Skip to content

Commit

Permalink
Merge branch 'release/1.0.11'
Browse files Browse the repository at this point in the history
  • Loading branch information
Ubuntu committed Aug 31, 2017
2 parents 9719ff4 + 2c13d25 commit f497b9f
Show file tree
Hide file tree
Showing 5 changed files with 11 additions and 11 deletions.
4 changes: 2 additions & 2 deletions luigi_task_executor/CNV.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ class ConsonanceTask(luigi.Task):

redwood_host = luigi.Parameter("storage.ucsc-cgl.org")
redwood_token = luigi.Parameter("must_be_defined")
dockstore_tool_running_dockstore_tool = luigi.Parameter(default="quay.io/ucsc_cgl/dockstore-tool-runner:1.0.20")
dockstore_tool_running_dockstore_tool = luigi.Parameter(default="quay.io/ucsc_cgl/dockstore-tool-runner:1.0.21")

workflow_version = luigi.Parameter(default="must be defined")

Expand Down Expand Up @@ -251,7 +251,7 @@ class CNVCoordinator(luigi.Task):
redwood_token = luigi.Parameter("must_be_defined")
redwood_host = luigi.Parameter(default='storage.ucsc-cgp.org')
image_descriptor = luigi.Parameter("must be defined")
dockstore_tool_running_dockstore_tool = luigi.Parameter(default="quay.io/ucsc_cgl/dockstore-tool-runner:1.0.20")
dockstore_tool_running_dockstore_tool = luigi.Parameter(default="quay.io/ucsc_cgl/dockstore-tool-runner:1.0.21")
tmp_dir = luigi.Parameter(default='/datastore')
max_jobs = luigi.Parameter(default='-1')
bundle_uuid_filename_to_file_uuid = {}
Expand Down
4 changes: 2 additions & 2 deletions luigi_task_executor/Protect.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ class ConsonanceTask(luigi.Task):

redwood_host = luigi.Parameter("storage.ucsc-cgl.org")
redwood_token = luigi.Parameter("must_be_defined")
dockstore_tool_running_dockstore_tool = luigi.Parameter(default="quay.io/ucsc_cgl/dockstore-tool-runner:1.0.20")
dockstore_tool_running_dockstore_tool = luigi.Parameter(default="quay.io/ucsc_cgl/dockstore-tool-runner:1.0.21")

workflow_version = luigi.Parameter(default="must be defined")

Expand Down Expand Up @@ -322,7 +322,7 @@ class ProtectCoordinator(luigi.Task):
redwood_token = luigi.Parameter("must_be_defined")
redwood_host = luigi.Parameter(default='storage.ucsc-cgp.org')
image_descriptor = luigi.Parameter("must be defined")
dockstore_tool_running_dockstore_tool = luigi.Parameter(default="quay.io/ucsc_cgl/dockstore-tool-runner:1.0.20")
dockstore_tool_running_dockstore_tool = luigi.Parameter(default="quay.io/ucsc_cgl/dockstore-tool-runner:1.0.21")
tmp_dir = luigi.Parameter(default='/datastore')
max_jobs = luigi.Parameter(default='-1')
bundle_uuid_filename_to_file_uuid = {}
Expand Down
4 changes: 2 additions & 2 deletions luigi_task_executor/RNA-Seq.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@
class ConsonanceTask(luigi.Task):
redwood_host = luigi.Parameter("storage.ucsc-cgp.org")
redwood_token = luigi.Parameter("must_be_defined")
dockstore_tool_running_dockstore_tool = luigi.Parameter(default="quay.io/ucsc_cgl/dockstore-tool-runner:1.0.20")
dockstore_tool_running_dockstore_tool = luigi.Parameter(default="quay.io/ucsc_cgl/dockstore-tool-runner:1.0.21")

workflow_version = luigi.Parameter(default="must be defined")

