Clone instead of wget for LINC calibraotr

tikk3r · Oct 13, 2023 · 4c070dc · 4c070dc
1 parent bea527a
commit 4c070dc
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/runners/run_LINC_calibrator.sh b/runners/run_LINC_calibrator.sh
@@ -145,8 +145,9 @@ else
     fi
 
     echo "Generating default pipeline configuration"
-    wget --no-http-keep-alive https://raw.githubusercontent.com/tikk3r/flocs/fedora-py3/runners/create_ms_list.py
-    singularity exec -B $PWD,$BINDPATHS $SIMG python create_ms_list.py --filter_baselines '*&' $DATADIR
+    git clone https://github.com/tikk3r/flocs.git
+
+    singularity exec -B $PWD,$BINDPATHS $SIMG python flocs/runners/create_ms_list.py --filter_baselines '*&' $DATADIR
     echo LINC starting
     echo export PYTHONPATH=\$LINC_DATA_ROOT/scripts:\$PYTHONPATH > jobrunner.sh
     echo 'cwltool --parallel --preserve-entire-environment --no-container --tmpdir-prefix=$TMPDIR --outdir=$RESULTSDIR --log-dir=$LOGSDIR $LINC_DATA_ROOT/workflows/HBA_calibrator.cwl mslist.json' >> jobrunner.sh