Nextflow pipeline to create GO/Phenotypes annotations for pangenomes #1070
Travis CI / Travis CI - Pull Request
succeeded
Mar 5, 2024 in 9m 32s
Build Passed
Details
This is a pull request build.
It is running a build against the merge commit, after merging #1070 Nextflow pipeline to create GO/Phenotypes annotations for pangenomes.
Any changes that have been made to the postreleasefix/112 branch before the build ran are also included.
Jobs and Stages
This build has two jobs, running in parallel.
| Job | Perl | ENV | OS | State |
|---|---|---|---|---|
| 5932.1 |
5.14 | AUTH_TOKEN=[secure] | Linux | passed |
| 5932.2 |
5.26 | AUTH_TOKEN=[secure] | Linux | passed |
Build Configuration
| Build Option | Setting |
|---|---|
| Language | Perl |
| Operating System | Linux (Trusty) |
| Perl Versions | 5.14, 5.26 |
Build Configuration
{
"language": "perl",
"os": [
"linux"
],
"dist": "trusty",
"perl": [
"5.14",
"5.26"
],
"env": [
"global=AUTH_TOKEN=[secure] jobs={:COVERALLS=>\"true\", :DB=>\"mysql\"}={:COVERALLS=>\"false\", :DB=>\"mysql\"}"
],
"sudo": false,
"addons": {
"apt": {
"packages": [
"unzip"
]
}
},
"services": [
"mysql"
],
"before_install": [
"export ENSEMBL_BRANCH=main",
"git clone --branch $ENSEMBL_BRANCH --depth 1 https://github.com/Ensembl/ensembl-test.git",
"git clone --branch $ENSEMBL_BRANCH --depth 1 https://github.com/Ensembl/ensembl.git",
"git clone --branch main --depth 1 https://github.com/Ensembl/ensembl-hive.git",
"git clone --branch $ENSEMBL_BRANCH --depth 1 https://github.com/Ensembl/ensembl-io.git",
"git clone --branch $ENSEMBL_BRANCH --depth 1 https://github.com/Ensembl/ensembl-funcgen.git",
"git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git",
"git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git",
"cd htslib",
"make",
"cd ..",
"export HTSLIB_DIR=$PWD/htslib",
"cd C_code/",
"make",
"cd ../",
"export CWD=$PWD",
"export DEPS=$HOME/dependencies",
"mkdir -p $DEPS",
"cd $DEPS",
"$CWD/travisci/get_dependencies.sh",
"cd $CWD"
],
"install": [
"export CWD=$PWD",
"export PERL5LIB=$PWD/bioperl-live:$PERL5LIB",
"export DEPS=$HOME/dependencies",
"export KENT_SRC=\"$DEPS/kent-335_base/src\"",
"export MACHTYPE=$(uname -m)",
"export CFLAGS=\"-fPIC\"",
"cd $DEPS",
"$CWD/travisci/build_c.sh",
"cd $CWD",
"cpanm --quiet --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile .",
"cpanm --quiet --installdeps --with-recommends --notest .",
"cpanm --quiet -n Devel::Cover::Report::Coveralls",
"cp travisci/MultiTestDB.conf.travisci modules/t/MultiTestDB.conf"
],
"script": [
"./travisci/harness.sh"
],
"jobs": {
"exclude": [
{
"perl": "5.14",
"env": [
{
"COVERALLS": "false",
"DB": "mysql"
}
]
},
{
"perl": "5.26",
"env": [
{
"COVERALLS": "true",
"DB": "mysql"
}
]
}
]
},
"notifications": {
"email": [
{
"on_success": "always",
"on_failure": "always"
}
],
"slack": [
{
"rooms": [
{
"secure": "ddpvJ5UJ+rEcllroQYpPg381+5iPDIt5VDlu1Zeepwx9KeUofJpGWO0H4SJjp75+3uKubEhaSJWnh0No296Lv8rtbZkji3rwmK/qxX3OtzVu9LtMx5+7MRQymI54D6j9gzZ2QKR0DW+K3GwBYR31KqmyZIhnKd0UeTVbEXuaQqVk2Oe4LdzZJkezNgdphuz3cFsaqd2fg85PXNgbfGLwdbGRDl+39m6wQ1nWqzTDqO/NECCeheev1OYTYXdM49rd6NyfMeUMZujwuix+YLN6Ph7ePTyxuheE+PQSvJkoFCxpnsly9rxqo/594RwcDa8OsJPLm8cN6+5L8zmb4M5UfGtUFHsK9usp96DguaadAG3esnkwdQ6QI2w8x/+3l1IesvnPJFTNtwU6iY9MvGKq6Zgb6X5tNVhrOYxV0Ixo1AB24wjd32AQWrOg2rvVpB9bIYisSlSdJJG9ON0tEykbcIOtG73PRhrgZHUswSN5lZuTf0beVnhH2Q3Lo5qbIGfsrQqG0G6/P7LgagkQ89qfexpGTSd6YfzjSyMmqcQ7dBl8/D1MtysQdHOL+R2zJB6JdFM6BZh78AzSExpQHs/do/0rObmPRM/8JcsyFgHrpWx7Ntbpy/vPKp9fGH/jOrif3Ex4Qxs0+buYR+IQpsiSqiVaTex9GOIZlwg7kuLlXdA="
}
]
}
]
}
}
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