File: .travis.yml

package info (click to toggle)
shovill 1.1.0-4
  • links: PTS, VCS
  • area: main
  • in suites: bullseye, sid
  • size: 6,408 kB
  • sloc: perl: 603; sh: 35; makefile: 4
file content (38 lines) | stat: -rw-r--r-- 1,067 bytes parent folder | download
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
language: perl

sudo: false

perl:
    - "5.26"

addons:
    apt:
        packages:
            - pigz
            - unzip
            - libstdc++6
            - liblzma5
            - libbz2-1.0
            - zlib1g-dev
            
install:
    - "export PATH=$PWD/.travis:$PWD/bin:$PATH"
    - "mkdir -p deps && cd deps && source install_deps.sh && cd .."
    - "pwd"
    - "echo $HOME"
    - "echo $PATH"
    - "find deps -executable -type f"

script:
    - "kmc"
    - "skesa --version"
    - "shovill --version"
    - "shovill --check"
    - "shovill --help"
    - "! shovill --doesnotexist"
    - "shovill --outdir out.spades --assembler spades --R1 test/R1.fq.gz --R2 test/R2.fq.gz --nostitch --noreadcorr --nocorr"
    - "grep '>' out.spades/contigs.fa"
    - "shovill --outdir out.megahit --assembler megahit --R1 test/R1.fq.gz --R2 test/R2.fq.gz --trim"
    - "grep '>' out.megahit/contigs.fa"
    - "shovill --outdir out.velvet --assembler velvet --R1 test/R1.fq.gz --R2 test/R2.fq.gz --ram 4 --noreadcorr --nocorr"
    - "grep '>' out.velvet/contigs.fa"