DESeq2 requires metadata sample name to match gene_count_matrix sample name will handle this in workflow to make things consistent
0 session initialised
1 session submitted (no change to conditions/samples/workflows allowed pass this stage)
2 workflow generated
3 workflow submitted to run
4 workflow finished
sudo apt-get install zlib1g-dev
sudo apt-get install libncurses5-dev
sudo apt-get install libbz2-dev
sudo apt-get install liblzma-devWe use python and pytest as the testing framework. All the tests are stored in ./tests. Before committing a new test, you should test your test locally first.
Assuming you have all dependencies met
run $ pytest ./tests
You should see something similar to the following:
$ pytest tests
============================= test session starts ==============================
platform linux -- Python 3.6.3, pytest-3.3.0, py-1.5.2, pluggy-0.6.0
rootdir: /home/travis/build/tonyyzy/RNASeq, inifile:
collected 1 item
tests/test_STAR_index_nodocker.py . [100%]
=========================== 1 passed in 2.01 seconds ===========================
The command "pytest tests" exited with 0.
rnaseq | |-- Genome_Index | |-- H. Sapiens | | |-- fasta | | |-- annotation | | |-- STAR_index | | |-- HISAT2_index | | | |-- P. Yoelii |-- data | | | |-- Session ID | |-- workflow1 | | |-- cwl file | | |-- yml file | | |-- analysis result directories | |-- fastq | | |-- file1.fastq | | |-- file2.fastq | | | |-- genome | |-- fasta | |-- annotation | |-- RNASeq (repository)