Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update SpliceAI GPU #983

Open
wants to merge 12 commits into
base: main
Choose a base branch
from

simulate_variation fix variable

bc55b80
Select commit
Loading
Failed to load commit list.
Open

Update SpliceAI GPU #983

simulate_variation fix variable
bc55b80
Select commit
Loading
Failed to load commit list.
Travis CI / Travis CI - Pull Request succeeded Aug 30, 2024 in 9m 58s

Build Passed

The build passed, just like the previous build.

Details

This is a pull request build.

It is running a build against the merge commit, after merging #983 Update SpliceAI GPU.
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
6155.1 5.14 AUTH_TOKEN=[secure] Linux passed
6155.2 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": "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"
          }
        ]
      }
    ]
  }
}