Commit 2fad2ce6 authored by Hervé  MENAGER's avatar Hervé MENAGER

upload all workflows from workflow-is-cwl/workflows to Galaxy

parent 2e533443
Pipeline #12591 passed with stages
in 10 minutes and 7 seconds
set -m
. /app/galaxy/.venv/bin/activate
cwltool --pack /app/workflow-is-cwl/workflows/cmsearch-multimodel-wf.cwl > /app/workflow-is-cwl/workflows/cmsearch-multimodel-wf.packed.cwl
cat /app/workflow-is-cwl/workflows/cmsearch-multimodel-wf.packed.cwl
for filename in /app/workflow-is-cwl/workflows/*.cwl; do
cwltool --pack $filename > "$filename.packed"
done
sh /app/start.sh &
GALAXY_PID=$!
echo "Galaxy PID is $GALAXY_PID"
......
from bioblend.galaxy import GalaxyInstance
import json
import sys, glob
BASE_URL='http://localhost:8080'
KEY='111111111111111111111'
gi = GalaxyInstance(url=BASE_URL, key=KEY)
cwl_wf = json.load(open('/app/workflow-is-cwl/workflows/cmsearch-multimodel-wf.packed.cwl','r'))
gi.workflows.import_workflow_dict(cwl_wf)
for filename in glob.glob('/app/workflow-is-cwl/workflows/*.cwl.packed'):
try:
cwl_wf = json.load(open(filename,'r'))
gi.workflows.import_workflow_dict(cwl_wf)
except:
print "failed uploading %s" % filename
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