-
Notifications
You must be signed in to change notification settings - Fork 40
/
.travis.yml
41 lines (39 loc) · 1.68 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
language: python
python:
# We don't actually use the Travis Python, but this keeps it organized.
- "3.8.6"
install:
# set up conda
- sudo apt-get update
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
- bash miniconda.sh -b -p $HOME/miniconda
- export PATH="$HOME/miniconda/bin:$PATH"
- hash -r
- conda config --set always_yes yes --set changeps1 no
- conda update -q conda
# clone metagem repo
- git clone https://github.com/franciscozorrilla/metaGEM.git && cd metaGEM
# set up mamba
- travis_wait 30 conda create --quiet --prefix ./envs/mamba mamba -c conda-forge && source activate envs/mamba
# set up metagem
- travis_wait 30 mamba env create --quiet --prefix ./envs/metagem -f envs/metaGEM_env.yml
- source activate envs/metagem
# This causes TRAVIS CI specific error, something to do with the setuptools version - pip install --quiet --user memote carveme smetana
- source deactivate && source activate envs/mamba
# set up metawrap
- travis_wait 30 mamba env create --quiet --prefix ./envs/metawrap -f envs/metaWRAP_env.yml
# set up prokka-roary
- travis_wait 30 mamba env create --quiet --prefix ./envs/prokkaroary -f envs/prokkaroary_env.yml
# set root dir
- echo -e "Setting current directory to root in config.yaml file ... \n" && root=$(pwd) && sed -i "2s~/.*$~$root~" config.yaml
# set scratch dir
- mkdir -p tmp
- echo -e "Setting tmp directory in config.yaml file ... \n" && scratch=$(pwd|sed 's|$|/tmp|g') && sed -i "3s~/.*$~$scratch~" config.yaml
script:
- source activate envs/metagem
# run createFolders
- snakemake createFolders -j1
# run downloadToy
- snakemake downloadToy -j1
# run fastp
- snakemake all -j1