Ecosyste.ms: Issues

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

GitHub / WrightonLabCSU/DRAM issues and pull requests

#389 - Add nf-core style testing suite for the Nextflow side of the code

Issue - State: open - Opened by madeline-scyphers 16 days ago
Labels: testing

#388 - Add logging in python side of DRAM

Issue - State: open - Opened by madeline-scyphers 16 days ago
Labels: documentation

#387 - Feature/kegg pep directory

Pull Request - State: closed - Opened by madeline-scyphers 19 days ago
Labels: enhancement

#386 - Question about DRAM-v output

Issue - State: open - Opened by deminatanja 20 days ago

#385 - Bugfix/path creation bug

Pull Request - State: closed - Opened by madeline-scyphers 20 days ago
Labels: bug

#384 - Update README.md to give notes about DRAM v2 public beta

Pull Request - State: closed - Opened by madeline-scyphers 20 days ago
Labels: documentation

#382 - Add much better logging throughout the pipeline

Issue - State: open - Opened by madeline-scyphers about 1 month ago
Labels: documentation

#381 - Add better input validation for input combinations that don't make sense

Issue - State: open - Opened by madeline-scyphers about 1 month ago
Labels: package, documentation

#380 - Create a DOI for the DRAM software with zenodo

Issue - State: open - Opened by madeline-scyphers about 1 month ago
Labels: package

#378 - When writing outputs or logs, if already exists, append with something

Issue - State: open - Opened by madeline-scyphers about 1 month ago
Labels: enhancement

#376 - Add close inactive issue workflow/action

Issue - State: open - Opened by madeline-scyphers about 1 month ago
Labels: CI/CD

#375 - Setup milestones for tracking issues and development progress

Issue - State: closed - Opened by madeline-scyphers about 1 month ago
Labels: documentation

#374 - DRAM visualization (product) tracking issue

Issue - State: open - Opened by madeline-scyphers about 1 month ago
Labels: package

#373 - DRAM v2 README has too much hard coded things in it (like the --help output)

Issue - State: open - Opened by madeline-scyphers about 1 month ago
Labels: documentation

#372 - DRAM trees and adjectives implementation

Issue - State: open - Opened by madeline-scyphers about 1 month ago
Labels: enhancement, process

#371 - Better user Nextflow Configuration override

Issue - State: open - Opened by madeline-scyphers about 1 month ago
Labels: configuration

#370 - Update environment.yml

Issue - State: open - Opened by madeline-scyphers about 1 month ago
Labels: package, refactor

#369 - Integrate whatever we feel is useful from the nf-core template

Issue - State: open - Opened by madeline-scyphers about 1 month ago - 1 comment
Labels: package, CI/CD, testing

#368 - Add back DRAM v1 testing suite for v2

Issue - State: open - Opened by madeline-scyphers about 1 month ago
Labels: CI/CD, testing

#367 - Update docs from Wiki for DRAM v2, probably move to readthedocs

Issue - State: open - Opened by madeline-scyphers about 1 month ago
Labels: documentation

#366 - Decouple DRAM v2 tool code from Nextflow code

Issue - State: open - Opened by madeline-scyphers about 1 month ago
Labels: package

#365 - KEGG db formatting process should allow passing in directory of pep files

Issue - State: closed - Opened by madeline-scyphers about 1 month ago
Labels: enhancement, database

#364 - Rename docs and configs from DRAM2 to just DRAM

Pull Request - State: closed - Opened by madeline-scyphers about 1 month ago
Labels: package

#363 - Dram-v on Virsorter2 output: pandas error, unexpected EOF, syntax error

Issue - State: open - Opened by deminatanja about 1 month ago - 1 comment

#361 - State of DRAM2

Issue - State: open - Opened by donovan-parks 2 months ago - 1 comment
Labels: Usage Question

#360 - DRAM-setup.py in v1.5.0 has invalid syntax

Issue - State: open - Opened by donovan-parks 2 months ago

#358 - Controlling CPU usage for the DRAM.py distill pipeline for DRAM v.1.5.0

Issue - State: open - Opened by nataliesarno 3 months ago - 1 comment
Labels: Usage Question

#357 - Pathway abundances?

Issue - State: open - Opened by Manso002 4 months ago

#356 - Changing order of genomes in DRAM distill HTML output

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

#354 - pop out errors when prepare databases

Issue - State: open - Opened by lingc31415 5 months ago

#353 - VOGDB does not import correctly

Issue - State: closed - Opened by nactopus 5 months ago - 1 comment

#352 - Fix install problem for vog db

Pull Request - State: open - Opened by SilasK 5 months ago - 2 comments

#350 - Selection logic for gene_id in amg_summery.tsv

Issue - State: open - Opened by diego00012138 5 months ago - 1 comment

#349 - errors when prepare database

Issue - State: open - Opened by mengyuan-JI 6 months ago - 4 comments

#348 - `genome_stats.tsv` has the wrong tRNA count for MIMAG standards

Issue - State: open - Opened by AroneyS 6 months ago - 3 comments

#346 - DRAM2 environment.yaml

Issue - State: open - Opened by SF-Dragon 7 months ago - 1 comment

#345 - How long does populating step take?

