Integration testing

Have created a list of tools that can be used to test new server deployments. Based upon 3 different training network workflows. The idea is that the tools will be installed using ephemeris, tested with ephemeris and then the workflows run on the tutorial data. This will test a new server on a wide variety of tools and we can use these tests again when upgrading resources etc to check on times and effects etc.

Workflows chosen

Located in workflows directory as .ga files. Install with Ephemeris workflow-install command. You will need an admin api key.

1. Calling variants in non-diploid systems
2. rna-seq reads to counts

List of tools

Located in all_tools.yml in tools directory. Instal with Ephemeris shed-tools install command. You will need an admin api key.

• rseqc revisions:
  • f437057e46f1

- **picard** revisions: - a1f0b3f4b781 - 2a17c789e0a5
- **samtools_idxstats** revisions: - 7a6034296ae9 - 04d5581db1f5
- **multiqc** revisions: - 5e33b465d8d5 - 1c2db0054039
- **collection_column_join** revisions: - 58228a4d58fe
- **fastqc** revisions: - c15237684a01 - e7b2202befea
- **cutadapt** revisions: - 660cffd8d92a
- **hisat2** revisions: - 6daca6da3059
- **featurecounts** revisions: - 1759d845181e
- **bwa** revisions: - 3fe632431b68
- **bamtools_filter** revisions: - cb20f99fd45b
- **freebayes** revisions: - ef2c525bd8cd
- **vcffilter** revisions: - fa24bf0598f4
- **vcf2tsv** revisions: - 285060661b45

Environment

Create a virtualenv (python3) with the dependencies from integration-testing/requirements.yml installed.

bash scripts/make_environment.sh

TO DO

• Write better bash script arg parsing