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
#333 - bioconvert genbank2gff3 erroneous tRNA parent if not gene feature before tRNA feature
Issue -
State: open - Opened by tuspjo over 1 year ago
#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
#289 - Move all test files from bioconvert to the test/ directory if possible
Issue -
State: closed - Opened by cokelaer 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