fix test

AroneyS · Aug 30, 2024 · 737b678 · 737b678
1 parent d124888
commit 737b678
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git 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 <https://github.com/Ecogenomics/GTDBTk>).
 CheckM2 database is the directory containing the CheckM2 database (see <https://github.com/chklovski/CheckM2>).
-These can also be downloaded automatically by Aviary using `aviary configure --download gtdb singlem checkm2` (see <https://github.com/rhysnewell/aviary>).
+These can also be downloaded automatically with `--download-databases` flag, which uses Aviary (`aviary configure --download gtdb singlem checkm2`, see <https://github.com/rhysnewell/aviary>).
+Note that the databases are very large.
 
 ```bash
 binchicken build \

diff --git 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 "