Issue - State: open - Opened by jianshu93 7 months ago - 3 comments

#344 - Need help in preparation of database

Issue - State: closed - Opened by sahilrishav2 7 months ago

#343 - Need help in processing of database

Issue - State: closed - Opened by sahilrishav2 7 months ago

#342 - Problem with database instalation (vog_latest_hmms.txt is empty)

Issue - State: open - Opened by ghost 7 months ago - 2 comments

#341 - Fail in processing vogdb

Issue - State: open - Opened by ShangLiii 8 months ago - 6 comments

#340 - VOGDB issue--extra enclosing folder

Issue - State: open - Opened by schmigle 8 months ago - 4 comments

#339 - Fix `DRAM-setup.py` v1.5.0 for missing `)`

Issue - State: open - Opened by npavlovikj 8 months ago - 5 comments

#338 - cazy annotation format for version 1.4.6

Issue - State: closed - Opened by Ales-ibt 8 months ago - 1 comment

#335 - problem about dramv-annotate

Issue - State: open - Opened by xjhzjucas 9 months ago - 3 comments

#334 - bug in `v.1.5.0` on the `DRAM-setup.py` help message

Issue - State: open - Opened by hariszaf 9 months ago - 1 comment

#333 - Continue the "prepare_database" process

Issue - State: open - Opened by chenyj8 9 months ago - 2 comments

#332 - hmmpress not found during prepare_databases

Issue - State: open - Opened by carleton-envbiotech 9 months ago - 1 comment

#331 - dbcan2 url gone ??

Issue - State: open - Opened by EricDeveaud 9 months ago - 3 comments

#330 - DRAM 1.5.0 installation issues

Issue - State: open - Opened by karenhn 10 months ago - 6 comments

#329 - annotate genes using faa fasta files

Issue - State: open - Opened by avera1988 10 months ago - 3 comments

#328 - key error: K01566 when using DRAM-v.py annotate

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

#327 - Is my DRAM_v run successful?

Issue - State: open - Opened by fhdbqr 10 months ago

#326 - DRAM-setup.py broke when upgrading to v1.5.0

Issue - State: closed - Opened by cjburgess 11 months ago - 2 comments

#324 - How to speed up the operation?

Issue - State: open - Opened by qkqk-hub 11 months ago

#323 - DRAM-v.py annotate

Issue - State: open - Opened by hgingras 11 months ago

#322 - Problem with DRAM databases installation

Issue - State: open - Opened by apazminov 11 months ago

#322 - Problem with DRAM databases installation

Issue - State: open - Opened by apazminov 11 months ago

#321 - Receiving a "No descriptions found for your id's" for GT2

Issue - State: open - Opened by carleton-envbiotech 11 months ago - 6 comments

#320 - Update DRAM-setup.py

Pull Request - State: closed - Opened by jrr-microbio 12 months ago

#319 - cazy annotations missing in distill heatmap

Issue - State: open - Opened by Aiswarya-prasad 12 months ago

#318 - Steps to download all the databases and setup manually in DRAM

Issue - State: open - Opened by srisvs33 12 months ago - 2 comments

#316 - Unable to specify database locations

Issue - State: open - Opened by lingrongjin 12 months ago

#315 - No file named viral_genome_summary.tsv and Liquor.html output by DRAM-v.py

Issue - State: closed - Opened by actledge about 1 year ago - 1 comment

#313 - Downloading CAMPER db

Issue - State: closed - Opened by ZarulHanifah about 1 year ago - 1 comment

#312 - AttributeError: 'Series' object has no attribute 'iteritems'

Issue - State: closed - Opened by mw55309 about 1 year ago - 1 comment

#311 - Figure output missing

Issue - State: closed - Opened by moyn413 about 1 year ago - 1 comment

#310 - DRAM running time

Issue - State: closed - Opened by pabloati about 1 year ago - 3 comments

#309 - I have some trouble in using DRAM.py annotate

Issue - State: closed - Opened by microbial-cookie about 1 year ago - 5 comments

#308 - Databases used in DRAM

Issue - State: closed - Opened by dcm9123 about 1 year ago - 1 comment

#306 - There are no expected target files under the annotation folder

Issue - State: closed - Opened by 778055611 about 1 year ago - 3 comments

#305 - KEGG Database preparation for DRAM

Issue - State: closed - Opened by jrr-microbio about 1 year ago - 7 comments
Labels: good first issue

#304 - Update environment.yaml

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

#303 - Update environment.yaml

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

#301 - dbCAN ERROR

Issue - State: open - Opened by francesco-ricci about 1 year ago

#300 - Thread usage and computational efficiency

Issue - State: open - Opened by ganiatgithub about 1 year ago

#299 - Error when setting up databases

Issue - State: open - Opened by microbial-cookie about 1 year ago

#298 - Error when setting up databases

Issue - State: open - Opened by microbial-cookie about 1 year ago - 5 comments

#297 - Permission error when setting up databases

Issue - State: closed - Opened by pabloati about 1 year ago - 3 comments

#296 - default prodigal command request

Issue - State: open - Opened by bck243 about 1 year ago

#295 - Errno 13

Issue - State: open - Opened by Valentin-Bio about 1 year ago

#294 - ValueError: duplicate headers in DRAM-v.py but not when running DRAM.py

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

#293 - scikit-bio release 0.5.9 brings up ImportError.

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

#292 - testing database

Issue - State: open - Opened by fujch7 over 1 year ago

#291 - description_db.sqlite is taking extremely long to write

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