From 4c070dc06e5a1ea097a27b2982320e4a0cc6a948 Mon Sep 17 00:00:00 2001 From: Frits Sweijen Date: Fri, 13 Oct 2023 13:16:38 +0200 Subject: [PATCH] Clone instead of wget for LINC calibraotr --- runners/run_LINC_calibrator.sh | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/runners/run_LINC_calibrator.sh b/runners/run_LINC_calibrator.sh index 218755f..af7f55c 100755 --- 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