fa7f9c797d595fce3ad0e8ef79c80533af7334cced64 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + build: + - bioconductor-biocparallel + - bioconductor-edger + - bioconductor-genefilter + - bioconductor-singlecellexperiment + - bioconductor-summarizedexperiment + - r-base + - r-copula + - r-glmnet + - r-softimpute + run: + - bioconductor-biocparallel + - bioconductor-edger + - bioconductor-genefilter + - bioconductor-singlecellexperiment + - bioconductor-summarizedexperiment + - r-base + - r-copula + - r-glmnet + - r-softimpute +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: ' Implements a general and flexible zero-inflated negative binomial model that can be used to provide a low-dimensional representations of single-cell RNA-seq data. The model accounts for zero inflation (dropouts), over-dispersion, and the count nature of the data. The model also accounts for the difference in library sizes and optionally for batch effects and/or other covariates, avoiding the need for pre-normalize the data.' From d5359094e2ee09be7fe93f50e2aebfc67b542bb6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?= Date: Mon, 30 Jul 2018 15:28:04 -0300 Subject: [PATCH 03/12] Fixed errors detected during linting --- recipes/bioconductor-zinbwave/meta.yaml | 3 +-- recipes/r-softimpute/meta.yaml | 7 +++---- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/recipes/bioconductor-zinbwave/meta.yaml b/recipes/bioconductor-zinbwave/meta.yaml index fcdee5dfc12ee..04d030f8732b0 100644 --- a/recipes/bioconductor-zinbwave/meta.yaml +++ b/recipes/bioconductor-zinbwave/meta.yaml @@ -6,7 +6,6 @@ package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: - fn: '{{ name }}_{{ version }}.tar.gz' url: - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' @@ -44,4 +43,4 @@ test: about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: ' Implements a general and flexible zero-inflated negative binomial model that can be used to provide a low-dimensional representations of single-cell RNA-seq data. The model accounts for zero inflation (dropouts), over-dispersion, and the count nature of the data. The model also accounts for the difference in library sizes and optionally for batch effects and/or other covariates, avoiding the need for pre-normalize the data.' + summary: 'Implements a general and flexible zero-inflated negative binomial model that can be used to provide a low-dimensional representations of single-cell RNA-seq data. The model accounts for zero inflation (dropouts), over-dispersion, and the count nature of the data. The model also accounts for the difference in library sizes and optionally for batch effects and/or other covariates, avoiding the need for pre-normalize the data.' diff --git a/recipes/r-softimpute/meta.yaml b/recipes/r-softimpute/meta.yaml index f7de2b582250a..f1af605b41317 100644 --- a/recipes/r-softimpute/meta.yaml +++ b/recipes/r-softimpute/meta.yaml @@ -6,7 +6,6 @@ package: name: r-softimpute version: {{ version|replace("-", "_") }} source: - fn: softImpute_{{ version }}.tar.gz url: - {{ cran_mirror }}/src/contrib/softImpute_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/softImpute/softImpute_{{ version }}.tar.gz @@ -39,14 +38,14 @@ test: - $R -e "library('softImpute')" # [not win] - "\"%R%\" -e \"library('softImpute')\"" # [win] about: - home: https://CRAN.R-project.org/package=softImpute + home: 'https://CRAN.R-project.org/package=softImpute' license: GPL-2 - summary: Iterative methods for matrix completion that use nuclear-norm regularization. There + summary: 'Iterative methods for matrix completion that use nuclear-norm regularization. There are two main approaches.The one approach uses iterative soft-thresholded