blobtoolkit/blobtoolkit issues and pull requests

#224 - attempting to fix issue #223

Pull Request - State: closed - Opened by tkchafin 8 months ago

#223 - Incompatibility with Busco 5.7

Issue - State: open - Opened by muffato 8 months ago - 10 comments

#222 - Develop

Pull Request - State: open - Opened by rjchallis 9 months ago

#221 - blobtoolkit pipeline error related to parsing of diamond_blastp output (hits.py, "end"=int(end) fails)

Issue - State: open - Opened by estolle 10 months ago - 1 comment

#220 - Release/4.3.10

Pull Request - State: closed - Opened by rjchallis 10 months ago

#219 - Fix parsing of start and end positions in blast hits

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

#218 - Viewer is not starting interactively or remotely

Issue - State: open - Opened by torstenstruck 10 months ago - 3 comments

#217 - Adding blobtk from the other Docker container

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

#215 - Question About Running the Pipeline: CONDA_DIR variable, and snake_env conda environment

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

#214 - Error Associated with chromedriver-binary-auto When Installing Using pip install blobtoolkit

Issue - State: closed - Opened by foreignsand about 1 year ago - 2 comments

#213 - Error with blobtools_create step

Issue - State: open - Opened by aureliendejode over 1 year ago - 16 comments

#212 - Blobtools viewer and installation

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

#211 - viewer and _tkinter?

Issue - State: open - Opened by BTBarney over 1 year ago - 1 comment

#210 - database search order (diamond blast)

Issue - State: open - Opened by gbdias over 1 year ago - 2 comments

#209 - Viewer not working

Issue - State: open - Opened by HanaMerch over 1 year ago - 3 comments

#208 - Diamond steps not working, Missing input files for rule run_diamond_blastx:

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

#207 - Issue running any filter command

Issue - State: open - Opened by aglendening over 1 year ago - 1 comment

#206 - Versions of snakemake and blobtoolkit

Issue - State: open - Opened by aureliendejode over 1 year ago - 1 comment

#205 - [generate-config] Error message when using an invalid accession number

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

#204 - Bug in `count_busco_genes.py`

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

#203 - blobtools command line view produces graph with no labels

Issue - State: closed - Opened by alexrvandam over 1 year ago - 3 comments

#202 - Best way to format uniprot data?

Issue - State: open - Opened by hans-vg over 1 year ago - 1 comment

#201 - Bug in window_stats.py

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

#200 - Skipping pipeline components?

Issue - State: open - Opened by jsoghigian over 1 year ago - 1 comment

#199 - Clarification for filtering of mapped vs. unmapped reads.

Issue - State: open - Opened by myco-bradshaw over 1 year ago - 1 comment

#198 - Issue with Viewer

Issue - State: closed - Opened by jferbe1 over 1 year ago - 2 comments

#197 - bump to python3.12?

Issue - State: open - Opened by jowodo over 1 year ago - 1 comment

#196 - "/usr/bin/bash: conda: command not found" when running the blobtoolkit.smk metapipeline

Issue - State: open - Opened by git-hobo almost 2 years ago - 5 comments

#195 - Error with Parsing taxdump

Issue - State: open - Opened by Edouard94 almost 2 years ago - 5 comments

#194 - BUSCO gene hits

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

#193 - Adding tiara

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

#192 - Add installation instructions to build from source

Issue - State: open - Opened by seb45tian almost 2 years ago - 3 comments

#191 - merge release 4.2.0

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

#190 - Issue184/Taxononmic-filtering-using---Inv-not-working

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

#189 - Catch TypeError when meta.json does not already exist

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

#188 - Feature/update-target-tree

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

#187 - Develop

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

#186 - pip install blobtoolkit[full] error: Failed building wheel for blobtk

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

#185 - pip install giving an error today

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

#184 - Taxononmic filtering using --Inv not working?

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

#183 - no-hits with species, genus and family level annotation

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

#182 - Larger legends for the blobplots

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

#181 - Viewer Loading then white/blank screen

Issue - State: open - Opened by jaylward2 about 2 years ago - 2 comments

#180 - Blobtools add --cov error.

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

#179 - Installation problem viewer

Issue - State: open - Opened by LR-2021 about 2 years ago - 8 comments

#178 - An error occurs when using blobtools create

Issue - State: closed - Opened by maruiqi0710 about 2 years ago - 1 comment
Labels: bug

#177 - Docker image missing mosdepth, despite presence in conda env.yaml

Issue - State: open - Opened by bricoletc about 2 years ago - 4 comments

#176 - Generating plots using blobtools view

Issue - State: open - Opened by NPPO-NL about 2 years ago - 2 comments

#175 - Can this software now check the sequencing contamination of fungi and other Eukaryote?

