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Bulk update 090119b #13002

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Jan 9, 2019
Merged

Bulk update 090119b #13002

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9eb84f3
A few more updates
dpryan79 Jan 9, 2019
892ba82
Fix python in dexseq, since the count script has system requirements …
dpryan79 Jan 9, 2019
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2 changes: 2 additions & 0 deletions build-fail-blacklist
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Original file line number Diff line number Diff line change
Expand Up @@ -943,6 +943,7 @@ recipes/bioconductor-opencyto
recipes/bioconductor-cytoml
recipes/bioconductor-platecore
recipes/bioconductor-ping
recipes/bioconductor-frgepistasis

# missing r-* deps
recipes/bioconductor-mcagui
Expand Down Expand Up @@ -989,6 +990,7 @@ recipes/bioconductor-damirseq
recipes/r-rcdk
recipes/bioconductor-gars
recipes/bioconductor-isogenegui
recipes/bioconductor-bridgebr

# Missing root dependency
recipes/bioconductor-xps
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4 changes: 3 additions & 1 deletion recipes/bioconductor-dexseq/meta.yaml
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Expand Up @@ -12,7 +12,7 @@ source:
- 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
md5: 0852b22f25f3a3be615c118a2d0de719
build:
number: 0
number: 1
rpaths:
- lib/R/lib/
- lib/
Expand Down Expand Up @@ -57,6 +57,8 @@ requirements:
- r-rcolorbrewer
- r-statmod
- r-stringr
- python <3
- 'htseq >=0.6.1,<0.10.0' # dexseq_count.py performes an overly simplistic version check
test:
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@nturaga Can you relay python 2 and htseq as system requirements upstream for the dexseq package? We noticed this during the 3.7 release as well. Those are both needed for the counting script to work, which is pretty integral for actually using the package.

commands:
- '$R -e "library(''{{ name }}'')"'
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2 changes: 2 additions & 0 deletions recipes/bioconductor-isolde/meta.yaml
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Expand Up @@ -21,9 +21,11 @@ requirements:
- r-base
run:
- r-base
- llvm-openmp # [osx]
build:
- {{ compiler('c') }}
- make
- llvm-openmp # [osx]
test:
commands:
- '$R -e "library(''{{ name }}'')"'
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6 changes: 3 additions & 3 deletions recipes/bioconductor-process/meta.yaml
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@@ -1,4 +1,4 @@
{% set version = "1.58.0" %}
{% set version = "1.58.1" %}
{% set name = "PROcess" %}
{% set bioc = "3.8" %}

Expand All @@ -10,7 +10,7 @@ source:
- 'https://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|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
md5: e0b3f4defaace7d76c7b0c95792dfa53
md5: a5b428d7ac389fb7f808711e6012b880
build:
number: 0
rpaths:
Expand Down Expand Up @@ -38,5 +38,5 @@ extra:
parent_recipe:
name: bioconductor-process
path: recipes/bioconductor-process
version: 1.56.0
version: 1.58.0

9 changes: 7 additions & 2 deletions recipes/bioconductor-sparsedossa/meta.yaml
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@@ -1,4 +1,4 @@
{% set version = "1.6.0" %}
{% set version = "1.6.1" %}
{% set name = "sparseDOSSA" %}
{% set bioc = "3.8" %}

Expand All @@ -10,7 +10,7 @@ source:
- 'https://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|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
md5: afa11ea4a0e219d6ad6c0e2049805e32
md5: 9e7046fa4bc0bd007589073a9784f89b
build:
number: 0
rpaths:
Expand Down Expand Up @@ -38,4 +38,9 @@ about:
home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
license: 'MIT + file LICENSE'
summary: 'The package is to provide a model based Bayesian method to characterize and simulate microbiome data. sparseDOSSA''s model captures the marginal distribution of each microbial feature as a truncated, zero-inflated log-normal distribution, with parameters distributed as a parent log-normal distribution. The model can be effectively fit to reference microbial datasets in order to parameterize their microbes and communities, or to simulate synthetic datasets of similar population structure. Most importantly, it allows users to include both known feature-feature and feature-metadata correlation structures and thus provides a gold standard to enable benchmarking of statistical methods for metagenomic data analysis.'
extra:
parent_recipe:
name: bioconductor-sparsedossa
path: recipes/bioconductor-sparsedossa
version: 1.6.0

9 changes: 7 additions & 2 deletions recipes/bioconductor-sparsenetgls/meta.yaml
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@@ -1,4 +1,4 @@
{% set version = "1.0.0" %}
{% set version = "1.0.1" %}
{% set name = "sparsenetgls" %}
{% set bioc = "3.8" %}

Expand All @@ -10,7 +10,7 @@ source:
- 'https://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'
md5: bac14ecd5a32e5618159719c549b9c1b
md5: 7ef7d3b5a974cbdcaca5c4db001fab0a
build:
number: 0
rpaths:
Expand Down Expand Up @@ -41,4 +41,9 @@ about:
home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
license: GPL-3
summary: 'The package provides methods of combining the graph structure learning and generalized least squares regression to improve the regression estimation. The main function sparsenetgls() provides solutions for multivariate regression with Gaussian distributed dependant variables and explanatory variables utlizing multiple well-known graph structure learning approaches to estimating the precision matrix, and uses a penalized variance covariance matrix with a distance tuning parameter of the graph structure in deriving the sandwich estimators in generalized least squares (gls) regression. This package also provides functions for assessing a Gaussian graphical model which uses the penalized approach. It uses Receiver Operative Characteristics curve as a visualization tool in the assessment.'
extra:
parent_recipe:
name: bioconductor-sparsenetgls
path: recipes/bioconductor-sparsenetgls
version: 1.0.0

6 changes: 3 additions & 3 deletions recipes/bioconductor-specl/meta.yaml
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@@ -1,4 +1,4 @@
{% set version = "1.16.0" %}
{% set version = "1.16.1" %}
{% set name = "specL" %}
{% set bioc = "3.8" %}

Expand All @@ -10,7 +10,7 @@ source:
- 'https://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|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
md5: 7a519bb898df6985b4ca6e40787c5730
md5: 774f0ddb159c33a064c365095404f807
build:
number: 0
rpaths:
Expand Down Expand Up @@ -44,5 +44,5 @@ extra:
parent_recipe:
name: bioconductor-specl
path: recipes/bioconductor-specl
version: 1.14.0
version: 1.16.0