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| author | Pjotr Prins | 2024-04-03 11:09:20 +0200 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2024-09-12 07:40:03 -0500 |
| commit | fd25b6bf205e4642cf5f6ba5ed0e0cad73efc0b6 (patch) | |
| tree | 63511ead7559cfcc360c9ea67229fd3931d3d92e | |
| parent | d623d931046495239c7ce9ec3024e028b2f26fde (diff) | |
| download | genenetwork3-fd25b6bf205e4642cf5f6ba5ed0e0cad73efc0b6.tar.gz | |
rqtl_wrapper: minor fixes
| -rw-r--r-- | README.md | 3 | ||||
| -rw-r--r-- | gn3/api/general.py | 2 | ||||
| -rw-r--r-- | tests/unit/test_commands.py | 4 |
3 files changed, 4 insertions, 5 deletions
@@ -122,11 +122,10 @@ See also instructions in [.guix.scm](.guix.scm). These configurations should be set in an external config file, pointed to with the environment variable GN3_CONF. - SPARQL_ENDPOINT (ex: "http://localhost:9082/sparql") -- RQTL_WRAPPER (ex: "~/genenetwork3/scripts/rqtl_wrapper.R") - XAPIAN_DB_PATH (ex: "/export/data/genenetwork/xapian") - TMPDIR -TMPDIR also needs to be set correctly for the R script(s) because they pass results on as files on the local system (previously there was an issue with it being set to /tmp instead of ~/genenetwork3/tmp) +TMPDIR also needs to be set correctly for the R script(s) because they pass results on as files on the local system (previously there was an issue with it being set to /tmp instead of ~/genenetwork3/tmp). Note that the Guix build system should take care of the paths. ## Command-Line Utility Scripts diff --git a/gn3/api/general.py b/gn3/api/general.py index 891f992..b984361 100644 --- a/gn3/api/general.py +++ b/gn3/api/general.py @@ -64,7 +64,7 @@ def run_r_qtl(geno_filestr, pheno_filestr): """Run r_qtl command using the written rqtl_wrapper program """ - rqtl_wrapper = 'scripts/rqtl_wrapper.R' + rqtl_wrapper = 'scripts/rqtl_wrapper.R' # This is a stub cmd = (f"Rscript {rqtl_wrapper} " f"{geno_filestr} {pheno_filestr}") return jsonify(run_cmd(cmd)), 201 diff --git a/tests/unit/test_commands.py b/tests/unit/test_commands.py index 4dd8735..de0918a 100644 --- a/tests/unit/test_commands.py +++ b/tests/unit/test_commands.py @@ -61,7 +61,7 @@ class TestCommands(unittest.TestCase): def test_compose_rqtl_cmd(self): """Test that the R/qtl cmd is composed correctly""" self.assertEqual( - compose_rqtl_cmd(rqtl_wrapper_cmd="rqtl-wrapper", + compose_rqtl_cmd(rqtl_wrapper_cmd="scripts/rqtl-wrapper", rqtl_wrapper_kwargs={ "g": "the_genofile", "p": "the_phenofile", @@ -74,7 +74,7 @@ class TestCommands(unittest.TestCase): rqtl_wrapper_bool_kwargs=[ "addcovar" ]), - ("Rscript rqtl-wrapper " + ("Rscript scripts/rqtl-wrapper " "--g the_genofile --p the_phenofile " "--model np --method ehk " "--nperm 2000 --scale Mb " |