ENCODE-DCC/caper

Issues

• caper installs tests into site-packages/tests which is too generic of a name

  #206 opened 17 days ago by detrout
  0

• Cannot run on lsf system, not sure if exit code 127 is the reason

  #196 opened a year ago by Jixuan-Huang
  6

• Compatibility Update for Caper with Google Batch Following Deprecation of Cloud Life Sciences

  #205 opened 6 months ago by TarjinderSingh
  0

• Changing `gcp-out-dir` when using `caper submit`

  #169 opened 7 months ago by TarjinderSingh
  1

• using slurm-extra-param and the leader job

  #204 opened 7 months ago by giardine
  0

• Setting $SINGULARITY_TMPDIR environment variable

  #203 opened a year ago by miller-alexander
  0

• --slurm-extra-param: expected one argument

  #202 opened a year ago by OrangeyO2
  1

• Caper run with scatter runs out of memory

  #201 opened a year ago by sdwang008
  2

• Relative paths to data files are not accessible by Singularity containers

  #184 opened 2 years ago by jgoodson
  4

• Caper conda forge

  #200 opened a year ago by atb1r21
  0

• Consider increasing minimum requirement of PyYAML to 6.0.1

  #197 opened a year ago by mihirsamdarshi
  2

• LSF job parameter error

  #192 opened 2 years ago by jwtobias
  3

• caper halted

  #195 opened a year ago by zji90
  0

• .caper_tmp slowly eating up space

  #193 opened a year ago by sufyazi
  1

• apptainer

  #191 opened 2 years ago by ad2n15
  1

• Error when specifying --slurm-leader-job-resource-param

  #190 opened 2 years ago by wkc1986
  1

• filelock._error.Timeout: The file lock '/home/zjin/.caper/womtool_jar/womtool-65.jar.lock' could not be acquired.

  #162 opened 2 years ago by gavinjzg
  4

• Normalization

  #187 opened 2 years ago by nicholas-moskwa
  0

• Newer cromwell versions

  #176 opened 2 years ago by TarjinderSingh
  2

• changes to sge_resource_param in config file don't make it through to backend.conf

  #177 opened 2 years ago by welchwilmerck
  2

• Missing `engine` in gcs configuration

  #180 opened 2 years ago by TarjinderSingh
  1

• caper init slurm not working

  #175 opened 2 years ago by mapostolides
  6

• cromwell works, caper doesn't

  #182 opened 2 years ago by mapostolides
  0

• Failed on test data -- make_conf.py not found

  #174 opened 2 years ago by jlparkI
  0

• Unable to write file due to disk space despite there being sufficient disk space via docker

  #173 opened 2 years ago by alesgarces22
  3

• pyyaml error when create_instance.sh

  #168 opened 2 years ago by TarjinderSingh
  3

• idr threshold

  #167 opened 3 years ago by shinlin77
  1

• intermediate file

  #166 opened 3 years ago by shinlin77
  0

• exit 1

  #165 opened 3 years ago by shinlin77
  0

• Invalid or corrupt jarfile

  #164 opened 3 years ago by lucasrocmoreira
  2

• cromwell error: java out of bounds

  #163 opened 3 years ago by shinlin77
  1

• getting Cromwell error

  #161 opened 3 years ago by shinlin77
  1

• Job doesn't submit with custom backend memory specification

  #133 opened 3 years ago by HenryCWong
  4

• UnboundLocalError: local variable 'p' referenced before assignment

  #160 opened 3 years ago by Al-Murphy
  2

• Disk quota exceeded on SCG (due to `nobody` user)

  #149 opened 3 years ago by leepc12
  0

• Setting up MYSQL Metadata database - Unable connect to local MySQL server through socket

  #146 opened 3 years ago by sfpacman
  1

• Caper (wgbs-pipeline) not finding make_metadata_csv.py and make_conf.py

  #145 opened 3 years ago by ebprideaux
  11

• Trouble using caper on scg

  #144 opened 3 years ago by asanghi7
  0

• Trying to run example json file

  #142 opened 3 years ago by lcamillo
  0

• Can GCP backend use Genomics API?

  #141 opened 3 years ago by yihming
  0

• Can Caper upload data for cloud backend?

  #140 opened 3 years ago by yihming
  4

• caper install

  #138 opened 3 years ago by yinshiyi
  0

• Can caper server use a custom Cromwell conf file?

  #136 opened 3 years ago by yihming
  2

• Cannot build a local path from file link on GCP GS

  #132 opened 3 years ago by yihming
  4

• Example WDL file

  #131 opened 3 years ago by lwtan90
  1

• ~/.caper/default.conf file isn't created after caper init

  #130 opened 3 years ago by xinmiaoyan
  1

• No such file or directory: 'singularity'

  #128 opened 3 years ago by HenryCWong
  12

• How does docker get called in caper?

  #126 opened 3 years ago by HenryCWong
  2

• Running caper within a docker container

  #125 opened 3 years ago by HenryCWong
  2

• Womtool validation doesn't raise an exception

  #124 opened 3 years ago by Bek
  1