Ecosyste.ms: Issues

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

GitHub / bioconvert/bioconvert issues and pull requests

#345 - maf2sam fails on comments `#`

Issue - State: open - Opened by mrossi1-ilmn about 2 months ago

#344 - Wrong install command

Issue - State: open - Opened by JCTorrat 6 months ago

#343 - gbk to faa

Issue - State: open - Opened by cokelaer 6 months ago

#342 - genbank2gff3 not recognizing gbff extension

Issue - State: open - Opened by tuspjo 8 months ago

#341 - error in nexus2newick

Issue - State: open - Opened by tsm-tsm 8 months ago

#340 - updated version that was fixed to 1.0.0

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

#339 - Failing to convert xlsx to csv

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

#338 - Update environment_rtd.yml

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

#337 - update requirements in methods

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

#336 - benchmark incorporates CPU/memory usage

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

#335 - Mamba can't find bioconvert

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

#334 - gbff2gft not work

Issue - State: open - Opened by ysuzuki1978 over 1 year ago - 2 comments

#332 - meme motif conversion

Issue - State: open - Opened by cokelaer over 1 year ago
Labels: enhancement, todo

#331 - Update README.rst

Pull Request - State: closed - Opened by ambuvjyn over 1 year ago - 2 comments

#330 - 3D genome data format conversion

Issue - State: open - Opened by wbszhu over 1 year ago - 1 comment
Labels: new converter

#329 - ERROR [bioconvert:125]

Issue - State: open - Opened by ysuzuki1978 over 1 year ago - 1 comment

#328 - add small logo

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

#327 - Dev

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

#326 - Fixing bam2fastq issue and update material for paper

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

#325 - Bam2fastq conversion

Issue - State: closed - Opened by khourhin over 1 year ago

#324 - Update metadata

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

#323 - General cleanup

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

#322 - Fixing CI for pdb2faa and gff32gtf

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

#321 - update CI

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

#320 - mamba installation not working

Issue - State: closed - Opened by yoann-dufresne over 1 year ago - 1 comment

#319 - modules using go are failing

Issue - State: closed - Opened by cokelaer over 1 year ago - 1 comment
Labels: bug, todo

#318 - Update doc to use mamba instead of conda

Issue - State: closed - Opened by cokelaer over 1 year ago
Labels: todo

#317 - Main

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

#316 - add pdb2faa

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

#315 - add pdb2faa and fix cram2sam

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

#314 - Main

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

#313 - add new conversion gff3 to gtf2

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

#312 - Create directories if included in output file

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

#311 - Switch master branch to 'main'

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

#310 - Correct license classifier.

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

#309 - Fixing CI actions

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

#308 - Refactoring

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

#307 - Set metadata for 0.6 release

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

#306 - Refactoring

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

#305 - Refactoring

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

#304 - PDB to FASTA or small molecules (MOL2, PDB, SDF to SMILES)

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

#303 - Include biocode to avoid dependency

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

#302 - Fixing dsrc and updating documentation

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

#301 - Refactoring

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

#300 - add biocode

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

#299 - Cleanup new benchmarking

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

#298 - Snakemake benchmark

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

#297 - Check how is used biocode and how it is installed

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

#296 - Save benchmark results in json file

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

#295 - benchmark modifications

Pull Request - State: closed - Opened by HugoCaro over 2 years ago
Labels: enhancement

#294 - Problems gz2bz2

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

#293 - black application

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

#292 - Fixing benchmark with extra options

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

#291 - benchmark do not handle method with extra argument

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

#290 - modification test

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

#288 - Refactoring (no need for validators)

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

#287 - move ABI files for testing

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

#286 - change benchmark progress bar

Pull Request - State: closed - Opened by HugoCaro over 2 years ago
Labels: enhancement

#285 - Doc conversions8

Pull Request - State: closed - Opened by HugoCaro over 2 years ago
Labels: enhancement

#284 - replace Progress (easydev) by tqdm

Issue - State: closed - Opened by cokelaer over 2 years ago
Labels: todo

#283 - Doc conversions7

Pull Request - State: closed - Opened by HugoCaro over 2 years ago
Labels: enhancement

