diff --git a/docs/setup.md b/docs/setup.md index d9c2a4b6..bcab44ea 100644 --- a/docs/setup.md +++ b/docs/setup.md @@ -14,7 +14,8 @@ SingleM metapackage is the metapackage downloaded by SingleM using `singlem data The latter databases are required only if you want to run Aviary directly using the `--run-aviary` argument. GTDB-Tk database is the directory containing the GTDB-Tk release (see ). CheckM2 database is the directory containing the CheckM2 database (see ). -These can also be downloaded automatically by Aviary using `aviary configure --download gtdb singlem checkm2` (see ). +These can also be downloaded automatically with `--download-databases` flag, which uses Aviary (`aviary configure --download gtdb singlem checkm2`, see ). +Note that the databases are very large. ```bash binchicken build \ diff --git a/test/test_manual.py b/test/test_manual.py index 9db52b8a..c6b1005a 100644 --- a/test/test_manual.py +++ b/test/test_manual.py @@ -206,9 +206,9 @@ def test_update_specific_coassembly_sra(self): def test_build_with_downloads(self): with in_tempdir(): # path_to_conda = os.path.abspath(".conda") - path_to_metapackage = "metapackage.smpkg" - path_to_checkm2_db = "checkm2_db" - path_to_gtdbtk_db = "gtdb_release" + path_to_metapackage = os.path.abspath("metapackage.smpkg") + path_to_checkm2_db = os.path.abspath("checkm2_db") + path_to_gtdbtk_db = os.path.abspath("gtdb_release") cmd = ( f"binchicken build "