databio/bulker issues and pull requests

#89 - Auto-refresh imports

Issue - State: open - Opened by nsheff over 1 year ago
Labels: enhancement, brainstorming

#88 - show which crates are imported

Issue - State: open - Opened by nsheff almost 2 years ago
Labels: enhancement

#87 - bioconductor_full -> bioconductor_docker

Pull Request - State: open - Opened by lwaldron about 2 years ago

#86 - Wrong flag in tutorial for file manifest

Issue - State: open - Opened by jemma-nelson over 2 years ago

#85 - Release 0.7.3

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

#84 - Tips for running bulker for multiple users?

Issue - State: closed - Opened by pvanheus almost 3 years ago - 9 comments
Labels: docs, likely-solved

#83 - No engine config chunk provided - Singularity error

Issue - State: closed - Opened by rcorces about 3 years ago - 12 comments

#82 - Add a more comprehensive reference for writing manifests

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

#81 - Add volumes from CLI

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

#80 - line 3: docker: command not found

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

#79 - map manifest concepts to container labels for zero-config defaults

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

#78 - Release 0.7.2

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

#77 - 0.7.1

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

#76 - Version 0.7.0 release

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

#75 - Add ability to add env var from command line

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

#74 - Allowing both piping and quotes in bulker run

Issue - State: open - Opened by nsheff over 3 years ago - 1 comment
Labels: enhancement, brainstorming

#73 - Auto-detect -t?

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

#72 - Might it be possible to automatically set -t ?

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

#71 - "/bin/bash: clang: command not found" on OSX 11

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

#70 - Sharing a bulker config file across users

Issue - State: closed - Opened by rcorces almost 4 years ago - 7 comments

#69 - Issues when $SHELL isnt bash or zsh

Issue - State: closed - Opened by rcorces almost 4 years ago - 3 comments

#68 - add bulker remove

Issue - State: closed - Opened by nsheff almost 4 years ago

#67 - How to manipulate volumes in bulker config

Issue - State: closed - Opened by rcorces almost 4 years ago - 6 comments

#66 - Don't use $HOME, hard-code it

Issue - State: open - Opened by nsheff almost 4 years ago - 3 comments

#65 - display commands in alphabetical order

Issue - State: closed - Opened by nsheff almost 4 years ago

#64 - Issues with bulker when submitting jobs on SGE

Issue - State: closed - Opened by gbloeb about 4 years ago - 10 comments

#63 - Bulker + CWL synergy and enhancement

Issue - State: open - Opened by nsheff about 4 years ago
Labels: brainstorming

#62 - drop the PEP compatible icon

Pull Request - State: closed - Opened by mr-c about 4 years ago

#61 - Recursive reloading

Issue - State: closed - Opened by nsheff about 4 years ago - 2 comments
Labels: enhancement

#60 - pull access denied for databio/bioconductor

Issue - State: closed - Opened by stolarczyk over 4 years ago - 3 comments
Labels: question

#59 - KeyError: 'singularity_fullpath'

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

#58 - verison 0.6.0

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

#57 - bulker activate fails with default config

Issue - State: closed - Opened by nsheff over 4 years ago
Labels: bug

#56 - /etc/sudoers.d is not shared from OS X and is not known to Docker.

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

#55 - trouble running on a cluster with singularity

Issue - State: closed - Opened by lwaldron over 4 years ago - 10 comments

#54 - associating many commands with a container

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

#53 - Loading/activating PEPATAC crate_Errors

Issue - State: open - Opened by Kmrouj over 4 years ago - 12 comments

#52 - container-specific exclusions

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

#51 - inspect requires crate name

Issue - State: closed - Opened by stolarczyk over 4 years ago - 22 comments
Labels: bug

#50 - bulker overwrites PS1

Issue - State: open - Opened by stolarczyk over 4 years ago - 6 comments
Labels: question

