refgenie/refgenconf issues and pull requests

#148 - Merge branch 0.12.3 into dev

Pull Request - State: closed - Opened by nsheff about 2 months ago

#147 - Fix plugin verbosity

Pull Request - State: open - Opened by nsheff about 2 months ago

#146 - All commands fail due to a 404 error for openapi.json

Issue - State: closed - Opened by ialbert 8 months ago - 1 comment

#145 - Adopt yacman v1

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

#144 - New refgenconf requires python 3.8

Issue - State: open - Opened by nsheff about 2 years ago - 1 comment

#143 - allow dashes in genome names

Pull Request - State: closed - Opened by mirpedrol about 2 years ago - 1 comment

#142 - Support for Python 3.10

Issue - State: open - Opened by fabianegli over 2 years ago - 3 comments

#141 - Populate of refgenie registry paths doesn't allow dashes in the genome name

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

#140 - Issue 139 raise more specific error for non existing asset

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

#139 - Refgenconf should give a more specific error when an non-existing asset is queried

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

#138 - Incorrect web link in upgrade message

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

#137 - Dev

Pull Request - State: open - Opened by nsheff over 2 years ago

#136 - Fix setuptools, release 0.12.2

Pull Request - State: closed - Opened by nsheff about 3 years ago - 1 comment

#135 - v0.12.1

Pull Request - State: closed - Opened by stolarczyk about 3 years ago - 1 comment

#134 - Missing dependency on tqdm

Issue - State: closed - Opened by natefoo about 3 years ago - 2 comments

#133 - get_tag_seek_keys() returns None - leading to potential TypeError: 'NoneType' object is not iterable

Issue - State: open - Opened by jpsmith5 about 3 years ago - 2 comments
Labels: bug

#132 - revamp looper plugin to accomodate multiple genomes

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

#131 - Remove RunTimeWarning

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

#130 - v0.12.0

Pull Request - State: closed - Opened by stolarczyk over 3 years ago - 5 comments

#129 - Looper plugin

Pull Request - State: closed - Opened by nsheff over 3 years ago - 7 comments

#128 - A list of seek keys

Issue - State: closed - Opened by nsheff over 3 years ago - 2 comments
Labels: question

#127 - v0.11.1

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

#126 - Refgenie populater plugin

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

#125 - tags in `RefGenConf.populate`?

Issue - State: closed - Opened by stolarczyk over 3 years ago - 2 comments
Labels: question, priority-high, likely-solved

#124 - Release 0.11.0

Pull Request - State: closed - Opened by nsheff over 3 years ago - 8 comments

#123 - using listr in remote mode

Issue - State: closed - Opened by stolarczyk over 3 years ago - 1 comment
Labels: likely-solved

#122 - alias links to log files appear to be wrong

Issue - State: closed - Opened by nsheff over 3 years ago - 4 comments
Labels: bug, likely-solved

#121 - seek remote assets return value

Issue - State: closed - Opened by stolarczyk over 3 years ago - 1 comment
Labels: question, priority-high

#120 - Improve error message for undefined alias

Issue - State: closed - Opened by nsheff over 3 years ago
Labels: docs, likely-solved

#119 - Database back-end for refgenieserver configuration

Issue - State: open - Opened by nsheff over 3 years ago - 2 comments

#118 - better missing ASDs communication in refgenie compare

Issue - State: closed - Opened by stolarczyk over 3 years ago - 3 comments
Labels: likely-solved

#117 - get ASDs.json (if missing) on any asset pull

Issue - State: open - Opened by stolarczyk over 3 years ago - 3 comments
Labels: enhancement

#116 - Fix deprecation warning

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

#115 - failed refgenie pull breaks the config

Issue - State: closed - Opened by stolarczyk almost 4 years ago - 1 comment
Labels: bug

#114 - Config upgrade bug: missing ASDs for genomes with no local fasta assets

Issue - State: closed - Opened by xuebingjie1990 almost 4 years ago

#113 - First pass at populator and looper plugin

Pull Request - State: closed - Opened by nsheff about 4 years ago - 14 comments

#112 - upgrade error on broken URL

Issue - State: closed - Opened by nsheff about 4 years ago - 6 comments

#111 - Dev config upgrade

Pull Request - State: closed - Opened by xuebingjie1990 about 4 years ago - 30 comments

#110 - init should create data and alias directories

Issue - State: closed - Opened by nsheff about 4 years ago - 1 comment
Labels: likely-solved

#109 - v0.9.3

Pull Request - State: closed - Opened by stolarczyk about 4 years ago - 1 comment

#108 - list function overloads python's built-in type

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

#107 - error in list_assets_by_genome

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

#106 - FileExistsError in initialize_genome

Issue - State: closed - Opened by stolarczyk over 4 years ago
Labels: likely-solved

#105 - Memory use of genome digest init

Issue - State: closed - Opened by nsheff over 4 years ago - 35 comments
Labels: likely-solved

#104 - allow forcing gzipped fasta

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

#103 - KeyError: 'aliases'

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

#102 - v0.10.0

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

#101 - update dev

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

#100 - v0.9.2

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

#99 - add genome_description upon asset pull

Issue - State: closed - Opened by nsheff over 4 years ago - 7 comments
Labels: enhancement

#98 - update dev

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

#97 - v0.9.1

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

#96 - bug in get_remote_data_str ?

