Ecosyste.ms: Issues

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GitHub / rkimoakbioinformatics/oakvar issues and pull requests

#57 - [BUG] Issue with annotators (cadd, hgvs)

Issue - State: closed - Opened by MariosGvr 3 months ago - 11 comments
Labels: bug

#56 - bug_fix_read_sql

Pull Request - State: closed - Opened by acmoudleysa 10 months ago - 1 comment

#55 - [BUG] `get_wgs_reader` method sometimes returns lowercase bases.

Issue - State: closed - Opened by sinmojito 10 months ago - 3 comments
Labels: bug

#54 - read_crv first row deletion fix

Pull Request - State: closed - Opened by sinmojito 11 months ago - 1 comment

#53 - fixed read_crv issue where polars was reading from previously opened …

Pull Request - State: closed - Opened by sinmojito 11 months ago - 1 comment

#52 - Adding tutorial images corresponding to v2.9.36 and updating tutorial accordingly.

Pull Request - State: closed - Opened by sinmojito 11 months ago - 1 comment

#51 - fixed the wsl2 issue where gui redirects to localhost instead of 0.0.0.0

Pull Request - State: closed - Opened by sinmojito 11 months ago - 1 comment

#50 - [BUG] Accessing GUI via 0.0.0.0 on WSL2

Issue - State: closed - Opened by sinmojito 11 months ago - 6 comments
Labels: bug

#49 - galaxy wrapper

Pull Request - State: closed - Opened by beatrizmclm about 1 year ago

#48 - [Feature] Small changes of GUI for uploading file and annotation button

Issue - State: closed - Opened by marfantyk about 1 year ago - 3 comments
Labels: enhancement

#47 - [Feature] one button for applying filters

Issue - State: closed - Opened by marfantyk about 1 year ago - 3 comments
Labels: enhancement

#45 - [BUG] problems with gene filters

Issue - State: closed - Opened by antonkulaga about 1 year ago - 2 comments
Labels: bug

#44 - Snakemake wrapper for ov run

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

#43 - Oakvar CWL workflow

Pull Request - State: closed - Opened by gehadkamel over 1 year ago - 6 comments

#42 - add first wdl workflow

Pull Request - State: closed - Opened by gehadkamel over 1 year ago - 8 comments

#41 - several users with empty login names are possible [BUG]

Issue - State: closed - Opened by antonkulaga over 1 year ago - 3 comments
Labels: bug

#40 - please change the icon for manually entering variants [Feature]

Issue - State: closed - Opened by antonkulaga over 1 year ago - 1 comment
Labels: enhancement

#39 - show dependencies of dependencies in selected modules[Feature]

Issue - State: open - Opened by antonkulaga over 1 year ago - 4 comments
Labels: enhancement

#38 - submission does not clean up [BUG]

Issue - State: closed - Opened by antonkulaga over 1 year ago - 1 comment
Labels: bug

#37 - [BUG] Error on "ov run exampleinput -a clinvar -t vcf"

Issue - State: open - Opened by lopatich over 1 year ago - 2 comments
Labels: bug

#36 - [Feature] there should be separate Log for reporters as well as some way to display progress

Issue - State: closed - Opened by antonkulaga over 1 year ago - 2 comments
Labels: enhancement

#35 - [BUG] Errors on "ov system setup" command

Issue - State: closed - Opened by marfantyk almost 2 years ago - 13 comments
Labels: bug

#34 - [BUG] polyphen2:2022.09.19 does not update

Issue - State: closed - Opened by antonkulaga almost 2 years ago - 3 comments
Labels: bug

#33 - [BUG] no dependency control for reporters

Issue - State: closed - Opened by antonkulaga almost 2 years ago - 6 comments
Labels: bug

#32 - make updating less confusing

Issue - State: closed - Opened by antonkulaga almost 2 years ago - 4 comments
Labels: bug

#31 - g.vcf support

Issue - State: open - Opened by antonkulaga almost 2 years ago - 7 comments
Labels: enhancement

