bgruening/galaxytools issues and pull requests

#1539 - Add --local option to Bismark Bowtie2 Wrapper (continuation from PR #1537)

Pull Request - State: open - Opened by jonasbucherETH 23 days ago - 1 comment

#1538 - Add pytorch-cuda requirement to flux tool

Pull Request - State: closed - Opened by arash77 25 days ago

#1537 - Add --local option to Bismark tool

Pull Request - State: closed - Opened by jonasbucherETH 25 days ago - 7 comments

#1536 - Refactor flux tool for improved model selection

Pull Request - State: closed - Opened by arash77 26 days ago

#1535 - add Single Cell shed category

Pull Request - State: closed - Opened by pavanvidem 27 days ago - 2 comments

#1534 - Updating tools/hictk from version 2.0.0 to 2.0.1

Pull Request - State: closed - Opened by gxydevbot 27 days ago - 1 comment

#1533 - [RFC] Add a Galaxy tool for TabPFN package (by Prof. Hutter's group)

Pull Request - State: open - Opened by anuprulez about 1 month ago

#1532 - Fix homepage URL for flux tool

Pull Request - State: closed - Opened by arash77 about 1 month ago

#1531 - Updating tools/rna_tools/rbpbench from version 0.8.1 to 1.0.1

Pull Request - State: open - Opened by gxydevbot about 1 month ago

#1530 - Updating tools/hictk from version 1.0.0 to 2.0.0

Pull Request - State: closed - Opened by gxydevbot about 1 month ago

#1529 - jbrowse2: fix for pif; deprecate blastxml

Pull Request - State: closed - Opened by fubar2 about 1 month ago - 3 comments

#1528 - Add fix_overlapping_genes functionality to AGAT tool

Pull Request - State: closed - Opened by SaimMomin12 about 1 month ago - 2 comments

#1527 - Add fix_overlapping_genes option to AGAT tool

Issue - State: closed - Opened by SaimMomin12 about 1 month ago

#1526 - Fixed issue in XML for tiara tool

Pull Request - State: closed - Opened by Minamehr about 1 month ago

#1525 - PTM Dephosphorylation Predictation Tool

Pull Request - State: open - Opened by haibkhn about 1 month ago - 4 comments

#1524 - Update motus DM .shed.yml

Pull Request - State: closed - Opened by paulzierep about 1 month ago

#1523 - Update ERGA EAR tool to v24.10.15

Pull Request - State: closed - Opened by SaimMomin12 about 1 month ago

#1522 - JBrowse2: Revert from pif indexes for paf

Pull Request - State: closed - Opened by fubar2 about 1 month ago - 14 comments

#1521 - Updating of gfastats tool to 1.3.8

Pull Request - State: closed - Opened by SaimMomin12 about 2 months ago

#1520 - fix LC_ALL in sort tool

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

#1519 - Updating .gitignore file

Pull Request - State: closed - Opened by SaimMomin12 about 2 months ago

#1518 - Sylph tool Wrapper

Pull Request - State: open - Opened by tcollins2011 about 2 months ago - 8 comments

#1517 - JBrowse2: fix tabix pif indexing

Pull Request - State: closed - Opened by fubar2 about 2 months ago - 2 comments

#1516 - JBrowse2: fix tabix pif indexing

Pull Request - State: closed - Opened by fubar2 about 2 months ago - 1 comment

#1515 - Tools/nextdenovo

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

#1514 - Updating tools/bioimaging from version 2.4.0 to 2.4.1

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

#1513 - JBrowse2: Speed up paf tracks with new tabix pif adapter.

Pull Request - State: closed - Opened by fubar2 about 2 months ago - 2 comments

#1512 - JBrowse2: add another required file for pulsar; remove label punctuation that can break JBrowse2 paths

