biosails · jerowe · Nov 20, 2017 · Nov 21, 2017 · Dec 5, 2017 · Dec 5, 2017
diff --git a/.travis.yml b/.travis.yml
@@ -5,29 +5,49 @@ services:
 install: scripts/travis-setup.sh
 cache:
   directories:
-  - "/home/travis/.conda/pkgs"
+  - "/opt/anaconda3/pkgs"
 jobs:
   include:
-  - stage: Linux+macOS
+  - stage: Linux
     if: "(type = push) AND ((branch IN (master, bulk)) OR (fork = true))"
     os: linux
-    script: scripts/travis-run.sh
+    script: travis_wait 30 scripts/travis-run-conda-build-all.sh
   - stage: Linux
     if: type = pull_request
     os: linux
-    script: scripts/travis-run.sh
+    script: travis_wait 30 scripts/travis-run-conda-build-all.sh
 env:
   global:
-  - SUBDAGS=1
-  - BIOCONDA_UTILS_TAG=master
-  - BIOCONDA_UTILS_BUILD_ARGS="--loglevel=info"
-  - BIOCONDA_UTILS_LINT_ARGS=
-  - MINICONDA_VER="4.3.21"
-  - ANACONDA_USER='nyuad-cgsb'
-  - GITHUB_USER='nyuad-cgsb'
-  - MY_TRAVIS_REPO_SLUG='biosails/biostacks'
-  - CONTAINER_NAMESPACE='nyuad_cgsb'
-  - CONDA_PKGS_DIRS='/home/travis/.conda/pkgs'
+  - MINICONDA_VER: '4.3.21'
+  - ANACONDA_USER: 'nyuad-cgsb'
+  - GITHUB_USER: 'nyuad-cgsb'
+  - MY_TRAVIS_REPO_SLUG: 'biosails/biostacks'
+  - CONTAINER_NAMESPACE: 'nyuad_cgsb'
+  - CONDA_PKGS_DIRS: '/opt/anaconda3/pkgs'
+  - CONDA_BLD_PATH: '/opt/anaconda3/conda-bld'
+  - CONDA_R: '3.4.1'
+  - CONDA_PERL: '5.22.0'
+  - CONDA_HTSLIB: "1.6"
+  - CONDA_BOOST: "1.64"
+  - CONDA_NPY: "112"
+  - CONDA_NCURSES: "5.9"
+  - CONDA_GSL: "1.16"
+  - CONDA_GMP: "5.1"
+  - CONDA_HDF5: "1.8.17"
+  - CONDA_ZLIB: "1.2.8"
+  - CONDA_BZIP2: "1.0"
+  - CONDA_XZ: "5.2"
+  # - SUBDAGS=1
+  # - BIOCONDA_UTILS_TAG=master
+  # - BIOCONDA_UTILS_BUILD_ARGS="--loglevel=debug"
+  # - BIOCONDA_UTILS_LINT_ARGS=
+  # - MINICONDA_VER="4.3.21"
+  # - ANACONDA_USER='nyuad-cgsb'
+  # - GITHUB_USER='nyuad-cgsb'
+  # - MY_TRAVIS_REPO_SLUG='biosails/biostacks'
+  # - CONTAINER_NAMESPACE='nyuad_cgsb'
+  # - CONDA_PKGS_DIRS='/opt/anaconda3/pkgs'
+  # - CONDA_BLD_PATH='/opt/anaconda3/conda-bld'
   - secure: 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
   - secure: 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
   - secure: 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

