Ecosyste.ms: Issues

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GitHub / molgenis/molgenis-compute issues and pull requests

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

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies, java

#289 - Bump httpclient from 4.2.5 to 4.5.13 in /molgenis-compute-core

Pull Request - State: open - Opened by dependabot[bot] over 3 years ago
Labels: dependencies, java

#288 - Submit.sh does not catch slurm/munge error

Issue - State: open - Opened by mmterpstra almost 4 years ago - 4 comments

#287 - Infinite loop on quoted strings containing comma's

Issue - State: open - Opened by mmterpstra almost 5 years ago

#285 - Bump httpclient from 4.2.5 to 4.3.6 in /molgenis-compute-core

Pull Request - State: closed - Opened by dependabot[bot] almost 5 years ago - 2 comments
Labels: dependencies

#284 - Bugfix for .../templates/slurm/submit.ftl

Pull Request - State: closed - Opened by pneerincx almost 5 years ago

#283 - bash submit.sh gives the error jobName: unbound variable

Issue - State: closed - Opened by npklein almost 5 years ago - 1 comment

#282 - Invalid parameter remapping in workflow.csv does not throw errors

Issue - State: open - Opened by mmterpstra about 5 years ago - 1 comment

#281 - Update compute.version from 17.08.1 to 19.01.1

Pull Request - State: closed - Opened by dennishendriksen almost 6 years ago

#280 - M6348 Configurable resource allocation

Pull Request - State: closed - Opened by dennishendriksen almost 6 years ago

#279 - Fix README build status link

Pull Request - State: closed - Opened by dennishendriksen almost 6 years ago

#278 - Update README.md

Pull Request - State: closed - Opened by mswertz almost 6 years ago

#277 - removing .env files

Issue - State: open - Opened by RoanKanninga about 7 years ago - 3 comments

#276 - Updated README.

Pull Request - State: closed - Opened by pneerincx over 7 years ago

#274 - Duplicate stepnames in workflow.csv do not throw errors

Issue - State: open - Opened by mmterpstra over 7 years ago

#273 - infinite loop on bad samplesheet header

Issue - State: open - Opened by mmterpstra over 7 years ago

#272 - Folding list work around does not work in all situations

Issue - State: open - Opened by npklein over 7 years ago

#271 - Add test that demonstrates #list parameter behavior

Pull Request - State: closed - Opened by fdlk almost 8 years ago - 2 comments

#269 - Updated tests for bug fix in SLURM header.

Pull Request - State: closed - Opened by pneerincx almost 8 years ago

#268 - Compute should give an exception when a custom header file does not exist

Issue - State: open - Opened by npklein almost 8 years ago
Labels: bug

#267 - Performance issue generating jobs

Issue - State: open - Opened by npklein about 8 years ago - 4 comments

#266 - Added example data that takes a very long time to generate

Pull Request - State: open - Opened by npklein about 8 years ago - 3 comments

#264 - Enable automatic numbering of generated scripts.

Issue - State: open - Opened by pneerincx about 8 years ago

#263 - Updated POM for new release tag.

Pull Request - State: closed - Opened by pneerincx about 8 years ago

#262 - Updates for SLURM with new cluster setup based on QoS.

Pull Request - State: closed - Opened by pneerincx about 8 years ago

#261 - Cleanup of submit_gaf.ftl and added set -e and set -u.

Pull Request - State: closed - Opened by pneerincx over 8 years ago

#260 - mmterpstra update makeTmpDir

Pull Request - State: closed - Opened by mmterpstra over 8 years ago - 1 comment

#259 - added timesheet to pipeline

Pull Request - State: closed - Opened by RoanKanninga over 8 years ago

#258 - fixing falsely TRAPPED message

Pull Request - State: closed - Opened by RoanKanninga over 8 years ago

#257 - added removing old submitted jobs from the queue

Pull Request - State: closed - Opened by RoanKanninga over 8 years ago

#255 - fixing variable declaration (noparse)

Pull Request - State: closed - Opened by RoanKanninga over 8 years ago

#254 - edited header, because mailing from a node doesnot work

Pull Request - State: closed - Opened by RoanKanninga over 8 years ago

#253 - fix #252

Pull Request - State: closed - Opened by RoanKanninga over 8 years ago

#251 - added error logging pipeline

Pull Request - State: closed - Opened by RoanKanninga over 8 years ago

#250 - added gaf footer template

Pull Request - State: closed - Opened by RoanKanninga over 8 years ago

#249 - Release 16.04.1 version numbering inconsistent.

Issue - State: open - Opened by fdlk over 8 years ago

#248 - fixing header

Pull Request - State: closed - Opened by RoanKanninga over 8 years ago

#247 - Empty line at samplesheet gives java.lang.ArrayIndexOutOfBoundsException

Issue - State: open - Opened by npklein over 8 years ago
Labels: bug

#246 - added custom header (containing projectname in the submitted job)

Pull Request - State: closed - Opened by RoanKanninga almost 9 years ago - 2 comments

#245 - Make clear how scripts are parsed

Issue - State: open - Opened by fdlk almost 9 years ago

#244 - Use Spring configuration

Issue - State: open - Opened by fdlk almost 9 years ago

#243 - Fix the documentation generators

Issue - State: open - Opened by fdlk almost 9 years ago

#242 - Remove obsolete command line options.