#282 - Doc conversion6

Pull Request - State: closed - Opened by HugoCaro over 2 years ago
Labels: enhancement

#281 - Doc conversions5

Pull Request - State: closed - Opened by HugoCaro over 2 years ago
Labels: enhancement

#280 - Fix conda env

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

#279 - Worflow gff22gff3

Pull Request - State: closed - Opened by HugoCaro over 2 years ago
Labels: enhancement

#278 - Doc conversions3

Pull Request - State: closed - Opened by HugoCaro over 2 years ago
Labels: enhancement

#277 - Workflow fasta2fastq

Pull Request - State: closed - Opened by HugoCaro over 2 years ago
Labels: enhancement

#276 - Fix CI actions

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

#275 - Creation of abi2fasta.yml and completion of the README.rst

Pull Request - State: closed - Opened by HugoCaro over 2 years ago
Labels: enhancement

#274 - Doc bam2sam

Pull Request - State: closed - Opened by HugoCaro over 2 years ago
Labels: in progress

#273 - Test bam2sam fails on CI. Commented for now but needs to be fixed

Issue - State: closed - Opened by cokelaer over 2 years ago
Labels: help wanted

#272 - remove travis

Issue - State: closed - Opened by cokelaer over 2 years ago
Labels: refactoring

#271 - move from argparse to click

Issue - State: closed - Opened by cokelaer over 2 years ago - 1 comment
Labels: refactoring

#270 - Revisit / update the singularity

Issue - State: closed - Opened by cokelaer over 2 years ago
Labels: refactoring

#269 - modified some files to use make html and fastq2fasta documentation

Pull Request - State: closed - Opened by HugoCaro over 2 years ago
Labels: enhancement

#268 - Fix rtd

Pull Request - State: closed - Opened by cokelaer over 2 years ago
Labels: enhancement

#267 - Changing the default method in the fastq2fasta.py file

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

#266 - method pyexcel-xls in csv2xls is failing

Issue - State: closed - Opened by cokelaer over 2 years ago
Labels: bug

#265 - Implementation of the "seqkit" method

Issue - State: closed - Opened by HugoCaro over 2 years ago
Labels: new method

#264 - add seqkit method

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

#263 - Fix RTD

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

#262 - naming of requirement_tools is ambiguous (should be merged with environment.yml)

Issue - State: closed - Opened by cokelaer over 2 years ago
Labels: enhancement

#261 - Regression error with BioPython in the fasta2genbank module

Issue - State: closed - Opened by cokelaer over 2 years ago
Labels: bug

#260 - Errors in the tutorial

Issue - State: closed - Opened by HugoCaro over 2 years ago - 1 comment
Labels: enhancement

#259 - Fixing CI

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

#258 - Ci stable version

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

#257 - Some questions about the command bioconvert --help

Issue - State: closed - Opened by Jianz9293 about 3 years ago - 4 comments

#256 - got many warnings when call bioconvert --help

Issue - State: closed - Opened by lufuhao about 3 years ago - 1 comment

#255 - License of the lib

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

#254 - gff32bed

Issue - State: open - Opened by khourhin about 4 years ago
Labels: new converter

#253 - Actually pass the sheet_name parameter to pyexcel

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

#252 - wrong infered output named

Issue - State: closed - Opened by cokelaer over 4 years ago - 2 comments
Labels: bug

#251 - Mybinder

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

#250 - fasta2clustal should handle input gz files

Issue - State: closed - Opened by Sdollin about 5 years ago - 1 comment
Labels: bug

#249 - RFE upgrade the doc for singularity 3 and python=3.6 for conda

Issue - State: closed - Opened by truatpasteurdotfr about 5 years ago - 4 comments

#244 - Update test_bam2bedgraph.py

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

#227 - embl2gff

Issue - State: open - Opened by cokelaer over 5 years ago - 1 comment
Labels: new converter

#179 - genbank2gff3

Issue - State: open - Opened by cokelaer about 6 years ago - 1 comment
Labels: enhancement