Expand Down Expand Up @@ -452,7 +452,7 @@ class RNASeqCoordinator(luigi.Task):
redwood_token = luigi.Parameter("must_be_defined")
redwood_host = luigi.Parameter(default='storage.ucsc-cgl.org')
image_descriptor = luigi.Parameter("must be defined")
dockstore_tool_running_dockstore_tool = luigi.Parameter(default="quay.io/ucsc_cgl/dockstore-tool-runner:1.0.20")
dockstore_tool_running_dockstore_tool = luigi.Parameter(default="quay.io/ucsc_cgl/dockstore-tool-runner:1.0.21")
tmp_dir = luigi.Parameter(default='/datastore')
max_jobs = luigi.Parameter(default='-1')
bundle_uuid_filename_to_file_uuid = {}
Expand Down
4 changes: 2 additions & 2 deletions luigi_task_executor/RNA-Seq_3_0_2-3.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@
class ConsonanceTask(luigi.Task):
redwood_host = luigi.Parameter("storage.ucsc-cgp.org")
redwood_token = luigi.Parameter("must_be_defined")
dockstore_tool_running_dockstore_tool = luigi.Parameter(default="quay.io/ucsc_cgl/dockstore-tool-runner:1.0.20")
dockstore_tool_running_dockstore_tool = luigi.Parameter(default="quay.io/ucsc_cgl/dockstore-tool-runner:1.0.21")

workflow_version = luigi.Parameter(default="must be defined")

Expand Down Expand Up @@ -460,7 +460,7 @@ class RNASeqCoordinator(luigi.Task):
redwood_token = luigi.Parameter("must_be_defined")
redwood_host = luigi.Parameter(default='storage.ucsc-cgl.org')
image_descriptor = luigi.Parameter("must be defined")
dockstore_tool_running_dockstore_tool = luigi.Parameter(default="quay.io/ucsc_cgl/dockstore-tool-runner:1.0.20")
dockstore_tool_running_dockstore_tool = luigi.Parameter(default="quay.io/ucsc_cgl/dockstore-tool-runner:1.0.21")
tmp_dir = luigi.Parameter(default='/datastore')
max_jobs = luigi.Parameter(default='-1')
bundle_uuid_filename_to_file_uuid = {}
Expand Down
6 changes: 3 additions & 3 deletions luigi_task_executor/run_Luigi_Deciders.sh
View file
Original file line number Diff line number Diff line change
Expand Up @@ -59,13 +59,13 @@ echo "Running Luigi RNA-Seq decider" >> ${LOG_FILE_PATH}/cron_decider_log.txt
# run the decider
#use the '--test-mode' switch to skip running Consonance
#This will be the new run commmand:
PYTHONPATH="${DECIDER_SOURCE_PATH}" luigi --module RNA-Seq RNASeqCoordinator --dockstore-tool-running-dockstore-tool "quay.io/ucsc_cgl/dockstore-tool-runner:1.0.20" --workflow-version "3.3.4-1.12.3" --touch-file-bucket ${TOUCH_FILE_DIRECTORY} --redwood-host ${STORAGE_SERVER} --redwood-token ${STORAGE_ACCESS_TOKEN} --es-index-host ${ELASTIC_SEARCH_SERVER} --es-index-port ${ELASTIC_SEARCH_PORT} --vm-instance-type "c4.8xlarge" --vm-region ${AWS_REGION} --program Treehouse --tmp-dir /datastore > "${LOG_FILE_PATH}"/cron_log_RNA-Seq_decider_stdout.txt 2> "${LOG_FILE_PATH}"/cron_log_RNA-Seq_decider_stderr.txt
PYTHONPATH="${DECIDER_SOURCE_PATH}" luigi --module RNA-Seq RNASeqCoordinator --dockstore-tool-running-dockstore-tool "quay.io/ucsc_cgl/dockstore-tool-runner:1.0.21" --workflow-version "3.3.4-1.12.3" --touch-file-bucket ${TOUCH_FILE_DIRECTORY} --redwood-host ${STORAGE_SERVER} --redwood-token ${STORAGE_ACCESS_TOKEN} --es-index-host ${ELASTIC_SEARCH_SERVER} --es-index-port ${ELASTIC_SEARCH_PORT} --vm-instance-type "c4.8xlarge" --vm-region ${AWS_REGION} --program Treehouse --tmp-dir /datastore > "${LOG_FILE_PATH}"/cron_log_RNA-Seq_decider_stdout.txt 2> "${LOG_FILE_PATH}"/cron_log_RNA-Seq_decider_stderr.txt

