Update ClinVar script to import somatic classifications + patch db schema 115 #1117
Travis CI / Travis CI - Pull Request
succeeded
Nov 21, 2024 in 10m 30s
Build Passed
Details
This is a pull request build.
It is running a build against the merge commit, after merging #1117 Update ClinVar script to import somatic classifications.
Any changes that have been made to the main branch before the build ran are also included.
Jobs and Stages
This build has two jobs, running in parallel.
| Job | Perl | ENV | OS | State |
|---|---|---|---|---|
| 6238.1 |
5.14 | AUTH_TOKEN=[secure] | Linux | passed |
| 6238.2 |
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"
}
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"slack": [
{
"rooms": [
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}
]
}
]
}
}
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