Pull Request - State: closed - Opened by fubar2 about 2 months ago - 1 comment

#1511 - Autoupdate errors

Issue - State: open - Opened by gxydevbot about 2 months ago - 5 comments

#1510 - Autoupdate errors

Issue - State: open - Opened by gxydevbot about 2 months ago

#1509 - Autoupdate errors

Issue - State: open - Opened by gxydevbot about 2 months ago

#1508 - Updating tools/gfastats from version 1.3.6 to 1.3.7

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

#1507 - Updating tools/agat from version 1.4.0 to 1.4.1

Pull Request - State: open - Opened by gxydevbot 2 months ago - 3 comments

#1506 - Try ci upgrade fiji

Pull Request - State: closed - Opened by lldelisle 2 months ago

#1505 - Saim momin12 tools/cellpose

Pull Request - State: closed - Opened by bgruening 2 months ago - 1 comment

#1504 - JBrowse2 update to 2.15.4

Pull Request - State: closed - Opened by fubar2 2 months ago - 2 comments

#1503 - update CI

Pull Request - State: closed - Opened by bgruening 2 months ago

#1502 - bump IntaRNA v3.4.1

Pull Request - State: closed - Opened by martin-raden 2 months ago - 2 comments

#1501 - Updating tools/image_processing/graphicsmagick from version 1.3.44 to 1.3.45

Pull Request - State: closed - Opened by gxydevbot 2 months ago

#1500 - Updating tools/flye from version 2.9.4 to 2.9.5

Pull Request - State: closed - Opened by gxydevbot 2 months ago

#1499 - upgrade Fiji, add ROI export to Analyze Particle, add filter tool and crop tool

Pull Request - State: closed - Opened by lldelisle 2 months ago - 25 comments

#1498 - Updating chemicaltoolbox/im-pipelines from version 1.1.4 to 1.1.6

Pull Request - State: open - Opened by gxydevbot 3 months ago - 4 comments

#1497 - Update chatgpt tool to v2

Pull Request - State: closed - Opened by arash77 3 months ago

#1496 - Integrate black forest labs FLUX.1 models into Galaxy

Pull Request - State: closed - Opened by arash77 3 months ago - 3 comments

#1495 - Updating the test data for tools/cellpose

Pull Request - State: open - Opened by SaimMomin12 3 months ago - 21 comments

#1494 - Updating tools/cellpose from version 3.0.10 to 3.0.11

Pull Request - State: closed - Opened by gxydevbot 3 months ago - 6 comments

#1493 - Updating tools/bioimaging from version 2.3.1 to 2.4.0

Pull Request - State: closed - Opened by gxydevbot 3 months ago - 4 comments

#1492 - Updating of the ERGA EAR tool

Pull Request - State: closed - Opened by SaimMomin12 3 months ago - 1 comment

#1491 - Make global scaling the JBrowse2 bigwig default

Pull Request - State: closed - Opened by fubar2 3 months ago - 1 comment

#1490 - split_file_to_collection hardcodes fastq output

Issue - State: open - Opened by mvdbeek 3 months ago

#1489 - Updating chemicaltoolbox/rdock from version 2013.1-0 to 2013.1

Pull Request - State: closed - Opened by gxydevbot 3 months ago - 8 comments

#1488 - Updating tools/image_processing/graphicsmagick from version 1.3.43 to 1.3.44

Pull Request - State: closed - Opened by gxydevbot 3 months ago

#1487 - Updating test data of Flye tool

Pull Request - State: closed - Opened by SaimMomin12 3 months ago - 4 comments

#1486 - Improve instructions for better results and better code readability in ChatGPT tool

Pull Request - State: closed - Opened by arash77 3 months ago - 3 comments

#1485 - add collection_type to input collection in JBrowse2

Pull Request - State: closed - Opened by fubar2 3 months ago - 1 comment

#1484 - update jbrowse2 to 2.13.1

Pull Request - State: closed - Opened by fubar2 3 months ago - 2 comments

#1483 - Updated test parameters and test data for flye tool

Pull Request - State: closed - Opened by SaimMomin12 3 months ago - 1 comment

#1482 - aragorn_out_to_gff3.py error when parsing genomes with tmRNA's

Issue - State: open - Opened by cdshaffer 3 months ago

#1481 - Restructuring and updating test data of locarna tool

Pull Request - State: closed - Opened by SaimMomin12 3 months ago

#1480 - tp_cut fails if cut by field is selected and a delimiter is provided

Issue - State: closed - Opened by mvdbeek 3 months ago - 2 comments

#1479 - openbabel tool updates

Pull Request - State: closed - Opened by hechth 3 months ago - 1 comment

#1478 - cannot find 'reference_genome' in toolshed.g2.bx.psu.edu/repos/bgruening/hicup_digester/hicup_digester/0.9.2+galaxy0