diff --git a/Dockerfile b/Dockerfile
@@ -0,0 +1,24 @@
+from continuumio/miniconda3
+
+ARG CONDA_PKG=local
+ENV CONDA_PKG ${CONDA_PKG}
+
+RUN echo ${CONDA_PKG}
+RUN which conda
+RUN conda info
+RUN mkdir -p /opt/conda/conda-bld/linux-64
+
+## We have to add the pkgs and the build-system
+COPY pkgs/* /opt/conda/pkgs/
+COPY conda-bld/linux-64/${CONDA_PKG} /opt/conda/conda-bld/linux-64
+
+RUN conda config --set always_yes yes --set changeps1 no
+RUN conda config --add channels r
+RUN conda config --add channels conda-forge
+RUN conda config --add channels bioconda
+RUN conda config --add channels nyuad-cgsb
+
+RUN ls -lah /opt/conda/conda-bld/linux-64
+RUN conda config --add channels file://opt/conda/conda-bld/linux-64
+RUN conda index /opt/conda/conda-bld/linux-64
+RUN conda install -y --use-local gencore_rnaseq
diff --git a/configs/bioconda_utils-requirements.txt b/configs/bioconda_utils-requirements.txt
@@ -0,0 +1,23 @@
+anaconda-client=1.6.3
+argh=0.26.2
+beautifulsoup4=4.6.0
+conda=4.3.21
+conda-build=2.1.16
+galaxy-lib=17.9.7
+jinja2=2.9.6
+jsonschema=2.5.1
+networkx=1.11
+pyaml=15.8.2
+pydotplus=2.0.2
+python=3.5.2
+requests=2.12.4
+sphinx
+docutils
+sphinx_rtd_theme
+involucro=1.1.2
+pandas=0.19.2
+numpy=1.12.1
+pygithub=1.29
+colorlog=2.10.*
+six=1.10.0
+alabaster=0.7.9
diff --git a/recipes/gencore_rnaseq/1.0/meta.yaml b/recipes/gencore_rnaseq/1.0/meta.yaml
@@ -0,0 +1,54 @@
+{% set name = "gencore_rnaseq" %}
+{% set version = "1.0" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+build:
+  number: 1
+  skip: True # [osx]
+
+requirements:
+  run:
+  ##Alignment
+  - samtools ==1.3.1
+  - kallisto ==0.43.0
+  # - cufflinks-patch ==2.2.1
+  # - bowtie2 ==2.2.8
+  # - tophat ==2.1.0
+  # - star ==2.5.2a
+  # - bcftools ==1.3.1
+  # - blat ==35
+  # - gatk ==3.6
+  # - picard ==2.5.0
+  # - prinseq ==0.20.4
+  # - vcftools ==0.1.14
+  # - bedtools ==2.25.0
+  # - vcflib ==1.0.0_rc1
+  # - bamtools ==2.4.0
+  # - seqtk ==1.2
+  ##Downstream processing
+  - r-base
+  # - r-essentials
+  # - r-cairo
+  # - bioconductor-deseq2
+  # - bioconductor-edger >=3.14.0
+  # - bioconductor-cummerbund >=2.16.0
+  # - bioconductor-genomicranges >=1.26.1
+  # - bioconductor-gviz >=1.16.5
+  # - bioconductor-biovizbase >=1.18.0
+  # - bioconductor-s4vectors >=0.12.0
+  # - bioconductor-ballgown >=2.2.0
+  # - htseq ==0.6.1.post1
+  # - hisat2 ==2.0.4
+  # - stringtie ==1.3.0
+
+test:
+  commands:
+    - bowtie2 --help 2>&1 | grep "bowtie"
+
+about:
+  home: 'https://cgsb.abudhabi.nyu.edu/'
+  license: BSD
+  summary: 'Gencore RnaSeq Module'
diff --git a/scripts/build_docs.py b/scripts/build_docs.py
@@ -0,0 +1,11 @@
+#!/usr/bin/env python
+
+from conda_build.config import Config
+from conda_build.metadata import MetaData
+from conda_build.render import render_recipe
+
+recipe_dir = 'recipes/gencore_rnaseq/1.0/meta.yaml'
+
+config =  Config(croot=recipe_dir, anaconda_upload=False, verbose=True,
+activate=False, debug=False, variant=None)
+metadata = render_recipe(recipe_dir, config=config)
diff --git a/scripts/travis-run-conda-build-all.sh b/scripts/travis-run-conda-build-all.sh
@@ -0,0 +1,54 @@
+#!/bin/bash
+set -euo pipefail
+# Set some defaults
+set +u
+[[ -z $DOCKER_ARG ]] && DOCKER_ARG=""
+[[ -z $TRAVIS ]] && TRAVIS="false"
+[[ -z $BIOCONDA_UTILS_LINT_ARGS ]] && BIOCONDA_UTILS_LINT_ARGS=""
+[[ -z $RANGE_ARG ]] && RANGE_ARG="--git-range master HEAD"
+[[ -z $DISABLE_BIOCONDA_UTILS_BUILD_GIT_RANGE_CHECK  ]] && DISABLE_BIOCONDA_UTILS_BUILD_GIT_RANGE_CHECK="false"
+[[ -z $SKIP_LINTING ]] && SKIP_LINTING=false
+[[ -z $UPLOAD_ARG ]] && UPLOAD_ARG=""
+set -u
+
+if [[ $TRAVIS_BRANCH != "master" && $TRAVIS_BRANCH != "bulk" && $TRAVIS_PULL_REQUEST == "false" && $TRAVIS_REPO_SLUG == "$MY_TRAVIS_REPO_SLUG" ]]
+then
+    echo ""
+    echo "Tests are skipped for pushes to the main bioconda-recipes repo."
+    echo "If you have opened a pull request, please see the full tests for that PR."
+    echo "See https://bioconda.github.io/build-system.html for details"
+    echo ""
+    exit 0
+fi
+
+
+# TODO Add another upload
+if [[ ( $TRAVIS_BRANCH == "master" || $TRAVIS_BRANCH == "bulk" ) && "$TRAVIS_PULL_REQUEST" == "false" && $TRAVIS_REPO_SLUG == "$MY_TRAVIS_REPO_SLUG" ]]
+then
+        UPLOAD_ARG="--upload-channels nyuad-cgsb "
+fi
+
+
+if [[ $DISABLE_BIOCONDA_UTILS_BUILD_GIT_RANGE_CHECK == "true" ]]
+then
+    echo
+    echo "DISABLE_BIOCONDA_UTILS_BUILD_GIT_RANGE_CHECK is true."
+    echo "A comprehensive check will be performed to see what needs to be built."
+    RANGE_ARG=""
+fi
+
+set -x
+
+export PATH=/home/travis/anaconda3/bin:$PATH
+conda install -y conda-build-all
+conda-build-all recipes --inspect-channels nyuad-cgsb $UPLOAD_ARG
+ls -lahR $CONDA_BLD_PATH
+
+echo "We should be building things now...."
+
+cp Dockerfile /opt/anaconda3
+cd /opt/anaconda3
+docker build --build-arg CONDA_PKG='gencore_rnaseq-1.0-r3.4.1_1.tar.bz2' -t 'gencore_rnaseq:1.0-r3.4.1_1' .
+
+docker images
+set +x
diff --git a/scripts/travis-run.sh b/scripts/travis-run.sh
@@ -8,7 +8,6 @@ set +u
 [[ -z $RANGE_ARG ]] && RANGE_ARG="--git-range master HEAD"
 [[ -z $DISABLE_BIOCONDA_UTILS_BUILD_GIT_RANGE_CHECK  ]] && DISABLE_BIOCONDA_UTILS_BUILD_GIT_RANGE_CHECK="false"
 [[ -z $SKIP_LINTING ]] && SKIP_LINTING=false
-# [[ -z $CONTAINER_NAMESPACE ]] && CONTAINER_NAMESPACE="nyuad_cgsb"
 set -u
 