svds to impute the missing values. The second approach uses alternating least squares. Both have an "EM" flavor, in that at each iteration the matrix is completed with the current estimate. For large matrices there is a special sparse-matrix class named "Incomplete" that efficiently handles all computations. The package includes procedures for centering and scaling rows, columns or both, and for computing low-rank SVDs - on large sparse centered matrices (i.e. principal components) + on large sparse centered matrices (i.e. principal components)' license_family: GPL2 From 20469daa3a57a2a61fee918a283bb532f8e9fabc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?= Date: Mon, 30 Jul 2018 15:45:31 -0300 Subject: [PATCH 04/12] Added the 'extras' section --- recipes/bioconductor-zinbwave/meta.yaml | 7 ++++++- recipes/r-softimpute/meta.yaml | 4 ++-- 2 files changed, 8 insertions(+), 3 deletions(-) diff --git a/recipes/bioconductor-zinbwave/meta.yaml b/recipes/bioconductor-zinbwave/meta.yaml index 04d030f8732b0..ac8a98c52aa7f 100644 --- a/recipes/bioconductor-zinbwave/meta.yaml +++ b/recipes/bioconductor-zinbwave/meta.yaml @@ -42,5 +42,10 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: Artistic-2.0 + license: 'Artistic-2.0' summary: 'Implements a general and flexible zero-inflated negative binomial model that can be used to provide a low-dimensional representations of single-cell RNA-seq data. The model accounts for zero inflation (dropouts), over-dispersion, and the count nature of the data. The model also accounts for the difference in library sizes and optionally for batch effects and/or other covariates, avoiding the need for pre-normalize the data.' + +extra: + identifiers: + - biotools:zinbwave + - doi:10.1038/s41467-017-02554-5 diff --git a/recipes/r-softimpute/meta.yaml b/recipes/r-softimpute/meta.yaml index f1af605b41317..52eeb265998be 100644 --- a/recipes/r-softimpute/meta.yaml +++ b/recipes/r-softimpute/meta.yaml @@ -39,7 +39,7 @@ test: - "\"%R%\" -e \"library('softImpute')\"" # [win] about: home: 'https://CRAN.R-project.org/package=softImpute' - license: GPL-2 + license: 'GPL-2' summary: 'Iterative methods for matrix completion that use nuclear-norm regularization. There are two main approaches.The one approach uses iterative soft-thresholded svds to impute the missing values. The second approach uses alternating least squares. Both @@ -48,4 +48,4 @@ about: "Incomplete" that efficiently handles all computations. The package includes procedures for centering and scaling rows, columns or both, and for computing low-rank SVDs on large sparse centered matrices (i.e. principal components)' - license_family: GPL2 + license_family: 'GPL2' From cf6529f32e2a254376fa3ffbbe48980ad021497d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?= Date: Mon, 30 Jul 2018 16:13:52 -0300 Subject: [PATCH 05/12] Removed Windows-specific lines from the r-softimpute recipe --- recipes/r-softimpute/meta.yaml | 15 +++------------ 1 file changed, 3 insertions(+), 12 deletions(-) diff --git a/recipes/r-softimpute/meta.yaml b/recipes/r-softimpute/meta.yaml index 52eeb265998be..609dd8e6feda1 100644 --- a/recipes/r-softimpute/meta.yaml +++ b/recipes/r-softimpute/meta.yaml @@ -11,32 +11,23 @@ source: - {{ cran_mirror }}/src/contrib/Archive/softImpute/softImpute_{{ version }}.tar.gz sha256: 98f5e66aefbf50a6a170421316a9f4b96651521a2196424245052340e75f9d1d build: - merge_build_host: True # [win] number: 0 rpaths: - lib/R/lib/ - lib/ requirements: build: - - {{ compiler('c') }} # [not win] - - {{ compiler('fortran') }} # [not win] - - {{native}}toolchain # [win] - - {{posix}}filesystem # [win] - - {{posix}}make - - {{posix}}sed # [win] - - {{posix}}coreutils # [win] - - {{posix}}zip # [win] + - {{ compiler('c') }} + - {{ compiler('fortran') }} host: - r-base - r-matrix run: - r-base - - {{native}}gcc-libs # [win] - r-matrix test: commands: - - $R -e "library('softImpute')" # [not win] - - "\"%R%\" -e \"library('softImpute')\"" # [win] + - $R -e "library('softImpute')" about: home: 'https://CRAN.R-project.org/package=softImpute' license: 'GPL-2' From d86ff7e792c1c90a59859473f81d6e6914244d74 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?