Ecosyste.ms: Issues

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

GitHub / dib-lab/dammit issues and pull requests

#245 - Two bug fixes so dammit can run

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

#244 - Add -L (follow redirects) to curl commands

Pull Request - State: open - Opened by pansapiens over 1 year ago

#243 - unable to install databases

Issue - State: open - Opened by peter0k over 1 year ago - 3 comments

#240 - Cap doit to <0.36.0 to avoid TaskLoader2

Pull Request - State: open - Opened by NickCrews about 2 years ago

#239 - TaskLoader issue

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

#238 - doit.cmd_base.py:TaskLoader

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

#237 - databases installation errors

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

#236 - Not recognizing BUSCO?

Issue - State: open - Opened by incoreygible almost 3 years ago

#235 - Failed install from conda-forge

Issue - State: closed - Opened by incoreygible almost 3 years ago

#233 - Download issue

Issue - State: open - Opened by mthang about 3 years ago

#232 - Optimized parameters for cmscan with Rfam

Pull Request - State: open - Opened by camillescott over 3 years ago

#231 - Failed to download a database

Issue - State: closed - Opened by josruirod over 3 years ago

#230 - No symbol dbm_open found in library libdb-6.2.so

Issue - State: open - Opened by pmoulos over 3 years ago - 1 comment

#229 - curl: (28) Failed to connect to cegg.unige.ch port 21: Connection timed out

Issue - State: open - Opened by hoelzer over 3 years ago - 14 comments

#228 - Add benchmark directive to each rule

Pull Request - State: open - Opened by bluegenes over 3 years ago

#227 - TypeError: an integer is required (got type bytes)

Issue - State: open - Opened by jtoy7 over 3 years ago - 2 comments

#226 - `--no-rename` tests and duplicate name error checking

Pull Request - State: closed - Opened by camillescott over 3 years ago

#225 - Solving environment: failed with repodata

Issue - State: open - Opened by PedroDaPos over 3 years ago - 1 comment

#223 - Update to BUSCO v5

Pull Request - State: closed - Opened by camillescott almost 4 years ago

#222 - Add a verbosity flag

Pull Request - State: closed - Opened by camillescott almost 4 years ago

#221 - Expose `--rename-regex` in main annotate CLI

Pull Request - State: closed - Opened by camillescott almost 4 years ago

#220 - Enable user to select whether to rename transcripts

Pull Request - State: closed - Opened by camillescott almost 4 years ago

#219 - Add support for Snakemake extra args to annotate and databases

Pull Request - State: closed - Opened by camillescott almost 4 years ago

#218 - TODO: Move target generation inside Snakefile

Issue - State: open - Opened by camillescott almost 4 years ago

#217 - TODO: Backmap renamed transcripts in final FASTA

Issue - State: closed - Opened by camillescott almost 4 years ago - 1 comment

#216 - TODO: support extra snakemake args

Issue - State: closed - Opened by camillescott almost 4 years ago

#215 - Attempt making paths portable

Pull Request - State: closed - Opened by camillescott almost 4 years ago

#214 - EXP: MacOS compatibility

Pull Request - State: open - Opened by camillescott almost 4 years ago

#213 - Implement basic GFF3 conversion for BUSCO results

Pull Request - State: closed - Opened by camillescott almost 4 years ago

#212 - Additional Cleanup

Pull Request - State: closed - Opened by camillescott almost 4 years ago

#211 - Implement caching for Snakemake-managed conda environments

Pull Request - State: closed - Opened by camillescott almost 4 years ago

#209 - TODO: migrate python logging to XDG spec

Issue - State: closed - Opened by camillescott almost 4 years ago - 1 comment

#208 - Migrate to github-actions

Pull Request - State: closed - Opened by camillescott almost 4 years ago

#207 - Environment suggestions

Pull Request - State: closed - Opened by luizirber almost 4 years ago - 2 comments

#206 - Staging for version 2.0

Pull Request - State: open - Opened by camillescott almost 4 years ago

#204 - Improvements to UI

Pull Request - State: closed - Opened by camillescott almost 4 years ago

#203 - TypeError: lastal_task() got an unexpected keyword argument 'pbs'

Issue - State: open - Opened by AntonioBaeza almost 4 years ago - 6 comments

#202 - Can I install newer versions of BUSCO than v2?

Issue - State: open - Opened by sformel about 4 years ago

#201 - Snakefile formatting and file hierarchy cleanup

Pull Request - State: closed - Opened by camillescott about 4 years ago

#199 - add'l integration tests

Pull Request - State: open - Opened by bluegenes about 4 years ago

#198 - Opeify

Pull Request - State: closed - Opened by camillescott about 4 years ago

#197 - [WIP] docs2.0

Pull Request - State: open - Opened by bluegenes about 4 years ago

#196 - Nuke it from orbit: general clean-up and bugfixing

Pull Request - State: closed - Opened by camillescott about 4 years ago

#195 - Please delete this issue

Issue - State: open - Opened by vragh over 4 years ago

#194 - TaskError - taskid:hmmscan:longest_orfs.pep.x.Pfam-A.hmm

Issue - State: open - Opened by sarah872 over 4 years ago

#193 - use mamba for conda installations

Pull Request - State: closed - Opened by bluegenes over 4 years ago

#192 - Get metalink working for database download

Issue - State: open - Opened by bluegenes over 4 years ago

#191 - Expose `--split-regex` from dammit rename-fasta to main dammit annotate pipeline

