Ecosyste.ms: Issues

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

GitHub / ENCODE-DCC/caper issues and pull requests

#204 - using slurm-extra-param and the leader job

Issue - State: open - Opened by giardine 10 months ago

#203 - Setting $SINGULARITY_TMPDIR environment variable

Issue - State: open - Opened by miller-alexander about 1 year ago

#202 - --slurm-extra-param: expected one argument

Issue - State: open - Opened by OrangeyO2 about 1 year ago - 1 comment

#201 - Caper run with scatter runs out of memory

Issue - State: closed - Opened by sdwang008 over 1 year ago - 2 comments

#200 - Caper conda forge

Issue - State: open - Opened by atb1r21 over 1 year ago

#199 - v2.3.2

Pull Request - State: closed - Opened by leepc12 over 1 year ago

#198 - remove pyyaml requirements from setup

Pull Request - State: closed - Opened by leepc12 over 1 year ago

#197 - Consider increasing minimum requirement of PyYAML to 6.0.1

Issue - State: closed - Opened by mihirsamdarshi over 1 year ago - 2 comments

#196 - Cannot run on lsf system, not sure if exit code 127 is the reason

Issue - State: open - Opened by Jixuan-Huang over 1 year ago - 6 comments

#195 - caper halted

Issue - State: open - Opened by zji90 over 1 year ago

#194 - Hotfix upgrade filelock

Pull Request - State: closed - Opened by leepc12 almost 2 years ago

#193 - .caper_tmp slowly eating up space

Issue - State: closed - Opened by sufyazi almost 2 years ago - 1 comment

#192 - LSF job parameter error

Issue - State: open - Opened by jwtobias almost 2 years ago - 3 comments

#191 - apptainer

Issue - State: open - Opened by ad2n15 almost 2 years ago - 1 comment

#190 - Error when specifying --slurm-leader-job-resource-param

Issue - State: closed - Opened by wkc1986 almost 2 years ago - 1 comment

#189 - v2.3.1

Pull Request - State: closed - Opened by leepc12 over 2 years ago

#188 - Relpath based on cwd in abspath

Pull Request - State: closed - Opened by leepc12 over 2 years ago

#187 - Normalization

Issue - State: open - Opened by nicholas-moskwa over 2 years ago

#186 - v2.2.3

Pull Request - State: closed - Opened by leepc12 over 2 years ago

#185 - Hotfix simpler conf file

Pull Request - State: closed - Opened by leepc12 over 2 years ago

#184 - Relative paths to data files are not accessible by Singularity containers

Issue - State: open - Opened by jgoodson over 2 years ago - 4 comments

#183 - v2.2.2

Pull Request - State: closed - Opened by leepc12 over 2 years ago

#182 - cromwell works, caper doesn't

Issue - State: open - Opened by mapostolides over 2 years ago

#181 - Hotfix issue 177, 180

Pull Request - State: closed - Opened by leepc12 over 2 years ago

#180 - Missing `engine` in gcs configuration

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

#179 - v2.2.1

Pull Request - State: closed - Opened by leepc12 over 2 years ago - 3 comments

#178 - Hotfix 177 sge resource param

Pull Request - State: closed - Opened by leepc12 over 2 years ago

#176 - Newer cromwell versions

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

#175 - caper init slurm not working

Issue - State: open - Opened by mapostolides over 2 years ago - 6 comments

#174 - Failed on test data -- make_conf.py not found

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

#172 - v2.2.0

Pull Request - State: closed - Opened by leepc12 over 2 years ago

#171 - Pipe 75 better hpc feature and troubleshotting

Pull Request - State: closed - Opened by leepc12 over 2 years ago

#170 - fix pyyaml install issue

Pull Request - State: closed - Opened by leepc12 over 2 years ago

#169 - Changing `gcp-out-dir` when using `caper submit`

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

#168 - pyyaml error when create_instance.sh

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

#167 - idr threshold

Issue - State: open - Opened by shinlin77 almost 3 years ago - 1 comment

#166 - intermediate file

Issue - State: closed - Opened by shinlin77 almost 3 years ago

#165 - exit 1

Issue - State: closed - Opened by shinlin77 almost 3 years ago

#164 - Invalid or corrupt jarfile

Issue - State: closed - Opened by lucasrocmoreira almost 3 years ago - 2 comments

