Merge pull request #90 from c-mertes/conda_package

Conda packaging

.travis.yml

@@ -1,68 +1,40 @@
 language: python
-sudo: required
 dist: xenial
 
-cache:
-  - directories:
-    - $HOME/R/Library
-    - /usr/bin/R
-    - $HOME/miniconda
-    - $HOME/htslib
-    - $HOME/bcftools
-
-env:
-  global:
-    - DROP_DIR=$(pwd)
-    - PROJECT_DIR="$HOME/project"
-    - MINICONDA_DIR="$HOME/miniconda"
-    - CONDA_SCRIPT="$MINICONDA_DIR/etc/profile.d/conda.sh"
-    - R_LIBS_USER="$HOME/R/Library"
-    - TAR="/bin/tar"
+#cache:
+#  - directories:
+#    - $HOME/miniconda
 
 python:
-  - "3.6.7"
+  - "3.7"
 
-addons:
-  apt:
-    packages:
-      - r-base
-      - libxml2-dev
-      - libcurl4-openssl-dev
-      - libssl-dev
-      - libblas-dev
-      - liblapack-dev
-      - gfortran
-      - graphviz
-      - pandoc
-      - tabix
-    sources:
-      - sourceline: 'deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran35/'
-        key_url: 'http://keyserver.ubuntu.com:11371/pks/lookup?op=get&search=0xe298a3a825c0d65dfd57cbb651716619e084dab9'
-    update: true
-
 install:
-  - cd $DROP_DIR
-#  - R -e "if ('FRASER' %in% rownames(installed.packages())) remove.packages('FRASER')"
-#  - R -e "if ('tMAE' %in% rownames(installed.packages())) remove.packages('tMAE')"
-  - Rscript travis/installRPackages.R drop/requirementsR.txt
-  - bash travis/install_bcftools.sh
-  - export PATH="$HOME/bcftools:$PATH"
-  - bcftools --version
-  - bash travis/install_conda.sh
-  - source $CONDA_SCRIPT
-  - conda activate drop_env
-  - pip install .
+  # Install Anaconda
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O /tmp/miniconda.sh
+  - bash /tmp/miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+
+  - conda config --add channels bioconda
+  - conda config --add channels conda-forge
 
-before_script:
-  - mkdir -p $PROJECT_DIR
-  - cd $PROJECT_DIR
-  - drop demo
+  # build package with cond
+  - conda install conda-build
+  - conda build conda.recipe --output-folder=$HOME/build
+  - conda config --add channels "file://${HOME}/build"
+
+  # test package
+  - source $HOME/miniconda/etc/profile.d/conda.sh
+  - conda create -q -n drop drop
+  - conda activate drop
 
 script: 
-  - cd $PROJECT_DIR
-  - snakemake -n
-  - snakemake aberrantExpression --cores 2
-  - snakemake aberrantSplicing --cores 2
-  - snakemake mae --cores 2
-  - snakemake --cores 2
-  - snakemake exportCounts --cores 2
+  - conda list 
+  - java -version
+  - gatk --help
+  - samtools --version
+  - bcftools --version
+  - drop --version
+  - python --version

conda.recipe/meta.yaml

@@ -0,0 +1,106 @@
+{% set name = "drop" %}
+{% set version = "0.9.0" %}
+
+package:
+  name: "{{ name|lower }}"
+  version: "{{ version }}"
+
+source:
+  path: ..
+
+build:
+  number: 0
+  script: 
+    - "{{ PYTHON }} -m pip install -vv git+https://github.com/gagneurlab/wbuild.git#egg=wbuild"
+    - "${R} -e 'BiocManager::install(\"mumichae/tMAE\", dependencies=FALSE, update=FALSE, ask=FALSE)'"
+    - "{{ PYTHON }} -m pip install . -vv"
+  rpaths:
+    - lib/R/lib/
+    - lib/
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+
+  host:
+    - python
+    - pip
+
+    # wbuild requirements
+    - pyyaml>=4.2b1
+    - pytest-runner
+
+    # tMAE requirements
+    - r-base>=4.0.0
+    - r-devtools
+    - r-biocmanager
+    - r-data.table
+    - r-ggplot2
+    - r-dplyr
+    - bioconductor-DESeq2
+    - bioconductor-GenomicScores 
+
+  run:
+    - python
+    - pandas
+    - Click>=7.0
+    - click-log
+    - python-dateutil
+
+    # snakemake/wbuild
+    - snakemake=>5.5.2
+    - pandoc
+    - graphviz
+    - pyyaml>=4.2b1
+
+    # command line tools
+    - tabix
+    - samtools>=1.7
+    - bcftools>=1.7
+    - gatk4>=4.0.4
+    - star>=2.7
+
+    # R dependencies
+    - r-base>=4.0.0
+    - r-rmarkdown
+    - r-knitr
+    - r-ggplot2
+    - r-ggthemes
+    - r-cowplot
+    - r-data.table
+    - r-dplyr
+    - r-tidyr
+    - r-magrittr
+    - r-devtools
+
+    # bioconductor packages
+    - bioconductor-deseq2
+    - bioconductor-GenomicScores
+    - bioconductor-outrider
+    - bioconductor-fraser
+    - bioconductor-variantannotation
+    - bioconductor-bsgenome.hsapiens.ucsc.hg19
+    #- bioconductor-mafdb.gnomad.r2.1.hs37d5
+    #- bioconductor-mafdb.gnomad.r2.1.grch38
+
+test:
+  imports:
+    - drop
+    - wbuild
+  commands:
+    - ${R} -e "library(tMAE)"
+    - wbuild --version
+    - drop --version
+
+about:
+  home: "https://gagneurlab-drop.readthedocs.io"
+  license: MIT
+  license_family: MIT
+  license_file: ../LICENSE
+  summary: "Detection of RNA Outliers Pipeline"
+  doc_url: 
+  dev_url: 
+
+extra:
+  recipe-maintainers:
+    - mumichae

setup.py

@@ -5,13 +5,6 @@
 with open("README.md", "r") as fh:
     long_description = fh.read()
 
-requirements = [
-    'wbuild @ git+https://github.com/gagneurlab/wBuild.git@master#egg=wbuild',
-    #'wbuild',
-    'snakemake==5.5.2',
-    'pandas',
-]
-
 extra_files = []
 for (path, directories, filenames) in os.walk('drop/'):
     directories[:] = [d for d in directories if not (d.startswith('.') or d == 'Data')]
@@ -32,8 +25,7 @@
     packages=setuptools.find_packages(include=["drop"]),
     entry_points={'console_scripts': ['drop=drop.cli:main']},
     package_data={'drop': extra_files},
-    include_package_data=True,
-    install_requires=requirements
+    include_package_data=True
 )