= Date: Mon, 30 Jul 2018 16:16:34 -0300 Subject: [PATCH 06/12] Forgot to remove some Windows-specific lines --- recipes/r-softimpute/meta.yaml | 2 -- 1 file changed, 2 deletions(-) diff --git a/recipes/r-softimpute/meta.yaml b/recipes/r-softimpute/meta.yaml index 609dd8e6feda1..4a42b83a8cf14 100644 --- a/recipes/r-softimpute/meta.yaml +++ b/recipes/r-softimpute/meta.yaml @@ -1,6 +1,4 @@ {% set version = '1.4' %} -{% set posix = 'm2-' if win else '' %} -{% set native = 'm2w64-' if win else '' %} package: name: r-softimpute From 86a8836eb8b64ecc43d3f77669306ec97b870a96 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?= Date: Mon, 30 Jul 2018 17:33:12 -0300 Subject: [PATCH 07/12] Fixed r-softimpute build.sh --- recipes/r-softimpute/build.sh | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) diff --git a/recipes/r-softimpute/build.sh b/recipes/r-softimpute/build.sh index cc966cfd3aaea..da43ce2168312 100644 --- a/recipes/r-softimpute/build.sh +++ b/recipes/r-softimpute/build.sh @@ -1,11 +1,4 @@ #!/bin/bash - -if [[ $target_platform =~ linux.* ]] || [[ $target_platform == win-32 ]] || [[ $target_platform == win-64 ]] || [[ $target_platform == osx-64 ]]; then - export DISABLE_AUTOBREW=1 - mv DESCRIPTION DESCRIPTION.old - grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - $R CMD INSTALL --build . -else - mkdir -p $PREFIX/lib/R/library/softImpute - mv * $PREFIX/lib/R/library/softImpute -fi +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +$R CMD INSTALL --build . \ No newline at end of file From 76ec8deb5b80c658c62ea6ac500138a1654ba3ab Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?= Date: Mon, 30 Jul 2018 18:33:43 -0300 Subject: [PATCH 08/12] Fix source url --- recipes/r-softimpute/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/r-softimpute/meta.yaml b/recipes/r-softimpute/meta.yaml index 4a42b83a8cf14..4f28418a2030c 100644 --- a/recipes/r-softimpute/meta.yaml +++ b/recipes/r-softimpute/meta.yaml @@ -5,8 +5,8 @@ package: version: {{ version|replace("-", "_") }} source: url: - - {{ cran_mirror }}/src/contrib/softImpute_{{ version }}.tar.gz - - {{ cran_mirror }}/src/contrib/Archive/softImpute/softImpute_{{ version }}.tar.gz + - https://cran.r-project.org/src/contrib/softImpute_{{ version }}.tar.gz + - https://cran.r-project.org/src/contrib/Archive/softImpute/softImpute_{{ version }}.tar.gz sha256: 98f5e66aefbf50a6a170421316a9f4b96651521a2196424245052340e75f9d1d build: number: 0 From 16e4cd0a3a6087aaf232b165a72e730a0626be40 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?= Date: Tue, 7 Aug 2018 09:27:21 -0300 Subject: [PATCH 09/12] Remove r-softimpute --- recipes/r-softimpute/build.sh | 4 ---- recipes/r-softimpute/meta.yaml | 40 ---------------------------------- 2 files changed, 44 deletions(-) delete mode 100644 recipes/r-softimpute/build.sh delete mode 100644 recipes/r-softimpute/meta.yaml diff --git a/recipes/r-softimpute/build.sh b/recipes/r-softimpute/build.sh deleted file mode 100644 index da43ce2168312..0000000000000 --- a/recipes/r-softimpute/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash -mv DESCRIPTION DESCRIPTION.old -grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/r-softimpute/meta.yaml