#163 - cromwell error: java out of bounds

Issue - State: closed - Opened by shinlin77 almost 3 years ago - 1 comment

#161 - getting Cromwell error

Issue - State: open - Opened by shinlin77 almost 3 years ago - 1 comment

#160 - UnboundLocalError: local variable 'p' referenced before assignment

Issue - State: closed - Opened by Al-Murphy almost 3 years ago - 2 comments

#159 - v2.1.3

Pull Request - State: closed - Opened by leepc12 about 3 years ago

#158 - Pip 1656 fix pip install

Pull Request - State: closed - Opened by leepc12 about 3 years ago

#157 - remove duplicate param in caper init

Pull Request - State: closed - Opened by leepc12 about 3 years ago

#156 - Hotfix gcp caper server

Pull Request - State: closed - Opened by leepc12 about 3 years ago

#155 - v2.1.2

Pull Request - State: closed - Opened by leepc12 about 3 years ago

#154 - fix stderr.background bug

Pull Request - State: closed - Opened by leepc12 about 3 years ago

#153 - v2.1.1

Pull Request - State: closed - Opened by leepc12 about 3 years ago

#152 - Pip 1643 fix sbatch stalling

Pull Request - State: closed - Opened by leepc12 about 3 years ago

#151 - v2.1.0

Pull Request - State: closed - Opened by leepc12 about 3 years ago

#150 - Pip 1640 fix gid issue

Pull Request - State: closed - Opened by leepc12 about 3 years ago

#149 - Disk quota exceeded on SCG (due to `nobody` user)

Issue - State: closed - Opened by leepc12 about 3 years ago

#148 - v2.0.0

Pull Request - State: closed - Opened by leepc12 over 3 years ago

#147 - Pip 1626 docker and conda in task runtime

Pull Request - State: closed - Opened by leepc12 over 3 years ago

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

Issue - State: closed - Opened by ebprideaux over 3 years ago - 11 comments

#144 - Trouble using caper on scg

Issue - State: closed - Opened by asanghi7 over 3 years ago

#143 - Add LSF

Pull Request - State: closed - Opened by HenryCWong over 3 years ago - 2 comments

#142 - Trying to run example json file

Issue - State: closed - Opened by lcamillo over 3 years ago

#141 - Can GCP backend use Genomics API?

Issue - State: open - Opened by yihming over 3 years ago

#140 - Can Caper upload data for cloud backend?

Issue - State: closed - Opened by yihming over 3 years ago - 4 comments

#139 - Modified cromwell for aws backend

Pull Request - State: closed - Opened by leepc12 over 3 years ago

#138 - caper install

Issue - State: closed - Opened by yinshiyi over 3 years ago

#137 - add description/troubleshooting for aws backend

Pull Request - State: closed - Opened by leepc12 over 3 years ago

#136 - Can caper server use a custom Cromwell conf file?

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

#135 - update doc for aws (to disable spot instances)

Pull Request - State: closed - Opened by leepc12 over 3 years ago

#134 - update doc for aws (about disabling spot instances)

Pull Request - State: closed - Opened by leepc12 over 3 years ago

#133 - Job doesn't submit with custom backend memory specification

Issue - State: closed - Opened by HenryCWong over 3 years ago - 4 comments

#132 - Cannot build a local path from file link on GCP GS

Issue - State: closed - Opened by yihming over 3 years ago - 4 comments

#131 - Example WDL file

Issue - State: closed - Opened by lwtan90 over 3 years ago - 1 comment

#130 - ~/.caper/default.conf file isn't created after caper init

Issue - State: open - Opened by xinmiaoyan over 3 years ago - 1 comment

#129 - v1.6.3

Pull Request - State: closed - Opened by leepc12 over 3 years ago

#128 - No such file or directory: 'singularity'

Issue - State: closed - Opened by HenryCWong over 3 years ago - 12 comments

#127 - Pip 1551 fix aws autoscaling

Pull Request - State: closed - Opened by leepc12 over 3 years ago

#126 - How does docker get called in caper?

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

#125 - Running caper within a docker container

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

#124 - Womtool validation doesn't raise an exception

Issue - State: open - Opened by Bek over 3 years ago - 1 comment

#123 - v1.6.2

Pull Request - State: closed - Opened by leepc12 over 3 years ago

#122 - v1.6.1

Pull Request - State: closed - Opened by leepc12 over 3 years ago

#121 - Pip 1548 install gsutil

Pull Request - State: closed - Opened by leepc12 over 3 years ago

#120 - Pip 1545 install gsutil

Pull Request - State: closed - Opened by leepc12 over 3 years ago

#118 - PBS qsub Node Specification Error

Issue - State: open - Opened by CriticalSci over 3 years ago - 4 comments

#117 - v1.6.1

Pull Request - State: closed - Opened by leepc12 almost 4 years ago

#116 - Hotfix to fix troubleshoot bug

Pull Request - State: closed - Opened by leepc12 almost 4 years ago

#115 - AWS backend

Pull Request - State: closed - Opened by leepc12 almost 4 years ago

#114 - increase server timeout

Pull Request - State: closed - Opened by leepc12 almost 4 years ago

#113 - v1.6.0

Pull Request - State: closed - Opened by leepc12 almost 4 years ago

#112 - Pip 1528 direct read from hocon

Pull Request - State: closed - Opened by leepc12 almost 4 years ago

#111 - v1.5.1

Pull Request - State: closed - Opened by leepc12 almost 4 years ago

#110 - Pip 1523 fix custom backend file

Pull Request - State: closed - Opened by leepc12 almost 4 years ago

#109 - v1.5.0

Pull Request - State: closed - Opened by leepc12 almost 4 years ago

#107 - fix for aws

Pull Request - State: closed - Opened by leepc12 almost 4 years ago