diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/api/general.py | 14 | ||||
| -rw-r--r-- | gn3/settings.py | 1 |
2 files changed, 15 insertions, 0 deletions
diff --git a/gn3/api/general.py b/gn3/api/general.py index a9a8da2..cebb2e3 100644 --- a/gn3/api/general.py +++ b/gn3/api/general.py @@ -6,6 +6,7 @@ from flask import jsonify from flask import request from gn3.fs_helpers import extract_uploaded_file +from gn3.commands import run_cmd general = Blueprint("general", __name__) @@ -50,3 +51,16 @@ TTL is set in the metadata file. If none is provided, the default is 1 week. if results.get("status") > 0: status = 500 return jsonify(results), status + + +@general.route("/qtl/run/<geno_filestr>/<pheno_filestr>", + methods=["POST"], + strict_slashes=False) +def run_r_qtl(geno_filestr, pheno_filestr): + """Run r_qtl command using the written rqtl_wrapper program + + """ + rqtl_wrapper = current_app.config["RQTL_WRAPPER"] + cmd = (f"Rscript {rqtl_wrapper} " + f"{geno_filestr} {pheno_filestr}") + return jsonify(run_cmd(cmd)), 201 diff --git a/gn3/settings.py b/gn3/settings.py index 7b3ffb7..2057ce1 100644 --- a/gn3/settings.py +++ b/gn3/settings.py @@ -10,6 +10,7 @@ CACHEDIR = "" REDIS_URI = "redis://localhost:6379/0" REDIS_JOB_QUEUE = "GN3::job-queue" TMPDIR = os.environ.get("TMPDIR", tempfile.gettempdir()) +RQTL_WRAPPER = "rqtl_wrapper.R" # SQL confs SQL_URI = os.environ.get("SQL_URI", "mysql://webqtlout:webqtlout@localhost/db_webqtl") |