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Travis Tests for ExoSeq #13
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| sudo: required | ||
| language: java | ||
| jdk: openjdk8 | ||
| services: | ||
| - docker | ||
| python: | ||
| - "2.7" | ||
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| cache: pip | ||
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| matrix: | ||
| fast_finish: true | ||
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| install: | ||
| - "./scripts/install.sh --tool $TOOL_INSTALL" | ||
| # Install nf-core/tools | ||
| - git clone https://github.com/nf-core/tools.git /tmp/nf-core-tools | ||
| - cd /tmp/nf-core-tools | ||
| - pip install --user -e . | ||
| # Get Kit Files | ||
| - wget -O kits.tar.bz2 https://qbic-intranet.am10.uni-tuebingen.de/owncloud/index.php/s/Qvku3etEqb3PW58/download | ||
| # Get tiny Reference Files | ||
| # Reset | ||
| - cd ${TRAVIS_BUILD_DIR}/tests | ||
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| env: | ||
| global: | ||
| - NXF_VER=0.27.6 SGT_VER=2.4.2 | ||
|
There was a problem hiding this comment. Should use the minimum version of Nextflow but also the latest, that way we catch new bugs triggered by new releases. |
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| matrix: | ||
| - PROFILE=docker TEST=TOOLS TOOL_INSTALL=ALL | ||
| - PROFILE=singularity TEST=TOOLS TOOL_INSTALL=ALL | ||
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| script: | ||
| - "nf-core lint ${TRAVIS_BUILD_DIR}" | ||
| - "./scripts/test.sh --profile $PROFILE --test $TEST" | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,42 @@ | ||
| #!/bin/bash | ||
| #Credit to the Sarek devs at https://github.com/SciLifeLab/Sarek | ||
| TOOL="all" | ||
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| while [[ $# -gt 0 ]] | ||
| do | ||
| key="$1" | ||
| case $key in | ||
| -t|--tool) | ||
| TOOL="$2" | ||
| shift # past argument | ||
| shift # past value | ||
| ;; | ||
| *) # unknown option | ||
| shift # past argument | ||
| ;; | ||
| esac | ||
| done | ||
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| # Install Nextflow | ||
| if [[ "$TOOL" = nextflow ]] || [[ "$TOOL" = all ]] | ||
| then | ||
| cd $HOME | ||
| curl -fsSL get.nextflow.io | bash | ||
| chmod +x nextflow | ||
| sudo mv nextflow /usr/local/bin/ | ||
| fi | ||
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| # Install Singularity | ||
| if [[ "$TOOL" = singularity ]] || [[ "$TOOL" = all ]] | ||
| then | ||
| sudo apt-get install squashfs-tools | ||
| cd $HOME | ||
| wget https://github.com/singularityware/singularity/releases/download/$SGT_VER/singularity-$SGT_VER.tar.gz | ||
| tar xvf singularity-$SGT_VER.tar.gz | ||
| cd singularity-$SGT_VER | ||
| ./configure --prefix=/usr/local | ||
| make | ||
| sudo make install | ||
| cd .. | ||
| rm -rf singularity-$SGT_VER* | ||
| fi |
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Maybe time to start playing with https://github.com/nf-core/test-datasets ?
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I just wondered how we should do that. My plan was to use the smallGrch37 by @maxulysse and @szilvajuhos https://github.com/szilvajuhos/smallRef, together with the Kit files and a very tiny small dataset that I already have. So maybe we should quickly have a decision on how to structure the test-datasets repository in a ticket there?
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By the way, https://github.com/SciLifeLab/Sarek-data is now used for testing in Sarek.
cf: SciLifeLab/Sarek#577