molgenis molgenis-compute issues

molgenis / molgenis-compute

MOLGENIS Compute is a framework for bioinformatics which enables large scale data and computational workflow management in a distributed execution environment.

http://wiki.gcc.rug.nl/wiki/ComputeStart

GNU Lesser General Public License v3.0

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issues

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Bump jsch from 0.1.50 to 0.1.54 in /molgenis-app-compute-db

#291 dependabot[bot] opened 2 years ago
0
Undeclared parameter exception is not case sensitive when scanning steps.

#290 mmterpstra opened 2 years ago
0
Bump httpclient from 4.2.5 to 4.5.13 in /molgenis-compute-core

#289 dependabot[bot] opened 3 years ago
0
Submit.sh does not catch slurm/munge error

#288 mmterpstra opened 3 years ago
4
Infinite loop on quoted strings containing comma's

#287 mmterpstra opened 4 years ago
0
Updated expected test results for recent bugfix in submit.ftl for slurm backend.

#286 pneerincx closed 4 years ago
0
Bump httpclient from 4.2.5 to 4.3.6 in /molgenis-compute-core

#285 dependabot[bot] closed 3 years ago
2
Bugfix for .../templates/slurm/submit.ftl

#284 pneerincx closed 4 years ago
0
bash submit.sh gives the error jobName: unbound variable

#283 npklein closed 4 years ago
1
Invalid parameter remapping in workflow.csv does not throw errors

#282 mmterpstra opened 4 years ago
1
Update compute.version from 17.08.1 to 19.01.1

#281 dennishendriksen closed 5 years ago
0
M6348 Configurable resource allocation

#280 dennishendriksen closed 5 years ago
0
Fix README build status link

#279 dennishendriksen closed 5 years ago
0
Update README.md

#278 mswertz closed 5 years ago
0
removing .env files

#277 RoanKanninga opened 6 years ago
3
Updated README.

#276 pneerincx closed 5 years ago
0
Updated templates for local and slurm backends and rewrote tests to produce output in a test specific subdir.

#275 pneerincx closed 7 years ago
0
Duplicate stepnames in workflow.csv do not throw errors

#274 mmterpstra opened 7 years ago
0
infinite loop on bad samplesheet header

#273 mmterpstra opened 7 years ago
0
Folding list work around does not work in all situations

#272 npklein opened 7 years ago
0
Add test that demonstrates #list parameter behavior

#271 fdlk closed 5 years ago
2
Updated Maven configs for version number and tar.gz. archive file with compiled app.

#270 pneerincx closed 7 years ago
0
Updated tests for bug fix in SLURM header.

#269 pneerincx closed 7 years ago
0
Compute should give an exception when a custom header file does not exist

#268 npklein opened 7 years ago
0
Performance issue generating jobs

#267 npklein opened 7 years ago
4
Added example data that takes a very long time to generate

#266 npklein opened 7 years ago
3
Added missing declaration in SLURM header.ftl of default for ${MC_failedFile}.

#265 pneerincx closed 7 years ago
0
Enable automatic numbering of generated scripts.

#264 pneerincx opened 7 years ago
0
Updated POM for new release tag.

#263 pneerincx closed 8 years ago
0
Updates for SLURM with new cluster setup based on QoS.

#262 pneerincx closed 8 years ago
0
Cleanup of submit_gaf.ftl and added set -e and set -u.

#261 pneerincx closed 8 years ago
0
mmterpstra update makeTmpDir

#260 mmterpstra closed 8 years ago
1
added timesheet to pipeline

#259 RoanKanninga closed 8 years ago
0
fixing falsely TRAPPED message

#258 RoanKanninga closed 8 years ago
0
added removing old submitted jobs from the queue

#257 RoanKanninga closed 8 years ago
0
updated header/footer and submit for backend localhost + small fix in…

#256 RoanKanninga closed 8 years ago
0
fixing variable declaration (noparse)

#255 RoanKanninga closed 8 years ago
0
edited header, because mailing from a node doesnot work

#254 RoanKanninga closed 8 years ago
0
fix #252

#253 RoanKanninga closed 8 years ago
0
while submitting via submit.sh should reset mailing procedure..

#252 RoanKanninga closed 8 years ago
0
added error logging pipeline

#251 RoanKanninga closed 8 years ago
0
added gaf footer template

#250 RoanKanninga closed 8 years ago
0
Release 16.04.1 version numbering inconsistent.

#249 fdlk opened 8 years ago
0
fixing header

#248 RoanKanninga closed 8 years ago
0
Empty line at samplesheet gives java.lang.ArrayIndexOutOfBoundsException

#247 npklein opened 8 years ago
0
added custom header (containing projectname in the submitted job)

#246 RoanKanninga closed 8 years ago
2
Make clear how scripts are parsed

#245 fdlk opened 8 years ago
0
Use Spring configuration

#244 fdlk opened 8 years ago
0
Fix the documentation generators

#243 fdlk opened 8 years ago
0
Remove obsolete command line options.

#242 fdlk opened 8 years ago
0