Issue - State: open - Opened by mvdbeek 3 months ago
Labels: bug

#1477 - Update ChatGPT tool

Pull Request - State: closed - Opened by arash77 3 months ago

#1476 - Chemical toolbox updates

Pull Request - State: closed - Opened by hechth 3 months ago - 13 comments

#1475 - Add ChatGPT Galaxy tool README file

Pull Request - State: closed - Opened by arash77 3 months ago

#1474 - add flexynesis

Pull Request - State: closed - Opened by nilchia 4 months ago - 10 comments

#1473 - Add sample numbers to confusion matrix plot

Pull Request - State: closed - Opened by anuprulez 4 months ago - 2 comments

#1472 - Switch AGAT output to gff3 and update to 1.4.0

Pull Request - State: closed - Opened by TomHarrop 4 months ago - 1 comment

#1471 - agat - should the output be GFF3?

Issue - State: closed - Opened by TomHarrop 4 months ago - 1 comment

#1470 - Fixing Linting errors of cellprofiler_v4

Pull Request - State: closed - Opened by SaimMomin12 4 months ago

#1469 - Integrates OpenAI's ChatGPT into Galaxy.

Pull Request - State: closed - Opened by arash77 4 months ago - 5 comments

#1468 - Updating tools/cellprofiler_v4 from version 4.2.6 to 4.2.7

Pull Request - State: closed - Opened by gxydevbot 4 months ago - 1 comment

#1467 - UniProt: batched access to id mapping

Pull Request - State: closed - Opened by bernt-matthias 4 months ago - 1 comment

#1466 - Update text-processing/replace_text_in_column examples

Issue - State: open - Opened by GomeChas 4 months ago

#1465 - update jbrowse2 to 2.13.0

Pull Request - State: closed - Opened by fubar2 4 months ago

#1464 - Updating tools/image_processing/imagej2 from version 20170530 to 20240614

Pull Request - State: open - Opened by gxydevbot 4 months ago - 2 comments

#1463 - Update tool - add keep_longest_isoform to agat

Pull Request - State: closed - Opened by tbrown91 4 months ago - 2 comments

#1462 - adding blobtk plotting functionality to the blobtoolkit

Pull Request - State: closed - Opened by SaimMomin12 4 months ago - 2 comments

#1461 - Added Blobtk tool

Pull Request - State: closed - Opened by SaimMomin12 4 months ago - 4 comments

#1460 - Fix for imagej relative path handling

Pull Request - State: closed - Opened by bernt-matthias 4 months ago - 1 comment

#1459 - CPAT: Added option to use reference genome from builtin references

Pull Request - State: closed - Opened by SaimMomin12 4 months ago - 2 comments

#1458 - CPAT tool options

Issue - State: closed - Opened by SaimMomin12 4 months ago - 1 comment

#1457 - Mitohifi fix

Pull Request - State: open - Opened by SaimMomin12 4 months ago - 9 comments

#1456 - Blobtoolkit can have trouble parsing raw Diamond results

Issue - State: open - Opened by jennaj 4 months ago

#1455 - Updating tools/rna_tools/locarna from version 1.9.2.3 to 2.0.1

Pull Request - State: closed - Opened by gxydevbot 4 months ago - 1 comment

#1454 - MitoHiFi defaulting to animal data

Issue - State: open - Opened by Hymenium 4 months ago - 1 comment

#1453 - Remove hifiasm from bgruening/galaxytools; moved to IUC

Pull Request - State: closed - Opened by SaimMomin12 5 months ago - 1 comment

#1452 - imagej2 enhance contrasts fails

Issue - State: closed - Opened by bernt-matthias 5 months ago - 5 comments

#1451 - Updating hifiasm tool to 0.19.9

Pull Request - State: closed - Opened by SaimMomin12 5 months ago - 2 comments

#1450 - A data manager for motus

Pull Request - State: closed - Opened by paulzierep 5 months ago - 1 comment

#1448 - Fix cut tool

Pull Request - State: closed - Opened by bernt-matthias 5 months ago - 8 comments

GitHub / bgruening/galaxytools issues and pull requests