#49 - bulker inspect fails on tagged crates

Issue - State: open - Opened by nsheff over 4 years ago
Labels: bug

#48 - Version 0.5.0

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

#47 - NameError: global name 'FileNotFoundError' is not defined

Issue - State: closed - Opened by lwaldron over 4 years ago - 12 comments

#46 - Bulker 'shell_prompt' adds slashes when its loaded

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

#45 - Bulker sources bashrc, updating PATH when it likely should not

Issue - State: closed - Opened by jpsmith5 over 4 years ago - 10 comments

#44 - custom bulker prompt

Issue - State: closed - Opened by jpsmith5 over 4 years ago - 33 comments

#43 - adding env vars via CLI

Issue - State: closed - Opened by nsheff over 4 years ago - 1 comment
Labels: enhancement

#42 - Bulker inspect currently active crate

Issue - State: open - Opened by nsheff over 4 years ago - 2 comments
Labels: enhancement

#41 - python console scripts are problematic

Issue - State: open - Opened by nsheff over 4 years ago

#40 - Release 0.4.0

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

#39 - bulker overrides default shell

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

#38 - --workdir="`pwd`" is ignored when invoking rstudio-server

Issue - State: closed - Opened by lwaldron almost 5 years ago - 7 comments

#37 - Under some circumstances, "No config found in env var: BULKERCFG"

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

#36 - network error for rstudio-server on waldronlab/bioconductor

Issue - State: closed - Opened by lwaldron almost 5 years ago - 6 comments

#35 - document the no_user and no_network modes

Issue - State: closed - Opened by nsheff almost 5 years ago
Labels: docs

#34 - document dealing with images with entrypoints

Issue - State: closed - Opened by nsheff almost 5 years ago
Labels: docs

#33 - images are not pulled; rivanna/singularity

Issue - State: closed - Opened by stolarczyk almost 5 years ago - 2 comments

#32 - Running bulker activate before load throws error

Issue - State: closed - Opened by jpsmith5 almost 5 years ago - 1 comment

#31 - bulker consumes double-slashes

Issue - State: closed - Opened by nsheff almost 5 years ago - 1 comment
Labels: bug

#30 - user id not working in container on MacOS

Issue - State: closed - Opened by nsheff almost 5 years ago - 51 comments

#29 - container-specific volumes not mounting

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

#28 - Running git in bulker

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

#27 - release 0.3

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

#26 - NameError: name 'create_folder' is not defined

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

#25 - make 'bulker load' printout more concise

Issue - State: closed - Opened by stolarczyk almost 5 years ago - 2 comments

#24 - Multiple registries

Issue - State: open - Opened by nsheff almost 5 years ago
Labels: enhancement

#23 - release 0.2.4

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

#22 - AttributeError: default_namespace

Issue - State: closed - Opened by nsheff almost 5 years ago - 2 comments

#21 - bulker init is broken

Issue - State: closed - Opened by nsheff almost 5 years ago - 1 comment
Labels: bug

#20 - host commands should not create an empty executable

Issue - State: closed - Opened by nsheff almost 5 years ago

#19 - update yacman requirement

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

#18 - 0.2.2

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

#17 - Error running demo

Issue - State: closed - Opened by lgatto about 5 years ago - 3 comments
Labels: bug

#16 - 0.2.1

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

#15 - no module named request

Issue - State: closed - Opened by nsheff about 5 years ago
Labels: bug

#14 - crate location should be relative to bulker config

Issue - State: closed - Opened by nsheff about 5 years ago

#13 - 0.2.0

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

#12 - 0.1.2

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

#11 - start travis

Issue - State: closed - Opened by nsheff about 5 years ago

#10 - 0.1.1

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

#9 - import domain for cascading manifests

Issue - State: closed - Opened by nsheff about 5 years ago - 2 comments
Labels: enhancement

#8 - bulker shell

Issue - State: closed - Opened by nsheff about 5 years ago - 5 comments
Labels: enhancement

#7 - Settings that are both tool-specific and host-specific

Issue - State: closed - Opened by nsheff about 5 years ago - 1 comment
Labels: enhancement

#6 - docs

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

#5 - 0.1.0

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

#4 - 0.0.3

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

#3 - 0.0.2

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

#2 - Some ideas

Issue - State: closed - Opened by nsheff about 5 years ago

#1 - container location api

Issue - State: open - Opened by nsheff about 5 years ago
Labels: enhancement

GitHub / databio/bulker issues and pull requests