Ecosyste.ms: Issues

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

GitHub / gem-pasteur/macsyfinder issues and pull requests

#77 - Make a test more flexible

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

#76 - [BUG] miscalculation of alignment coverage

Issue - State: closed - Opened by jpjarnoux 3 months ago - 8 comments
Labels: bug

#75 - [HELP] unordered vs ordered_replicon with TXSS models and the inter-gene-max-space parameter

Issue - State: closed - Opened by gabepen 3 months ago - 1 comment
Labels: help wanted

#73 - [BUG] timeout parameter is missing/not povided in parallel_macsyfinder.nf

Issue - State: closed - Opened by bryan-brancotte 9 months ago - 1 comment
Labels: bug

#72 - GA score threshold missing in some CasFinder profile [HELP]

Issue - State: closed - Opened by jpjarnoux 9 months ago - 1 comment
Labels: help wanted

#71 - Generating results.macsyfinder.json file for MacSyView!

Issue - State: closed - Opened by NabilAsyraf98 9 months ago - 1 comment
Labels: bug

#70 - [FEAT] New release to fix bugs in package manager installations

Issue - State: closed - Opened by LucasPaoli 10 months ago - 8 comments
Labels: enhancement

#69 - [BUG] `_scan_profiles` strips `h` and `m` from profile name

Issue - State: closed - Opened by ezherman 11 months ago - 4 comments
Labels: bug

#68 - [HELP] Maxyfinder fails to run

Issue - State: closed - Opened by sujeetpowar 12 months ago - 3 comments
Labels: help wanted

#67 - [BUG]How to get rid of github API throttling？

Issue - State: closed - Opened by Revolution233 about 1 year ago
Labels: bug

#66 - [FEAT] supress duplicated log messages

Issue - State: closed - Opened by bneron about 1 year ago
Labels: enhancement

#65 - [FEAT] Should we use pyhmmer ?

Issue - State: closed - Opened by jeanrjc about 1 year ago - 3 comments
Labels: enhancement

#64 - FAA files do not always reflect the real order of the genes

Issue - State: open - Opened by najwataib about 1 year ago - 2 comments
Labels: enhancement

#63 - [FEAT] Enable MacSyFinder to run on zipped FASTA files

Issue - State: closed - Opened by saphia over 1 year ago - 3 comments
Labels: enhancement

#62 - [BUG] TXSScan + macsyfinder extremely long on some genomes

Issue - State: open - Opened by NelleV over 1 year ago
Labels: bug

#61 - [FEAT] Add a `--force` option to remove the folder in which macsyfinder writes results

Issue - State: closed - Opened by NelleV over 1 year ago
Labels: enhancement

#60 - [BUG] Macsyfinder with python subprocess kill main process on error

Issue - State: closed - Opened by celliern almost 2 years ago
Labels: bug

#59 - [HELP] macsydata install TXSS

Issue - State: closed - Opened by plasminogene almost 2 years ago - 2 comments
Labels: help wanted

#58 - [BUG] test_extract_concurent fail with "cannot join current thread"

Issue - State: closed - Opened by nileshpatra almost 2 years ago - 3 comments
Labels: bug

#57 - CVE-2007-4559 Patch

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

#56 - Something is wrong with the operation

Issue - State: closed - Opened by tu1120 about 2 years ago - 5 comments
Labels: help wanted

#55 - Gembase format

Issue - State: closed - Opened by mozammel47 about 2 years ago - 2 comments
Labels: help wanted

#54 - [Question] Why using --cpu 0 in hmmer ?

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

#53 - [BUG] MacSyFinder does not deal well when a replicon has a single protein.

Issue - State: closed - Opened by jeanrjc over 2 years ago - 5 comments
Labels: bug

#52 - [HELP] Error parsing models

Issue - State: closed - Opened by alexweisberg over 2 years ago - 4 comments
Labels: help wanted

#51 - unrecognized argument in test run

Issue - State: closed - Opened by usr2 over 2 years ago - 1 comment

#50 - [HELP] OSError: [Errno 39] Directory not empty when installing models

Issue - State: closed - Opened by ShailNair over 2 years ago - 4 comments
Labels: help wanted

#49 - [HELP]

Issue - State: closed - Opened by Aluminio-visto over 2 years ago - 3 comments
Labels: help wanted

#48 - Error using the docker gempasteur/macsyfinder:2.0rc7

Issue - State: closed - Opened by yuxiangtan over 2 years ago - 10 comments
Labels: bug

#47 - [HELP] .json file

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

#46 - [HELP] error when installing models

Issue - State: closed - Opened by schmittel over 2 years ago - 3 comments
Labels: help wanted