#30 - Error during setup in excelreporter

Issue - State: closed - Opened by Alex-Karmazin almost 2 years ago - 1 comment
Labels: bug

#29 - OakVar do not uninstalling completely

Issue - State: closed - Opened by Alex-Karmazin almost 2 years ago - 4 comments
Labels: bug

#28 - Duplicating rows when us annotators

Issue - State: closed - Opened by Alex-Karmazin almost 2 years ago - 12 comments
Labels: bug

#27 - Pagenation not loading data

Issue - State: closed - Opened by Alex-Karmazin almost 2 years ago - 3 comments
Labels: bug

#26 - [Feature] hot reload

Issue - State: open - Opened by antonkulaga almost 2 years ago - 3 comments
Labels: enhancement

#25 - No drop-down list in the filter tab

Issue - State: closed - Opened by OlgaBorysova almost 2 years ago - 4 comments
Labels: bug

#24 - feature request [can be done in collaboration with us]: support for PRS modules

Issue - State: open - Opened by antonkulaga almost 2 years ago - 1 comment
Labels: enhancement

#23 - feature request: function to group by genotype

Issue - State: open - Opened by antonkulaga almost 2 years ago - 1 comment
Labels: enhancement

#22 - feature request: presets for annotators and reporters

Issue - State: closed - Opened by antonkulaga almost 2 years ago - 2 comments
Labels: enhancement

#21 - feature request: use of pagination instead of 100K variants limit

Issue - State: closed - Opened by antonkulaga almost 2 years ago - 2 comments
Labels: enhancement

#20 - feature request: the tab with available reports should be displayed in annotators results

Issue - State: closed - Opened by antonkulaga almost 2 years ago - 9 comments
Labels: enhancement

#19 - feature request: adding new annotator to already annotated vcf

Issue - State: open - Opened by antonkulaga almost 2 years ago - 3 comments
Labels: enhancement

#18 - feature request: autodetect option for reference genome

Issue - State: closed - Opened by antonkulaga almost 2 years ago - 2 comments
Labels: enhancement

#17 - Problem updating dbsnp

Issue - State: closed - Opened by Alex-Karmazin almost 2 years ago - 4 comments
Labels: enhancement

#16 - Problem occurred while setting up the system

Issue - State: closed - Opened by lnalinaf almost 2 years ago - 22 comments
Labels: bug

#15 - JSON Error in stacktrace

Issue - State: closed - Opened by Alex-Karmazin almost 2 years ago - 6 comments
Labels: bug

#14 - improvement of UI loading speed (minor issue)

Issue - State: closed - Opened by antonkulaga almost 2 years ago - 12 comments

#13 - minor ui bug with system update

Issue - State: closed - Opened by antonkulaga almost 2 years ago - 4 comments
Labels: bug

#12 - Error during processing vcf file.

Issue - State: closed - Opened by Alex-Karmazin almost 2 years ago - 29 comments
Labels: bug

#11 - 'list' object has no attribute 'rstrip' in multiple modules

Issue - State: closed - Opened by antonkulaga almost 2 years ago - 12 comments
Labels: bug

#10 - oakvar.exceptions.BadFormatError: error: All samples have the reference genotype.

Issue - State: closed - Opened by antonkulaga almost 2 years ago - 12 comments

#9 - minor bug with non-standard home folders

Issue - State: closed - Opened by antonkulaga almost 2 years ago - 4 comments
Labels: bug

#8 - NameError: name 'stage_handler' is not defined

Issue - State: closed - Opened by antonkulaga almost 2 years ago - 7 comments

#7 - no favicon.ico error in wcravat.log

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

#6 - Error on starting job

Issue - State: closed - Opened by Alex-Karmazin almost 2 years ago - 3 comments
Labels: bug

#5 - ov gui leads to crashes

Issue - State: closed - Opened by antonkulaga almost 2 years ago - 4 comments

#4 - ov system setup can be blocked by email not coming

Issue - State: closed - Opened by antonkulaga almost 2 years ago - 4 comments

#3 - After setup there is no module webapps

Issue - State: closed - Opened by Alex-Karmazin about 2 years ago - 6 comments