#Run the ProTECT decider:
PYTHONPATH="${DECIDER_SOURCE_PATH}" luigi --module Protect ProtectCoordinator --dockstore-tool-running-dockstore-tool "quay.io/ucsc_cgl/dockstore-tool-runner:1.0.20" --workflow-version "2.5.5-1.12.3" --touch-file-bucket ${TOUCH_FILE_DIRECTORY} --redwood-host ${STORAGE_SERVER} --redwood-token ${STORAGE_ACCESS_TOKEN} --es-index-host ${ELASTIC_SEARCH_SERVER} --es-index-port ${ELASTIC_SEARCH_PORT} --vm-instance-type "c4.8xlarge" --vm-region ${AWS_REGION} --project TARGET --tmp-dir /datastore --test-mode > "${LOG_FILE_PATH}"/cron_log_Protect_decider_stdout.txt 2> "${LOG_FILE_PATH}"/cron_log_Protect_decider_stderr.txt
PYTHONPATH="${DECIDER_SOURCE_PATH}" luigi --module Protect ProtectCoordinator --dockstore-tool-running-dockstore-tool "quay.io/ucsc_cgl/dockstore-tool-runner:1.0.21" --workflow-version "2.5.5-1.12.3" --touch-file-bucket ${TOUCH_FILE_DIRECTORY} --redwood-host ${STORAGE_SERVER} --redwood-token ${STORAGE_ACCESS_TOKEN} --es-index-host ${ELASTIC_SEARCH_SERVER} --es-index-port ${ELASTIC_SEARCH_PORT} --vm-instance-type "c4.8xlarge" --vm-region ${AWS_REGION} --project TARGET --tmp-dir /datastore --test-mode > "${LOG_FILE_PATH}"/cron_log_Protect_decider_stdout.txt 2> "${LOG_FILE_PATH}"/cron_log_Protect_decider_stderr.txt


PYTHONPATH="${DECIDER_SOURCE_PATH}" luigi --module CNV CNVCoordinator --dockstore-tool-running-dockstore-tool "quay.io/ucsc_cgl/dockstore-tool-runner:1.0.20" --workflow-version "v1.0.0" --touch-file-bucket ${TOUCH_FILE_DIRECTORY} --redwood-host ${STORAGE_SERVER} --redwood-token ${STORAGE_ACCESS_TOKEN} --es-index-host ${ELASTIC_SEARCH_SERVER} --es-index-port ${ELASTIC_SEARCH_PORT} --vm-instance-type "c4.8xlarge" --vm-region ${AWS_REGION} --project WCDT --tmp-dir /datastore --test-mode > "${LOG_FILE_PATH}"/cron_log_CNV_decider_stdout.txt 2> "${LOG_FILE_PATH}"/cron_log_CNV_decider_stderr.txt
PYTHONPATH="${DECIDER_SOURCE_PATH}" luigi --module CNV CNVCoordinator --dockstore-tool-running-dockstore-tool "quay.io/ucsc_cgl/dockstore-tool-runner:1.0.21" --workflow-version "v1.0.0" --touch-file-bucket ${TOUCH_FILE_DIRECTORY} --redwood-host ${STORAGE_SERVER} --redwood-token ${STORAGE_ACCESS_TOKEN} --es-index-host ${ELASTIC_SEARCH_SERVER} --es-index-port ${ELASTIC_SEARCH_PORT} --vm-instance-type "c4.8xlarge" --vm-region ${AWS_REGION} --project WCDT --tmp-dir /datastore --test-mode > "${LOG_FILE_PATH}"/cron_log_CNV_decider_stdout.txt 2> "${LOG_FILE_PATH}"/cron_log_CNV_decider_stderr.txt


#execute commands to run addtional deciders in the extra folder
Expand Down

0 comments on commit f497b9f

Please sign in to comment.