cgat-developers/cgat-core

Issues

• sqlalchemy>=2

  #173 opened a year ago by jscaber
  0

• why sourcing the bashrc profile on cluster?

  #172 opened a year ago by bio-la
  17

• running local on macos time: illegal option -- -

  #171 opened a year ago by bio-la
  5

• running local on macos

  #165 opened 2 years ago by bio-la
  7

• TypeError: handle_sigint() got multiple values for argument 'pool'

  #146 opened a year ago by IanSudbery
  6

• Changing time requested for job

  #168 opened a year ago by lucygarner
  7

• Variable substitution in Ruffus decorator?

  #155 opened a year ago by lucygarner
  3

• Implementing LSF compatibility by creating new class in cluster.py

  #133 opened a year ago by jdparker101
  5

• Issue with BenchmarkData causing pipelines to stall.

  #147 opened a year ago by jjriley1
  1

• Missing header in E.start() using optparse

  #159 opened a year ago by AndreasHeger
  0

• to_cluster=False in P.load

  #162 opened a year ago by IanSudbery
  0

• How can I convert a parameter from the YAML file into an R vector

  #166 opened a year ago by lucygarner
  3

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

  #167 opened a year ago by lucygarner
  1

• help overwriting SLURM default params

  #164 opened 2 years ago by bio-la
  5

• pipeline printing our options as the defaults

  #152 opened 2 years ago by Acribbs
  1

• missing pipeline action svg

  #156 opened 2 years ago by AndreasHegerGenomics
  1

• cgat-core not compatible with py3.10

  #153 opened 3 years ago by AndreasHeger
  1

• Profiling files sent to home directory on CBRG server

  #151 opened 3 years ago by lucygarner
  11

• COmmand line arguments not overriding defaults

  #132 opened 3 years ago by david-cgat
  23

• How to add additional argument to qsub.

  #150 opened 3 years ago by crichgriffin
  6

• Add logging.exception to cgatcore.experiment module

  #143 opened 3 years ago by AndreasHegerGenomics
  0

• citation.cff file

  #144 opened 3 years ago by sebastian-luna-valero
  0

• Conda env can't be specified by directory

  #136 opened 4 years ago by IanSudbery
  1

• pytest failing with new v6.0.0

  #129 opened 4 years ago by Acribbs
  1

• two different conda pacakges

  #131 opened 4 years ago by IanSudbery
  3

• PBSPro error: drmaa.errors.InternalException: code 1: PBS is not configured to maintain job history

  #122 opened 4 years ago by antoniojbt
  5

• document virtual tsv module

  #121 opened 4 years ago by Acribbs
  0

• apsw dependency missing from conda package

  #126 opened 4 years ago by AndreasHegerGenomics
  2

• Depedency versions - pyyaml

  #116 opened 4 years ago by IanSudbery
  1

• Kubernates integration

  #111 opened 5 years ago by Acribbs
  2

• Tests failing with Python 3.8

  #105 opened 5 years ago by sebastian-luna-valero
  22

• Provide wrapper functors to allow re-use of the same function in ruffus

  #88 opened 5 years ago by AndreasHeger
  1

• drmaa.errors.InvalidAttributeValueException

  #102 opened 5 years ago by amayer21
  14

• The optparse module is deprecated

  #96 opened 5 years ago by Acribbs
  1

• Error while finding module specification for 'cgatcore.csv2db'

  #98 opened 5 years ago by antoniojbt
  6

• Is it possible to install a previous version of cgat-core?

  #85 opened 5 years ago by agammage
  4

• Add ability to import yaml files inside yaml file

  #86 opened 5 years ago by AndreasHeger
  0

• Add suffix argument to experiment.get_output_file

  #87 opened 5 years ago by AndreasHeger
  0

• collecting benchmark data pbspro

  #83 opened 6 years ago by antoniojbt
  2

• installation test errors

  #69 opened 6 years ago by antoniojbt
  10

• Time stamps not updating on rerun tasks

  #75 opened 6 years ago by IanSudbery
  9

• Executing bashrc

  #47 opened 6 years ago by IanSudbery
  5

• Update docs

  #67 opened 6 years ago by Acribbs
  1

• Torque implementation incomplete

  #62 opened 6 years ago by IanSudbery
  1

• Memory usage by Tables.concatenate_tables

  #52 opened 6 years ago by IanSudbery
  2

• Error during installation of cgat-core

  #59 opened 6 years ago by kevinrue
  4

• cgat-core executable no longer available

  #57 opened 6 years ago by jscaber
  0

• add functionality to specify input files on command line

  #54 opened 6 years ago by AndreasHeger
  0

• update and now issues running pipelines

  #51 opened 6 years ago by Acribbs
  2

• tmpdir missing parameter accessed

  #50 opened 6 years ago by Acribbs
  1