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Hervé MENAGER
galaxy-cwl-is-docker
Commits
2fad2ce6
Commit
2fad2ce6
authored
Jun 16, 2019
by
Hervé MENAGER
Browse files
upload all workflows from workflow-is-cwl/workflows to Galaxy
parent
2e533443
Pipeline
#12591
passed with stages
in 10 minutes and 7 seconds
Changes
2
Pipelines
1
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start_galaxy_and_upload_material.sh
View file @
2fad2ce6
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
"
...
...
upload_material.py
View file @
2fad2ce6
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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