-
Notifications
You must be signed in to change notification settings - Fork 1
/
.travis.yml
39 lines (33 loc) · 1.6 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
language: perl
sudo: true
addons:
apt:
packages:
- r-base
- r-base-dev
perl:
- "5.14"
install:
- wget https://github.com/jgm/pandoc/releases/download/1.19.2.1/pandoc-1.19.2.1-1-amd64.deb
- sudo dpkg -i pandoc-1.19.2.1-1-amd64.deb
- wget https://cran.r-project.org/src/base/R-3/R-3.4.0.tar.gz
- tar -xvf R-3.4.0.tar.gz
- pushd R-3.4.0 && ./configure --with-readline=no --with-x --with-cairo --prefix=/usr && make && sudo make install && popd
- sudo Rscript -e "install.packages(c('DT', 'ggplot2', 'ggpubr', 'ggrepel', 'markdown', 'Matrix', 'reshape', 'rmarkdown', 'scales', 'XML'), repos='https://www.stats.bris.ac.uk/R/')"
- sudo Rscript -e "source('http://bioconductor.org/biocLite.R')" -e "biocLite(c('GenomicRanges', 'graph', 'limma', 'SummarizedExperiment', 'S4Vectors'))"
- sudo Rscript -e "source('http://bioconductor.org/biocLite.R')" -e "biocLite(c('DESeq2', 'topGO'))"
- git clone --branch v1.1.3 https://github.com/sanger-pathogens/deago.git
- pushd deago && git archive --format=tar.gz --prefix=deago-1.1.3/ v1.1.3 >deago-1.1.3.tar.gz && popd
- pushd deago && sudo Rscript -e "install.packages('deago-1.1.3.tar.gz', repos = NULL, type='source')" && popd
before_script:
- "export DISPLAY=:99.0"
- "sh -e /etc/init.d/xvfb start"
- sleep 3 # give xvfb some time to start
- cpanm --quiet --notest Dist::Zilla::App::Command::cover
- cpanm --quiet --notest --skip-satisfied Devel::Cover::Report::Codecov
script:
- "dzil authordeps --missing | cpanm --notest"
- "dzil listdeps --missing | cpanm --notest"
- "dzil test"
after_success:
- dzil cover -test -report codecov