weix-cshl
commented
5 years ago Build Python virtual Environment: Python2.6 doesn't support sqlalchemy. The most recent Python 3.4 support the dependent packages sqlalchemy sqlsoup argparse html, but is not compatible with the atac pipeline script. python2.7 works just fine. But Peter pointed out
"Python 2.7 will be end of life on January 1st, 2020. I assume they know this at Ensembl, but you might ask them if they have any plans to update their code to make it python3 compatible (they may not since their instructions refer to using Apache 2.2 which has been unsupported since January 2018). "
Working directory
brie:/usr/local/ensembl-96/eg-assemblyconverter/
eg-assemblyconverter]$ vi mysql_servers.py
Modify the configuration to point database server to our local ones, test the script
(atacVE) [weix@brie eg-assemblyconverter]$ python atac_ensembl.py show-species EnsemblPlants
['aegilops_tauschii', 'amborella_trichopoda', 'arabidopsis_lyrata', 'arabidopsis_thaliana', 'brachypodium_distachyon', 'brassica_oleracea', 'brassica_rapa', 'chlamydomonas_reinhardtii', 'cyanidioschyzon_merolae', 'glycine_max', 'hordeum_vulgare', 'leersia_perrieri', 'medicago_truncatula', 'musa_acuminata', 'oryza_barthii', 'oryza_brachyantha', 'oryza_glaberrima', 'oryza_glumaepatula', 'oryza_indica', 'oryza_longistaminata', 'oryza_meridionalis', 'oryza_nivara', 'oryza_punctata', 'oryza_rufipogon', 'oryza_sativa', 'ostreococcus_lucimarinus', 'physcomitrella_patens', 'populus_trichocarpa', 'prunus_persica', 'selaginella_moellendorffii', 'setaria_italica', 'solanum_lycopersicum', 'solanum_tuberosum', 'sorghum_bicolor', 'theobroma_cacao', 'triticum_aestivum', 'triticum_urartu', 'vitis_vinifera', 'zea_mays']
Got the SOP from Bruno, following the documentation with help from Peter. EnsGen-ProjectingAcrossAssembly2019Apr.pdf EnsGen-AssemblyMapping2019Apr.pdf