Issue - State: closed - Opened by camillescott over 4 years ago
Labels: enhancement

#190 - seqid inconsistency with --no-rename between shmlast and other programs

Issue - State: open - Opened by camillescott over 4 years ago
Labels: bug

#189 - add wrapper tests

Pull Request - State: closed - Opened by bluegenes over 4 years ago

#188 - Update Tests

Pull Request - State: closed - Opened by camillescott over 4 years ago

#187 - `damit annotate` Exited with exit code 140

Issue - State: open - Opened by CeciliaDeng over 4 years ago - 2 comments

#186 - Plot busco

Pull Request - State: closed - Opened by bluegenes over 4 years ago

#184 - produce final annotation files!

Pull Request - State: closed - Opened by bluegenes over 4 years ago

#183 - Error: sqlite3 unable to open database file

Issue - State: open - Opened by blasks over 4 years ago - 4 comments

#182 - try using a snakemake profile to set cluster run params

Issue - State: open - Opened by bluegenes over 4 years ago

#180 - Init snakemake report

Pull Request - State: open - Opened by bluegenes over 4 years ago

#179 - [MRG] change busco wrapper to enable config

Pull Request - State: closed - Opened by bluegenes over 4 years ago

#178 - Enable user databases, busco databases

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

#177 - Unify click and argparse interfaces

Pull Request - State: closed - Opened by camillescott over 4 years ago - 2 comments

#176 - get mkdocs theme via gh-actions

Pull Request - State: closed - Opened by bluegenes over 4 years ago - 2 comments

#175 - Add conversion rules

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

#174 - Convert to Click

Issue - State: closed - Opened by camillescott over 4 years ago - 1 comment

#173 - docs docs docs

Issue - State: closed - Opened by bluegenes over 4 years ago - 1 comment

#172 - Use mkdocs submodule

Issue - State: closed - Opened by camillescott over 4 years ago - 1 comment

#171 - Update requirements

Pull Request - State: closed - Opened by camillescott over 4 years ago

#170 - Add rename rule to snakemake workflow.

Issue - State: closed - Opened by bluegenes over 4 years ago

#169 - Add task to convert transcript names *back* to original names (post annotation)

Issue - State: closed - Opened by bluegenes over 4 years ago - 2 comments

#168 - Write busco v4 rule

Issue - State: closed - Opened by bluegenes over 4 years ago - 1 comment

#167 - Update `requirements.txt` and conda environments.

Issue - State: closed - Opened by camillescott over 4 years ago

#166 - Add conversion rules to snakemake.

Issue - State: closed - Opened by camillescott over 4 years ago

#165 - Add wrappers for components.

Issue - State: closed - Opened by camillescott over 4 years ago

#164 - Running PR for Snakemakeification

Pull Request - State: open - Opened by camillescott over 4 years ago

#162 - Fixes for #161

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

#161 - BUSCO v2 database download fails, but gets marked as done

Issue - State: open - Opened by eburgueno over 4 years ago

#160 - script killed at fasta-annotate step

Issue - State: closed - Opened by DrPintoThe2nd almost 5 years ago

#159 - error

Issue - State: closed - Opened by christa88 almost 5 years ago

#156 - new install fails

Issue - State: closed - Opened by macmanes about 5 years ago - 2 comments

#154 - lastdb:uniref90

Issue - State: open - Opened by AEG4 about 5 years ago - 1 comment

#152 - Update bioconda package

Issue - State: closed - Opened by ppericard over 5 years ago - 1 comment

#151 - Fix typo in Inferal vs. Infernal

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

#150 - OSError: [Errno30]

Issue - State: open - Opened by davidjquispe over 5 years ago - 1 comment

#149 - parse out gff3 - no modules named pandas

Issue - State: closed - Opened by seboles over 5 years ago - 3 comments

#148 - KeyError: 'query_name'

Issue - State: closed - Opened by MDSharma over 5 years ago - 2 comments

#147 - BUSCO V1 database curl urls changed

Issue - State: open - Opened by schomakerra over 5 years ago - 1 comment

#146 - OrthoDBv10

Pull Request - State: open - Opened by rix133 over 5 years ago

#141 - can't install multiple busco databases at once

Issue - State: open - Opened by bluegenes almost 6 years ago

#140 - database install fails with n_threads

Issue - State: open - Opened by bluegenes almost 6 years ago - 1 comment

#139 - pandas sorting, GFF3Parser problem

Issue - State: open - Opened by johnsolk almost 6 years ago - 5 comments

#138 - citation?

Issue - State: closed - Opened by johnsolk almost 6 years ago - 2 comments

#136 - dammit install on bioconda

Issue - State: closed - Opened by desmondramirez almost 6 years ago - 11 comments

#111 - run_BUSCO.py running problem

Issue - State: closed - Opened by BiodeB over 6 years ago - 7 comments