From baa6ac4d8642880c65e8d7912841e4fabeeab8d9 Mon Sep 17 00:00:00 2001
From: xtrojak <trojak@mail.muni.cz>
Date: Fri, 20 Aug 2021 12:09:33 +0200
Subject: [PATCH 1/2] Added conda env config files

---
 conda/environment-build.yaml | 25 +++++++++++++
 conda/environment-dev.yaml   | 24 ++++++++++++
 conda/meta.yaml              | 72 ++++++++++++++++++++++++++++++++++++
 3 files changed, 121 insertions(+)
 create mode 100644 conda/environment-build.yaml
 create mode 100644 conda/environment-dev.yaml
 create mode 100644 conda/meta.yaml

diff --git a/conda/environment-build.yaml b/conda/environment-build.yaml
new file mode 100644
index 00000000..8d2037d9
--- /dev/null
+++ b/conda/environment-build.yaml
@@ -0,0 +1,25 @@
+name: recetox-aplcms-build
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - anaconda-client
+  - conda-build
+  - conda-verify
+  - r-base >=3.5
+  - r-mass
+  - r-rgl
+  - bioconductor-mzR
+  - r-splines2
+  - r-doparallel
+  - r-foreach
+  - r-iterators
+  - r-snow
+  - r-gbm
+  - r-e1071
+  - r-randomForest
+  - r-rocr
+  - r-rocs
+  - r-rcpp
+  - r-arrow
\ No newline at end of file
diff --git a/conda/environment-dev.yaml b/conda/environment-dev.yaml
new file mode 100644
index 00000000..9be08f8e
--- /dev/null
+++ b/conda/environment-dev.yaml
@@ -0,0 +1,24 @@
+name: recetox-aplcms
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - r-base >= 3.5
+  - r-devtools
+  - r-biocmanager
+  - r-mass
+  - r-rgl
+  - bioconductor-mzR
+  - r-splines2
+  - r-doparallel
+  - r-foreach
+  - r-iterators
+  - r-snow
+  - r-gbm
+  - r-e1071
+  - r-randomForest
+  - r-rocr
+  - r-rocs
+  - r-rcpp
+  - r-arrow
\ No newline at end of file
diff --git a/conda/meta.yaml b/conda/meta.yaml
new file mode 100644
index 00000000..2be3d0e8
--- /dev/null
+++ b/conda/meta.yaml
@@ -0,0 +1,72 @@
+{% set name = "recetox-aplcms" %}
+{% set version = "0.9.3" %}
+{% set github = "https://github.com/RECETOX/recetox-aplcms" %}
+
+package:
+  name: "r-{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  path: ./
+
+build:
+  number: 0
+  noarch: generic
+  rpaths:
+    - lib/
+    - lib/R/lib/
+  script: R CMD INSTALL --build .
+
+
+requirements:
+  host:
+    - r-base >=3.5
+    - r-mass
+    - r-rgl
+    - bioconductor-mzR
+    - r-splines2
+    - r-doparallel
+    - r-foreach
+    - r-iterators
+    - r-snow
+    - r-gbm
+    - r-e1071
+    - r-randomForest
+    - r-rocr
+    - r-rocs
+    - r-rcpp
+
+  run:
+    - r-base >= 3.5
+    - r-devtools
+    - r-biocmanager
+    - r-mass
+    - r-rgl
+    - bioconductor-mzR
+    - r-splines2
+    - r-doparallel
+    - r-foreach
+    - r-iterators
+    - r-snow
+    - r-gbm
+    - r-e1071
+    - r-randomForest
+    - r-rocr
+    - r-rocs
+    - r-rcpp
+    - r-arrow
+
+test:
+  commands:
+    - $R -e "library(recetox.recetox-aplcms)"
+
+about:
+  home: "{{ github }}"
+  license: GPL2.0
+  summary: apLCMS is a software which generates a feature table from a batch of LC/MS spectra. A modified fork of the original apLCMS by Tianwei Yu.
+
+extra:
+  maintainers:
+    - RECETOX/conda
+  identifiers:
+    - doi:10.1093/bioinformatics/btp291

From c6d58d2b8fcf72c115c2d977b664c147bf92b924 Mon Sep 17 00:00:00 2001
From: xtrojak <trojak@mail.muni.cz>
Date: Wed, 25 Aug 2021 08:53:28 +0200
Subject: [PATCH 2/2] Fixed issues in meta file such that conda build works

---
 conda/meta.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/conda/meta.yaml b/conda/meta.yaml
index 2be3d0e8..5caebbf1 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -7,7 +7,7 @@ package:
   version: "{{ version }}"
 
 source:
-  path: ./
+  path: ..
 
 build:
   number: 0
@@ -37,7 +37,7 @@ requirements:
     - r-rcpp
 
   run:
-    - r-base >= 3.5
+    - r-base >=3.5
     - r-devtools
     - r-biocmanager
     - r-mass
@@ -58,7 +58,7 @@ requirements:
 
 test:
   commands:
-    - $R -e "library(recetox.recetox-aplcms)"
+    - $R -e "library(recetox.aplcms)"
 
 about:
   home: "{{ github }}"