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.travis.yml
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.travis.yml
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os: linux
sudo: required
jdk:
- openjdk8
services:
- docker
branches:
only:
- master
language: go
go:
- "1.13"
python:
- "3.7"
addons:
apt:
packages:
- flawfinder
- squashfs-tools
- uuid-dev
- libuuid1
- libffi-dev
- libssl-dev
- libssl1.0.0
- libarchive-dev
- libgpgme11-dev
- libseccomp-dev
homebrew:
packages:
- squashfs
update: true
sudo: required
#dist: trusty
matrix:
include:
- python: "2.6"
- python: "3.5"
before_install:
- sudo chmod u+x .travis/*.sh
- /bin/bash .travis/setup.sh
install:
- sudo apt-get -qq update
- sudo apt-get -qq -y install graphviz realpath
script:
- curl -fsSL get.nextflow.io | bash
- singularity pull --name biocontainers-adapterremoval-v2.2.0-1-deb_cv1.img.pulling.1606372209985 docker://biocontainers/adapterremoval:v2.2.0-1-deb_cv1
- travis_wait ./nextflow run eDNAFlow.nf --reads "./testData2_Play/test_30000reads.fastq" --barcode "./testData2_Play/se_bc*" --blast_db "`realpath ./testData2_Play/fake_db/fakeDB.fasta`" --lulu "lulu.R"
- travis_wait 50 ./nextflow run eDNAFlow.nf --taxonomyAssignment --zotuTable "./testData2_Play/curated_zotuTable_2test_LCAscript.tab" --blastFile "./testData2_Play/blastResult_2test_LCAscript.tab" --lca_qcov '100' --lca_pid '98' --lca_diff '1' --lca_output "lca_result"