b/recipes/r-softimpute/meta.yaml deleted file mode 100644 index 4f28418a2030c..0000000000000 --- a/recipes/r-softimpute/meta.yaml +++ /dev/null @@ -1,40 +0,0 @@ -{% set version = '1.4' %} - -package: - name: r-softimpute - version: {{ version|replace("-", "_") }} -source: - url: - - https://cran.r-project.org/src/contrib/softImpute_{{ version }}.tar.gz - - https://cran.r-project.org/src/contrib/Archive/softImpute/softImpute_{{ version }}.tar.gz - sha256: 98f5e66aefbf50a6a170421316a9f4b96651521a2196424245052340e75f9d1d -build: - number: 0 - rpaths: - - lib/R/lib/ - - lib/ -requirements: - build: - - {{ compiler('c') }} - - {{ compiler('fortran') }} - host: - - r-base - - r-matrix - run: - - r-base - - r-matrix -test: - commands: - - $R -e "library('softImpute')" -about: - home: 'https://CRAN.R-project.org/package=softImpute' - license: 'GPL-2' - summary: 'Iterative methods for matrix completion that use nuclear-norm regularization. There - are two main approaches.The one approach uses iterative soft-thresholded svds to - impute the missing values. The second approach uses alternating least squares. Both - have an "EM" flavor, in that at each iteration the matrix is completed with the - current estimate. For large matrices there is a special sparse-matrix class named - "Incomplete" that efficiently handles all computations. The package includes procedures - for centering and scaling rows, columns or both, and for computing low-rank SVDs - on large sparse centered matrices (i.e. principal components)' - license_family: 'GPL2' From 67d2dcaba9c221018681d5cdde05ebd8150a10b7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?= Date: Fri, 10 Aug 2018 11:21:48 -0300 Subject: [PATCH 10/12] Add gsl dependency --- recipes/bioconductor-zinbwave/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/bioconductor-zinbwave/meta.yaml b/recipes/bioconductor-zinbwave/meta.yaml index ac8a98c52aa7f..3774c1dc79273 100644 --- a/recipes/bioconductor-zinbwave/meta.yaml +++ b/recipes/bioconductor-zinbwave/meta.yaml @@ -27,6 +27,7 @@ requirements: - r-copula - r-glmnet - r-softimpute + - gsl >=3.4 run: - bioconductor-biocparallel - bioconductor-edger @@ -37,6 +38,7 @@ requirements: - r-copula - r-glmnet - r-softimpute + - gsl >=3.4 test: commands: - '$R -e "library(''{{ name }}'')"' From a60ae1af7521c38cce2bc0c3a76ac85778814a19 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ant=C3=B4nio=20Camargo?= Date: Fri, 10 Aug 2018 12:46:02 -0300 Subject: [PATCH 11/12] Fix gsl version --- recipes/bioconductor-zinbwave/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/bioconductor-zinbwave/meta.yaml b/recipes/bioconductor-zinbwave/meta.yaml index 3774c1dc79273..191577efae938 100644 --- a/recipes/bioconductor-zinbwave/meta.yaml +++ b/recipes/bioconductor-zinbwave/meta.yaml @@ -27,7 +27,7 @@ requirements: - r-copula - r-glmnet - r-softimpute - - gsl >=3.4 + - gsl >=2.4 run: - bioconductor-biocparallel - bioconductor-edger @@ -38,7 +38,7 @@ requirements: - r-copula - r-glmnet - r-softimpute - - gsl >=3.4 + - gsl >=2.4 test: commands: - '$R -e "library(''{{ name }}'')"' From 3b0fb97f9abbb8a65c935f3877f5833742f3d0e2 Mon Sep 17 00:00:00 2001 From: apcamargo Date: Fri, 10 Aug 2018 15:55:10 -0300 Subject: [PATCH 12/12] skip macOS build --- recipes/bioconductor-zinbwave/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/bioconductor-zinbwave/meta.yaml b/recipes/bioconductor-zinbwave/meta.yaml index 191577efae938..e7ef7e0c7f251 100644 --- a/recipes/bioconductor-zinbwave/meta.yaml +++ b/recipes/bioconductor-zinbwave/meta.yaml @@ -13,6 +13,7 @@ source: sha256: 2ac640227b3adc489086fa7f9c797d595fce3ad0e8ef79c80533af7334cced64 build: number: 0 + skip: true # [osx] rpaths: - lib/R/lib/ - lib/