Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / cgat-developers/cgat-core issues and pull requests

#198 - Ac slurm

Pull Request - State: open - Opened by Acribbs 16 days ago - 1 comment

#197 - SLURM issues with latest version

Issue - State: open - Opened by snsansom 17 days ago - 14 comments

#196 - Added suffic to output_file

Pull Request - State: closed - Opened by Acribbs 23 days ago

#195 - Ac document

Pull Request - State: closed - Opened by Acribbs about 1 month ago

#194 - Ac document

Pull Request - State: closed - Opened by Acribbs about 1 month ago

#193 - Updatd will_run_on_cluster to now warn if to_cluster is active but DR…

Pull Request - State: closed - Opened by Acribbs about 1 month ago

#192 - jobs are not being submitted to the cluster

Issue - State: closed - Opened by snsansom about 1 month ago - 3 comments

#191 - added container (docker) functionality to the run statement

Pull Request - State: closed - Opened by Acribbs 2 months ago - 1 comment

#190 - debug github actions openssl

Pull Request - State: closed - Opened by Acribbs 2 months ago

#189 - Ac docchange

Pull Request - State: closed - Opened by Acribbs 2 months ago

#188 - Documentation not building

Issue - State: closed - Opened by IanSudbery 2 months ago - 5 comments

#187 - Ac docs

Pull Request - State: closed - Opened by Acribbs 3 months ago

#186 - added CGAT logo back into docs

Pull Request - State: closed - Opened by Acribbs 3 months ago

#185 - Ac docs

Pull Request - State: closed - Opened by Acribbs 3 months ago

#184 - updated mkdocs to work with dynamin importing documentation

Pull Request - State: closed - Opened by Acribbs 3 months ago

#183 - Ac docs

Pull Request - State: closed - Opened by Acribbs 3 months ago

#182 - Ac kubernetes

Pull Request - State: closed - Opened by Acribbs 3 months ago - 10 comments

#181 - mambaforge is depricated and need miniforge for action builds

Pull Request - State: closed - Opened by Acribbs 3 months ago

#180 - Ac canceljob

Pull Request - State: closed - Opened by Acribbs 3 months ago - 4 comments

#179 - included S3 decorators

Pull Request - State: closed - Opened by Acribbs 3 months ago - 3 comments

#178 - Ac tests

Pull Request - State: closed - Opened by Acribbs 3 months ago

#177 - cgat-0.7.2 fails to install in fresh env due to missing Numpy dependency

Issue - State: closed - Opened by ns-rse 3 months ago - 3 comments

#176 - Bump actions/download-artifact from 2 to 4.1.7 in /.github/workflows

Pull Request - State: closed - Opened by dependabot[bot] 5 months ago
Labels: dependencies

#175 - update to v0.6.16

Pull Request - State: closed - Opened by Acribbs 10 months ago

#174 - sqlalchemy 2.0 fix

Pull Request - State: closed - Opened by jscaber over 1 year ago - 4 comments

#173 - sqlalchemy>=2

Issue - State: closed - Opened by jscaber over 1 year ago

#172 - why sourcing the bashrc profile on cluster?

Issue - State: closed - Opened by bio-la over 1 year ago - 17 comments

#171 - running local on macos time: illegal option -- -

Issue - State: closed - Opened by bio-la over 1 year ago - 5 comments

#170 - increase version to 0.6.15

Pull Request - State: closed - Opened by AndreasHeger almost 2 years ago

#169 - Fix python 3.10 support

Pull Request - State: closed - Opened by tschoonj almost 2 years ago - 4 comments

#168 - Changing time requested for job

Issue - State: closed - Opened by lucygarner about 2 years ago - 7 comments

#167 - Do global variables need to be written in capitals in `cgat-core` pipelines?