Issue - State: open - Opened by fdlk almost 9 years ago

#241 - FoldParametersImpl is duplicate code

Issue - State: open - Opened by fdlk almost 9 years ago
Labels: bug

#240 - Update compute.version to 15.12.4

Pull Request - State: closed - Opened by mark-de-haan almost 9 years ago

#238 - changed mem-per-cpu to mem in header + fixes in tests

Pull Request - State: closed - Opened by RoanKanninga almost 9 years ago

#237 - changed mem-per-cpu to mem in header

Pull Request - State: closed - Opened by RoanKanninga almost 9 years ago

#235 - Add license

Issue - State: closed - Opened by fdlk almost 9 years ago

#234 - Fix dependencies during runtime

Pull Request - State: closed - Opened by mark-de-haan almost 9 years ago

#233 - Add inclusion of dependencies in assembly file

Pull Request - State: closed - Opened by mark-de-haan almost 9 years ago

#231 - [r1.3.0] Add GS collections to molgenis_compute.sh

Pull Request - State: closed - Opened by mark-de-haan almost 9 years ago - 1 comment

#230 - [master] Update app-db compute dependency

Pull Request - State: closed - Opened by mark-de-haan almost 9 years ago

#229 - Update master version to 1.4.0-SNAPSHOT

Pull Request - State: closed - Opened by mark-de-haan almost 9 years ago

#228 - [r1.3.0] Update poms to version 1.3.0

Pull Request - State: closed - Opened by mark-de-haan almost 9 years ago - 1 comment

#226 - New map for efficient memory usage, massive speed improvements

Pull Request - State: closed - Opened by mark-de-haan almost 9 years ago

#225 - Fix tests for updated SLURM submit.ftl

Pull Request - State: closed - Opened by mark-de-haan almost 9 years ago

#224 - updated submit.ftl

Pull Request - State: closed - Opened by RoanKanninga almost 9 years ago

#223 - Removed dotdotslash from submit template

Pull Request - State: closed - Opened by RoanKanninga almost 9 years ago - 1 comment

#221 - Removed SNAPSHOT

Pull Request - State: closed - Opened by mark-de-haan almost 9 years ago

#220 - Set hardcoded jar path to new compute version

Pull Request - State: closed - Opened by mark-de-haan almost 9 years ago

#219 - Update compute master pom

Pull Request - State: closed - Opened by mark-de-haan almost 9 years ago

#218 - Update app db pom

Pull Request - State: closed - Opened by mark-de-haan almost 9 years ago

#217 - Update POM

Pull Request - State: closed - Opened by mark-de-haan almost 9 years ago

#215 - Compute fails if project is checked out in directory with spaces in the name

Issue - State: open - Opened by fdlk almost 9 years ago
Labels: bug

#214 - Feature/intern strings

Pull Request - State: closed - Opened by fdlk almost 9 years ago - 1 comment

#213 - Log location of generated scripts to command line

Pull Request - State: closed - Opened by mark-de-haan almost 9 years ago

#212 - Fix declared dependencies

Issue - State: open - Opened by fdlk almost 9 years ago

#211 - Banner

Pull Request - State: closed - Opened by mark-de-haan almost 9 years ago

#210 - Removed version numbers from assembly.xml

Pull Request - State: closed - Opened by mark-de-haan almost 9 years ago

#209 - Update molgenis_compute.sh lib versions

Pull Request - State: closed - Opened by mark-de-haan almost 9 years ago

#208 - Fix runtime errors due to libraries with old versions

Pull Request - State: closed - Opened by mark-de-haan almost 9 years ago

#207 - Fix test

Pull Request - State: closed - Opened by fdlk almost 9 years ago

#206 - Revert "Might fix failing test on Jenkins??"

Pull Request - State: closed - Opened by mark-de-haan almost 9 years ago

#205 - Might fix failing test on Jenkins??

Pull Request - State: closed - Opened by mark-de-haan almost 9 years ago

#203 - Fix #202 Log lines repeated in tests

Pull Request - State: closed - Opened by fdlk almost 9 years ago

#202 - Log lines repeated in tests

Issue - State: closed - Opened by fdlk almost 9 years ago
Labels: bug

#201 - Test files contain references to system-dependent directories.

Issue - State: closed - Opened by fdlk almost 9 years ago - 1 comment

#200 - Added project variable in the name of the submitted job

Pull Request - State: closed - Opened by RoanKanninga almost 9 years ago

#196 - The Parameter map entities should be normalized to save memory

Issue - State: open - Opened by mark-de-haan almost 9 years ago
Labels: bug, technical-debt

#195 - user_ prefix and protocol_prefix make the parameter map entities too big

Issue - State: closed - Opened by mark-de-haan almost 9 years ago
Labels: bug, technical-debt

#193 - Bug fixes and performance enhancements

Pull Request - State: closed - Opened by mark-de-haan almost 9 years ago

#190 - remove hardcoded patch, spellingfix

Pull Request - State: closed - Opened by npklein almost 9 years ago - 1 comment

#186 - When using lists, two parameter sets result in all Parameters being expanded. Even in Protocols where this is not needed

Issue - State: closed - Opened by mark-de-haan about 9 years ago - 4 comments
Labels: bug, first-priority

#182 - molgenis_compute.sh refers to invalid jar and invalid package

Issue - State: closed - Opened by dennishendriksen over 9 years ago - 1 comment
Labels: bug