Issue - State: closed - Opened by nsheff over 4 years ago - 6 comments
Labels: bug, likely-solved

#95 - v0.9.0

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

#94 - v0.8.0

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

#93 - Adding values that aren't file paths

Issue - State: open - Opened by nsheff over 4 years ago - 1 comment
Labels: priority-low

#92 - Plugins

Pull Request - State: closed - Opened by nsheff over 4 years ago - 8 comments

#91 - Listing recipe requirements from within python

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

#90 - malformed string error

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

#89 - TypeError: tag must be str; got unicode

Issue - State: closed - Opened by nsheff over 4 years ago - 1 comment
Labels: bug, likely-solved, py2

#88 - v0.7.0

Pull Request - State: closed - Opened by stolarczyk over 4 years ago - 3 comments

#87 - Allow list_remote() to work with list of servers. Currently only returning values from first available URL.

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

#86 - mimic CLI terminology in RefGenConf object's methods

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

#84 - list_local is returning strings

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

#83 - Get a list of recipes within python

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

#82 - get_asset terminology

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

#81 - list_remote broken.

Issue - State: closed - Opened by nsheff over 4 years ago - 3 comments
Labels: bug

#80 - v0.6.2

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

#79 - v0.6.1

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

#78 - v0.6.0

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

#77 - updating config file in pull_asset

Issue - State: closed - Opened by nsheff about 5 years ago - 3 comments
Labels: enhancement, likely-solved

#76 - error on slow downloads

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

#75 - add a refgenie asset programmatically?

Issue - State: closed - Opened by jpsmith5 about 5 years ago - 10 comments
Labels: brainstorming

#74 - v0.5.4

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

#73 - colon is overloaded in tqdm progress bar description

Issue - State: closed - Opened by stolarczyk about 5 years ago
Labels: priority-low

#71 - Deal with HTTPError error (missing archives on the server)

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

#70 - chk_digest_update_child checks and writes asset relationship multiple times

Issue - State: closed - Opened by stolarczyk about 5 years ago
Labels: bug, likely-solved

#69 - pull_asset changes RGC object attribute outside of init

Issue - State: closed - Opened by stolarczyk about 5 years ago - 1 comment
Labels: bug, likely-solved

#68 - v0.5.3

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

#67 - v0.5.2

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

#66 - documentation updates

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

#65 - Random Errors in output

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

#64 - use openapi.json for standardizing interface to refgenie server

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

#63 - pulling an asset with parents should populate their asset_children

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

#62 - empty dir produced after a negative answer to "large archive" question

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

#61 - v0.5.0

Pull Request - State: closed - Opened by stolarczyk about 5 years ago - 7 comments

#60 - default seek keys

Issue - State: closed - Opened by nsheff about 5 years ago - 6 comments

#58 - create an empty RefGenConf object

Issue - State: closed - Opened by stolarczyk over 5 years ago - 2 comments
Labels: question

#57 - Genome checksums to dev

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

#56 - bug in refgenie seek

Issue - State: closed - Opened by nsheff over 5 years ago - 1 comment

#55 - update unit tests

Issue - State: closed - Opened by stolarczyk over 5 years ago
Labels: tests

#54 - add 'tag' to pull_asset

Issue - State: closed - Opened by nsheff over 5 years ago - 3 comments
Labels: likely-solved

#53 - `get_asset` will need a new optional arg, `tag`, which if set to None, returns the default asset.

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

#52 - `update_assets(` will need a signature change to accommodate:

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

#51 - add tag layer to the config format

Issue - State: closed - Opened by stolarczyk over 5 years ago - 1 comment

#50 - add setdefault method

Issue - State: closed - Opened by stolarczyk over 5 years ago - 2 comments
Labels: enhancement, likely-solved

#49 - release 0.4.0

Pull Request - State: closed - Opened by nsheff over 5 years ago - 1 comment

#47 - correct tests

Issue - State: closed - Opened by stolarczyk over 5 years ago - 1 comment
Labels: priority-high, tests, likely-solved

#43 - python2 error

Issue - State: closed - Opened by nsheff over 5 years ago - 3 comments
Labels: bug, likely-solved

#32 - archive_data fetch as a "request validation" step

Issue - State: closed - Opened by stolarczyk over 5 years ago
Labels: brainstorming

GitHub / refgenie/refgenconf issues and pull requests