# SOLVED: Broken tutorial: Getting started with the LSST Science Pipelines **URL:** \ **Category:** Support\ **Tags:** butler\ **Created:** [September 12, 2023, 1:06pm UTC](https://www.rubin.community/t/solved-broken-tutorial-getting-started-with-the-lsst-science-pipelines/7926 "2023-09-12T13:06:25Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![aetviita](https://sea2.discourse-cdn.com/flex002/user_avatar/www.rubin.community/aetviita/32/2659_2.png) [@aetviita](https://www.rubin.community/u/aetviita)\ **Post date:** [September 12, 2023, 1:06pm UTC](https://www.rubin.community/t/solved-broken-tutorial-getting-started-with-the-lsst-science-pipelines/7926/1 "2023-09-12T13:06:26Z")
Hi, I’m trying to run the tutorial for the LSST Science pipelines and have trouble following these instructions: [Getting started tutorial part 1: setting up the Butler data repository — LSST Science Pipelines](https://pipelines.lsst.io/getting-started/data-setup.html) Namely the command: git clone -b v25\_0\_1 [GitHub - lsst/rc2\_subset: A small subset of the RC2 dataset for running DRP](https://github.com/lsst/rc2_subset) fails with the error: fatal: Remote branch v25\_0\_1 not found in upstream origin and if I ignore the branch and proceed I get the following error when trying to initialize butler: Failed to instantiate Butler from config file:///home/viitanen/tutorial\_lsst\_pipelines/rc2\_subset/SMALL\_HSC/butler.yaml. Traceback (most recent call last): File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/engine/base.py”, line 1910, in \_execute\_context self.dialect.do\_execute( File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/engine/default.py”, line 736, in do\_execute cursor.execute(statement, parameters) sqlite3.DatabaseError: file is not a database The above exception was the direct cause of the following exception: Traceback (most recent call last): File “”, line 1, in File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/share/eups/Linux64/daf\_butler/ga7f022ee40+2007041a77/python/lsst/daf/butler/\_butler.py”, line 282, in **init** self.registry = Registry.fromConfig( File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/share/eups/Linux64/daf\_butler/ga7f022ee40+2007041a77/python/lsst/daf/butler/registry/\_registry.py”, line 230, in fromConfig return registry\_cls.fromConfig(config, butlerRoot, writeable, defaults) File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/share/eups/Linux64/daf\_butler/ga7f022ee40+2007041a77/python/lsst/daf/butler/registries/sql.py”, line 207, in fromConfig managers = managerTypes.loadRepo(database) File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/share/eups/Linux64/daf\_butler/ga7f022ee40+2007041a77/python/lsst/daf/butler/registry/managers.py”, line 242, in loadRepo with database.declareStaticTables(create=False) as context: File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/contextlib.py”, line 135, in **enter** return next(self.gen) File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/share/eups/Linux64/daf\_butler/ga7f022ee40+2007041a77/python/lsst/daf/butler/registry/interfaces/\_database.py”, line 678, in declareStaticTables context = StaticTablesContext(self, connection) File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/share/eups/Linux64/daf\_butler/ga7f022ee40+2007041a77/python/lsst/daf/butler/registry/interfaces/\_database.py”, line 118, in **init** self.\_tableNames = frozenset(self.\_inspector.get\_table\_names(schema=self.\_db.namespace)) File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/engine/reflection.py”, line 266, in get\_table\_names return self.dialect.get\_table\_names( File “”, line 2, in get\_table\_names File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/engine/reflection.py”, line 55, in cache ret = fn(self, con, \*args, \*\*kw) File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/dialects/sqlite/base.py”, line 1993, in get\_table\_names rs = connection.exec\_driver\_sql(s) File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/engine/base.py”, line 1770, in exec\_driver\_sql return self.\_exec\_driver\_sql( File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/engine/base.py”, line 1674, in \_exec\_driver\_sql ret = self.\_execute\_context( File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/engine/base.py”, line 1953, in \_execute\_context self._handle\_dbapi\_exception( File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/engine/base.py”, line 2134, in handle\_dbapi\_exception util.raise( File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/util/compat.py”, line 211, in raise_ raise exception File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/engine/base.py”, line 1910, in \_execute\_context self.dialect.do\_execute( File “/home/viitanen/mambaforge/envs/lsst-scipipe-5.0.1/lib/python3.10/site-packages/sqlalchemy/engine/default.py”, line 736, in do\_execute cursor.execute(statement, parameters) sqlalchemy.exc.DatabaseError: (sqlite3.DatabaseError) file is not a database [SQL: SELECT name FROM sqlite\_master WHERE type=‘table’ ORDER BY name] (Background on this error at: [Error Messages — SQLAlchemy 1.4 Documentation](https://sqlalche.me/e/14/4xp6)) For installing the LSST Science Pipelines I followed the instructions here: [Install with lsstinstall and eups distrib — LSST Science Pipelines](https://pipelines.lsst.io/install/lsstinstall.html) and verified that the issue is not due to git LFS, i.e. running the final git clone here [Configuring Git LFS for downloading LSST data packages — LSST Science Pipelines](https://pipelines.lsst.io/install/git-lfs.html) finishes without errors. Best, -akke ---
**Author:** ![timj](https://sea2.discourse-cdn.com/flex002/user_avatar/www.rubin.community/timj/32/10_2.png) [@timj](https://www.rubin.community/u/timj)\ **Post date:** [September 12, 2023, 2:46pm UTC](https://www.rubin.community/t/solved-broken-tutorial-getting-started-with-the-lsst-science-pipelines/7926/2 "2023-09-12T14:46:49Z")
> [@aetviita](#): > > file is not a database This error almost always means that the file was not downloaded properly from LFS. What size is it? It is a small file with some text in it pointing at a LFS object? ---
**Author:** ![aetviita](https://sea2.discourse-cdn.com/flex002/user_avatar/www.rubin.community/aetviita/32/2659_2.png) [@aetviita](https://www.rubin.community/u/aetviita)\ **Post date:** [September 12, 2023, 3:45pm UTC](https://www.rubin.community/t/solved-broken-tutorial-getting-started-with-the-lsst-science-pipelines/7926/3 "2023-09-12T15:45:03Z")
The problem was indeed with LFS. After including the credentials, one needs to run git lfs install in order to complete the initialization. This information is currently missing from the setup instruction [Configuring Git LFS for downloading LSST data packages — LSST Science Pipelines](https://pipelines.lsst.io/install/git-lfs.html) After running the command above, the tutorial seems to work.