Issue - State: closed - Opened by lucygarner over 2 years ago - 1 comment

#166 - How can I convert a parameter from the YAML file into an R vector

Issue - State: closed - Opened by lucygarner over 2 years ago - 3 comments

#165 - running local on macos

Issue - State: closed - Opened by bio-la over 2 years ago - 7 comments

#164 - help overwriting SLURM default params

Issue - State: closed - Opened by bio-la over 2 years ago - 5 comments

#163 - Add submitting load to the cluster as an option

Pull Request - State: closed - Opened by IanSudbery over 2 years ago

#162 - to_cluster=False in P.load

Issue - State: closed - Opened by IanSudbery over 2 years ago

#161 - restore retval issue when using argparse, version 0.6.13

Pull Request - State: closed - Opened by AndreasHeger over 2 years ago

#160 - Fix missing header

Pull Request - State: closed - Opened by AndreasHeger over 2 years ago - 1 comment

#159 - Missing header in E.start() using optparse

Issue - State: closed - Opened by AndreasHeger over 2 years ago

#158 - The pipeline outputs the global params before they are updated. The p…

Pull Request - State: closed - Opened by Acribbs almost 3 years ago

#157 - Adds pipeline action svg

Pull Request - State: closed - Opened by sebastian-luna-valero almost 3 years ago

#156 - missing pipeline action svg

Issue - State: closed - Opened by AndreasHegerGenomics almost 3 years ago - 1 comment

#155 - Variable substitution in Ruffus decorator?

Issue - State: closed - Opened by lucygarner almost 3 years ago - 3 comments

#154 - Py310 compatibility

Pull Request - State: closed - Opened by AndreasHeger almost 3 years ago - 4 comments

#153 - cgat-core not compatible with py3.10

Issue - State: closed - Opened by AndreasHeger almost 3 years ago - 1 comment

#152 - pipeline printing our options as the defaults

Issue - State: closed - Opened by Acribbs almost 3 years ago - 1 comment
Labels: bug

#151 - Profiling files sent to home directory on CBRG server

Issue - State: closed - Opened by lucygarner almost 3 years ago - 11 comments

#150 - How to add additional argument to qsub.

Issue - State: closed - Opened by crichgriffin over 3 years ago - 6 comments

#149 - bump version

Pull Request - State: closed - Opened by Acribbs over 3 years ago

#148 - use safeload instead of load for yaml

Pull Request - State: closed - Opened by Acribbs over 3 years ago

#147 - Issue with BenchmarkData causing pipelines to stall.

Issue - State: closed - Opened by jjriley1 over 3 years ago - 1 comment

#146 - TypeError: handle_sigint() got multiple values for argument 'pool'

Issue - State: closed - Opened by IanSudbery over 3 years ago - 6 comments

#145 - Fixes #143

Pull Request - State: closed - Opened by sebastian-luna-valero over 3 years ago

#144 - citation.cff file

Issue - State: closed - Opened by sebastian-luna-valero over 3 years ago

#142 - OSError returned when DRMAA API cannot access the lib path

Pull Request - State: closed - Opened by Acribbs over 3 years ago

#141 - bumped version to 0.6.8

Pull Request - State: closed - Opened by Acribbs over 3 years ago

#140 - added pytests for missing tests

Pull Request - State: closed - Opened by Acribbs over 3 years ago

#139 - updated tests

Pull Request - State: closed - Opened by Acribbs over 3 years ago

#138 - remove travis tests

Pull Request - State: closed - Opened by Acribbs almost 4 years ago

#137 - Allow abitrary location for conda env

Pull Request - State: closed - Opened by IanSudbery almost 4 years ago - 1 comment

#136 - Conda env can't be specified by directory

Issue - State: closed - Opened by IanSudbery almost 4 years ago - 1 comment

#135 - updated github actions to play around with install script

Pull Request - State: closed - Opened by Acribbs almost 4 years ago - 11 comments