Issue - State: closed - Opened by maruiqi0710 about 2 years ago

#174 - Error while trying to add "TypeError: '<' not supported between instances of 'NoneType' and 'int'"

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

#173 - opening the viewer on local machine from docker on remote server

Issue - State: closed - Opened by jaylward2 about 2 years ago - 13 comments

#172 - ERROR: Unable to parse /blobtoolkit/databases/ncbi_taxdump/nodes.dmp

Issue - State: closed - Opened by jaylward2 about 2 years ago - 1 comment

#171 - UI Design Issues

Issue - State: open - Opened by RexRowan about 2 years ago

#170 - Website Down

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

#169 - blobtools view issue

Issue - State: open - Opened by marco91sol about 2 years ago - 6 comments

#168 - Update-dependencies

Pull Request - State: closed - Opened by rjchallis about 2 years ago

#167 - blobtools view on remote server

Issue - State: open - Opened by rotifergirl about 2 years ago - 2 comments

#166 - UserWarning: Contig names in the Busco file did not match dataset identifiers, but when contig names are the same.

Issue - State: open - Opened by molikd over 2 years ago - 7 comments

#165 - Issues generating figures using the command line

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

#164 - skip tsv fields if field name is not recognised

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

#163 - make extract-busco-genes work on an untarred busco directory

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

#162 - use kwargs to call filter functions (fixes #161)

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

#161 - Issue in running any filter commands

Issue - State: closed - Opened by myco-bradshaw over 2 years ago - 1 comment
Labels: bug

#160 - Generating plots on the command line example

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

#159 - use assembly level from meta to set contig/scaffold label in snail plot

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

#158 - Editing source code when installed using pip

Issue - State: open - Opened by sheinasim over 2 years ago - 17 comments

#157 - selenium.common.exceptions.TimeoutException during `view` operation in Docker

Issue - State: open - Opened by bgruening over 2 years ago - 1 comment

#156 - Bump pytest from 6.2.5 to 7.2.2

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago - 1 comment

#155 - Issue with view when trying to export snail plot

Issue - State: open - Opened by MikeSanJose over 2 years ago - 1 comment

#154 - Issue running blast for taxonomical classification - no output

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

#153 - Update link to github commit in Detail view

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

#152 - Bump fastjsonschema from 2.15.3 to 2.16.3

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago - 1 comment

#151 - Bump setuptools from 65.6.3 to 67.4.0

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago - 1 comment

#150 - Bump selenium from 4.7.2 to 4.8.2

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago - 1 comment

#149 - Feature/replace-pysam

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

#148 - Error in npm install

Issue - State: open - Opened by r-poloni over 2 years ago - 16 comments

#147 - Request for AND not OR filtering

Issue - State: open - Opened by ChristophePatterson over 2 years ago - 1 comment

#146 - Bump http-cache-semantics from 4.1.0 to 4.1.1 in /src/viewer

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies, javascript

#145 - Feature/add-api-endpoints

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

#144 - Release-4.0.2

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

#143 - Develop

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

#142 - Release/4.0.0

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

#141 - Bump cookiejar from 2.1.3 to 2.1.4 in /src/viewer

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies, javascript

#140 - Bump cookiejar from 2.1.3 to 2.1.4 in /src/api

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies, javascript

#139 - Bump pysam from 0.19.1 to 0.20.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 2 comments

#138 - Bump blobtoolkit-core from 0.1.0 to 0.1.2

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 2 comments

#137 - Feature/split-packaging

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

#136 - Bump pytest from 6.2.5 to 7.2.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 2 comments

#135 - Switching out taxa from other to plot on graph, --sort_first from blobtools1

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

#134 - Bump json5 from 2.2.1 to 2.2.3 in /src/api

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies, javascript

#133 - Bump json5 from 1.0.1 to 1.0.2 in /src/viewer

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies, javascript

#132 - Bump ujson from 5.4.0 to 5.7.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 2 comments

#131 - Pipeline Install on cluster

Issue - State: closed - Opened by gitcruz over 2 years ago - 8 comments

#130 - Bump setuptools from 49.2.0 to 65.5.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies, python

#129 - Bump ujson from 5.4.0 to 5.6.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 2 comments

#128 - Bump express from 4.17.2 to 4.17.3 in /src/packaged-viewer

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies, javascript

#127 - replace rgba colours with rgb + fill-opacity

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

#126 - SVG files not displayed properly in Ai, Gimp, Inkscape, and Corel Vector

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

#125 - Bump qs and express in /src/packaged-viewer

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies, javascript

#124 - Bump qs and formidable in /src/api

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies, javascript

GitHub / blobtoolkit/blobtoolkit issues and pull requests