 if [[ $TRAVIS_BRANCH != "master" && $TRAVIS_BRANCH != "bulk" && $TRAVIS_PULL_REQUEST == "false" && $TRAVIS_REPO_SLUG == "$MY_TRAVIS_REPO_SLUG" ]]
@@ -74,7 +73,8 @@ export PATH=/anaconda/bin:$PATH
 # for local testing.
 if [[ $TRAVIS_OS_NAME == "linux" && $TRAVIS == "true" ]]
 then
-    DOCKER_ARG="--docker --mulled-test"
+    DOCKER_ARG="--mulled-test"
+    #DOCKER_ARG=" --mulled-test"
 fi
 
 # When building master or bulk, upload packages to anaconda and quay.io.
@@ -111,6 +111,6 @@ fi
 
 set -x
 pip install --upgrade  git+https://github.com/jerowe/bioconda-utils.git@develop
-bioconda-utils build recipes config.yml $UPLOAD_ARG $DOCKER_ARG $BIOCONDA_UTILS_BUILD_ARGS $RANGE_ARG || echo "Build Failed!"
+bioconda-utils build recipes config.yml  $UPLOAD_ARG $DOCKER_ARG $BIOCONDA_UTILS_BUILD_ARGS $RANGE_ARG || echo "Build Failed!"
 docker images
 set +x
diff --git a/scripts/travis-setup.sh b/scripts/travis-setup.sh
@@ -24,12 +24,20 @@ done
 SCRIPT_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
 
 pip install pyyaml
-sudo mkdir /anaconda
-sudo chown -R $USER /anaconda
-$SCRIPT_DIR/../simulate-travis.py --bootstrap /anaconda --overwrite
-/anaconda/bin/conda index /anaconda/conda-bld/linux-64 /anaconda/conda-bld/osx-64
-/anaconda/bin/conda config --add channels file://anaconda/conda-bld
-/anaconda/bin/conda install -y r-base r-essentials openjdk perl bioconductor-biobase
-
-/anaconda/bin/conda info
-ls -lah /home/travis/.conda/pkgs
+
+sudo chown -R $USER /opt/anaconda3
+
+wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh --quiet -O miniconda.sh
+bash miniconda.sh -b -p /home/travis/anaconda3
+export PATH="/home/travis/anaconda3/bin:$PATH"
+hash -r
+conda config --set always_yes yes --set changeps1 no
+conda config --add channels r
+conda config --add channels conda-forge
+conda config --add channels bioconda
+conda config --add channels nyuad-cgsb
+
+# conda index /home/travis/anaconda3/conda-bld/linux-64
+# conda config --add channels file://home/travis/anaconda3/conda-bld
+conda install -y r-base r-essentials openjdk perl bioconductor-biobase nodejs
+npm install -g marked-man