#134 - Ac fixtests

Pull Request - State: closed - Opened by Acribbs almost 4 years ago - 1 comment

#133 - Implementing LSF compatibility by creating new class in cluster.py

Issue - State: closed - Opened by jdparker101 almost 4 years ago - 5 comments

#132 - COmmand line arguments not overriding defaults

Issue - State: closed - Opened by david-cgat about 4 years ago - 23 comments

#131 - two different conda pacakges

Issue - State: closed - Opened by IanSudbery about 4 years ago - 3 comments

#130 - Update version.py

Pull Request - State: closed - Opened by Acribbs over 4 years ago

#129 - pytest failing with new v6.0.0

Issue - State: closed - Opened by Acribbs over 4 years ago - 1 comment

#128 - updated requirements

Pull Request - State: closed - Opened by Acribbs over 4 years ago

#127 - Ac deps

Pull Request - State: closed - Opened by Acribbs over 4 years ago

#126 - apsw dependency missing from conda package

Issue - State: closed - Opened by AndreasHegerGenomics over 4 years ago - 2 comments

#125 - Monitoring interval

Pull Request - State: closed - Opened by JDiprose over 4 years ago

#124 - enable configurable monitoring interval

Pull Request - State: closed - Opened by JDiprose over 4 years ago - 2 comments

#123 - Modified GEVENT_TIMEOUT_WAIT

Pull Request - State: closed - Opened by Acribbs over 4 years ago

#121 - document virtual tsv module

Issue - State: closed - Opened by Acribbs over 4 years ago

#120 - Ac virt

Pull Request - State: closed - Opened by Acribbs over 4 years ago

#119 - Raise error if the job is aborted

Pull Request - State: closed - Opened by snsansom over 4 years ago - 2 comments

#118 - Ac db

Pull Request - State: closed - Opened by Acribbs over 4 years ago - 1 comment

#117 - Ac pyyaml

Pull Request - State: closed - Opened by Acribbs over 4 years ago

#116 - Depedency versions - pyyaml

Issue - State: closed - Opened by IanSudbery over 4 years ago - 1 comment

#115 - Ah fix resourceusagecollection when error

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

#114 - bumped version to 0.6.5

Pull Request - State: closed - Opened by Acribbs about 5 years ago

#113 - bugfix add_pipe_args in cgatcore.table

Pull Request - State: closed - Opened by sebastian-luna-valero about 5 years ago

#112 - Update P.execute()

Pull Request - State: closed - Opened by sebastian-luna-valero about 5 years ago - 3 comments

#111 - Kubernates integration

Issue - State: closed - Opened by Acribbs about 5 years ago - 5 comments

#110 - Ac readthedocs

Pull Request - State: closed - Opened by Acribbs about 5 years ago

#109 - {AH} remove nose

Pull Request - State: closed - Opened by AndreasHeger about 5 years ago

#108 - Ah test pipeline cli

Pull Request - State: closed - Opened by AndreasHeger about 5 years ago

#107 - Bugfix: use the `ruffus_return_dag` function defined in scope

Pull Request - State: closed - Opened by paulbrodersen about 5 years ago - 3 comments

#106 - updated basicConfig so that it now picks up logformat

Pull Request - State: closed - Opened by Acribbs about 5 years ago

#105 - Tests failing with Python 3.8

Issue - State: closed - Opened by sebastian-luna-valero about 5 years ago - 22 comments

#104 - argparse table.py

Pull Request - State: closed - Opened by jscaber over 5 years ago - 12 comments

#103 - Fixing peek params for non-cgat-flow repositories

Pull Request - State: open - Opened by stydodt over 5 years ago - 11 comments

#102 - drmaa.errors.InvalidAttributeValueException

Issue - State: closed - Opened by amayer21 over 5 years ago - 14 comments

#101 - Ac argparse

Pull Request - State: closed - Opened by Acribbs over 5 years ago - 13 comments

#100 - Update travis.yml

Pull Request - State: closed - Opened by Acribbs over 5 years ago

#99 - Ah tidy up cluster error handling

Pull Request - State: closed - Opened by AndreasHeger over 5 years ago