forked from peterjc/pico_galaxy
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy path.travis.yml
150 lines (141 loc) · 6.24 KB
/
.travis.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
# This is a special configuration file to run tests on Travis-CI via
# GitHub notifications when changes are committed.
#
# For technical details, see http://travis-ci.org/ and this blog post
# for background,
# http://blastedbio.blogspot.com/2013/09/using-travis-ci-for-testing-galaxy-tools.html
# Galaxy currently only supports Python 2.7
language: python
cache: pip
jobs:
include:
- stage: lint
python: "2.7"
before_install:
- "if grep -P '\t' *.rst */*/*.rst; then echo 'Tabs are bad, please use four spaces in RST files.'; false; fi"
- "if grep -P '\t' */*/*.xml; then echo 'Tabs are bad, please use four spaces in XML files.'; false; fi"
- "if grep -P '\t' */*/.shed.yml; then echo 'Tabs are bad, please use four spaces in shed YAML files.'; false; fi"
- "if grep -n -r '[[:blank:]]$' *.rst */*/*.rst; then echo 'Please remove trailing whitespace in RST files.'; false; fi"
- "if grep -n -r '[[:blank:]]$' */*/*.xml; then echo 'Please remove trailing whitespace in XML files.'; false; fi"
- "if grep -n -r '[[:blank:]]$' */*/.shed.yml; then echo 'Please remove trailing whitespace in shed YAML files.'; false; fi"
install:
- pip install --upgrade pip setuptools
- pip install flake8 flake8-blind-except flake8-docstrings flake8-rst-docstrings restructuredtext-lint
- echo "Using flake8 to check Python code"
- flake8 .
- echo "Using restructuredtext-lint to check our RST files"
- restructuredtext-lint .
- pip install planemo
script:
- echo "Using planemo lint to check for obvious tool errors"
- planemo shed_lint --tools --fail_level error --ensure_metadata -r ${TRAVIS_BUILD_DIR}
- stage: test
python: "2.7"
env: GALAXY_BRANCH=master
- stage: test
python: "2.7"
env: GALAXY_BRANCH=dev
- stage: deploy
before_install:
- echo "Removing tools we're not testing or deploying"
- for line in $(cat .tt_skip); do rm -rf $line; done
- for line in $(cat .deploy_skip); do rm -rf $line; done
install:
- pip install --upgrade pip setuptools
- pip install planemo
script:
- if [ "$TRAVIS_PULL_REQUEST" == "false" ] && [ "$TRAVIS_BRANCH" == "master" ]; then planemo shed_update --shed_target testtoolshed --force_repository_creation --check_diff --shed_key_from_env TTS_KEY -r datatypes/ tools/ workflows/; fi
# Deployment
# ==========
# This is done with the new TravisCI stages feature, see
# https://blog.travis-ci.com/2017-05-11-introducing-build-stages
#
# Assumes you have set $TTS_KEY in the TravisCI interface,
# and that the test stage passed.
#
# As the deploy is run on a new VM, remove black-listed tools.
#
#
# Planemo Lint
# ============
#
# Planemo can be run to check tools separately from Galaxy, and this
# is fast so we do it *before* the slow process of installing Galaxy
# and running the tool tests.
#
#
# Installing Galaxy
# =================
#
# We want to test with specific branches of Galaxy, so we install it.
#
# Installing Tool Dependencies
# ============================
#
# We also need to install our tool dependencies, e.g. samtools binaries,
# which we will do manually rather than via a (local) Galaxy Tool Shed.
# Tool dependencies defined in this repository can be installed via
# "planemo dependency_script", however we still have to worry about
# dependencies normally done via the Tool Shed (e.g. Biopython,
# mummer) or assumed to be present by Galaxy itself (e.g. samtools).
before_install:
- pip install --upgrade pip setuptools
- pip install planemo requests
- echo "Removing tools we're not going to test"
- for line in $(cat .tt_skip); do rm -rf $line; done
- echo "Fixing permissions on Python eggs cache folder"
- mkdir -p "$HOME/.python-eggs"
- chmod 700 "$HOME/.python-eggs"
- echo "Downloading and setting up dependencies..."
- export INSTALL_DIR=/tmp/dep_install && mkdir $INSTALL_DIR
- export DOWNLOAD_CACHE=/tmp/download_cache && mkdir $DOWNLOAD_CACHE
- planemo dependency_script -r ${TRAVIS_BUILD_DIR}/packages/ ${TRAVIS_BUILD_DIR}/tools/
- bash dep_install.sh
- source env.sh
- echo "Installing MUMmer and its dependencies..."
- sudo apt-get -qq update
- sudo apt-get install -y gnuplot ghostscript
- cd ${TRAVIS_BUILD_DIR}
- wget http://downloads.sourceforge.net/project/mummer/mummer/3.23/MUMmer3.23.tar.gz
- tar -zxvf MUMmer3.23.tar.gz
- cd MUMmer3.23 && make check && make install
- export PATH=$PWD:$PATH
- echo "Installing samtools..."
- cd ${TRAVIS_BUILD_DIR} && mkdir samtools && cd samtools
- wget http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.19-Linux-x86_64.tgz
- tar -zxvf samtools-0.1.19-Linux-x86_64.tgz
- export PATH=$PWD/bin/:$PATH
- echo "Fetching Galaxy ${GALAXY_BRANCH} branch..."
- cd ${TRAVIS_BUILD_DIR}
- wget https://codeload.github.com/galaxyproject/galaxy/tar.gz/${GALAXY_BRANCH}
- tar -zxvf ${GALAXY_BRANCH} | tail
- cd galaxy-${GALAXY_BRANCH}
- echo "Getting Galaxy to install our Python dependencies..."
- echo biopython >> requirements.txt
# Configuring tools within Galaxy
# ===============================
#
# We don't have any special datatypes, and planemo should take care
# of all the test files...
#
# Note https://github.com/galaxyproject/planemo/issues/530 workaround
install:
- cd ${TRAVIS_BUILD_DIR}/galaxy-${GALAXY_BRANCH}
- export GALAXY_TEST_UPLOAD_ASYNC=false
- export GALAXY_TEST_DB_TEMPLATE=https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0127.sqlite
# Explicitly use sample files to generate default *.loc files
- for f in ${TRAVIS_BUILD_DIR}/tool-data/*.loc.sample; do cp "$f" "${f%.sample}"; done
# Then explicitly override them with any non-sample *.loc files
- cp ${TRAVIS_BUILD_DIR}/tool-data/*.loc ${TRAVIS_BUILD_DIR}/galaxy-${GALAXY_BRANCH}/tool-data/
# Then explicitly override them with any test *.loc files
# - cp ${TRAVIS_BUILD_DIR}/test-data/*.loc ${TRAVIS_BUILD_DIR}/galaxy-${GALAXY_BRANCH}/tool-data/
# Testing tools in Galaxy
# =======================
#
# Having setup our Galaxy, and tools, now just call planemo test.
script:
- cd ${TRAVIS_BUILD_DIR}
- planemo --version
- planemo test --no_dependency_resolution --galaxy_root ${TRAVIS_BUILD_DIR}/galaxy-${GALAXY_BRANCH} --skip_venv tools/
notifications:
email: false