#45 - how to use models

Issue - State: closed - Opened by bneron over 2 years ago - 1 comment
Labels: help wanted

#44 - change genes order in xml definition

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

#43 - Problem when running macsyfinder 2.0 for TXSS identification

Issue - State: closed - Opened by zhangyumeng1sjtu almost 3 years ago - 2 comments

#42 - "summary_best_solution" takes too long for large inputs

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

#40 - AttributeError: module 'colorlog' has no attribute 'logging'

Issue - State: closed - Opened by dineshkumarsrk about 3 years ago - 2 comments

#39 - crash when no mandatory/accessory/neutral genes are found

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

#38 - Latest colorlog release breaks macsydata on fresh macsyfinder installs

Issue - State: closed - Opened by Alexandre-Herve about 3 years ago - 2 comments

#37 - Models compatible with version 1

Issue - State: closed - Opened by sarah872 about 3 years ago - 2 comments
Labels: question

#36 - I can't install macsyfinder(v2.0rcl) sucessfully.

Issue - State: closed - Opened by lkj66666 over 3 years ago - 8 comments

#35 - Whether it is possible to run the singularity version for the Conjugation models?

Issue - State: closed - Opened by biofuture almost 4 years ago - 3 comments
Labels: question

#34 - How can I get the modle from the macsyfinder v2.0?

Issue - State: closed - Opened by lkj66666 almost 4 years ago - 9 comments

#33 - conda installation?

Issue - State: closed - Opened by cschu almost 4 years ago - 6 comments
Labels: question

#32 - Proper input format

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

#31 - Input sequence

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

#30 - Incompatibility with BLAST+ 2.10.0

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

#29 - Where can I find the Python3 port

Issue - State: closed - Opened by tillea almost 5 years ago - 8 comments

#28 - Installation test error.

Issue - State: closed - Opened by OmarCabrero about 5 years ago

#26 - Cannot install: python error

Issue - State: closed - Opened by vbrover about 5 years ago - 1 comment

#25 - No module named 'ConfigParser'

Issue - State: closed - Opened by YanpingHu about 5 years ago - 1 comment

#24 - No TXSS secretion system predicted

Issue - State: closed - Opened by yjiakang about 5 years ago - 1 comment

#23 - zip the hhmer results folder automatically

Issue - State: closed - Opened by genomesandMGEs over 5 years ago

#22 - Macsyfinder installation problem

Issue - State: closed - Opened by edusoto over 5 years ago - 4 comments

#21 - Please port to Python3

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

#20 - Other system modules

Issue - State: closed - Opened by sarah872 over 6 years ago - 3 comments

#19 - Problem when using extract

Issue - State: closed - Opened by altaetran over 6 years ago - 3 comments

#18 - fix typo

Pull Request - State: closed - Opened by bgoas over 6 years ago

#17 - Test occurs problems

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

#16 - Define system with two genes that hit the same HMM

Issue - State: closed - Opened by brymerr921 almost 7 years ago - 5 comments

#15 - Bug? Unordered db_type does not consider genes from system_ref

Issue - State: closed - Opened by lguy about 7 years ago - 1 comment

#14 - Gene column in the .report file

Issue - State: closed - Opened by lguy about 7 years ago - 1 comment
Labels: enhancement

#13 - verbosity option doesn't seem to affect the run

Issue - State: closed - Opened by lguy about 7 years ago - 1 comment
Labels: bug

#12 - test fail test_GembaseHMMReport_extract_concurent

Issue - State: closed - Opened by spleonard1 over 7 years ago

#11 - Problems Installing MacSyFinder

Issue - State: closed - Opened by tkarasov over 7 years ago - 10 comments

#10 - macsyfinder does not stop and exit in error when hmmsearch fail

Issue - State: closed - Opened by bneron over 8 years ago
Labels: bug

#9 - Add HMMER filtering criteria at the gene level: evalue and coverage

Issue - State: closed - Opened by saphia almost 9 years ago
Labels: enhancement

#8 - Create a new class of abstract systems "GeneBaseSystem"

Issue - State: closed - Opened by saphia almost 9 years ago - 1 comment
Labels: enhancement

#7 - Improve documentation: graph of classes

Issue - State: closed - Opened by saphia almost 9 years ago
Labels: enhancement

#6 - New input data type: all fastas in a folder analysed in a single macsyfinder run.

Issue - State: closed - Opened by saphia almost 9 years ago - 5 comments
Labels: enhancement

#5 - Creation of a new gene status "annotated" or "neutral"

Issue - State: closed - Opened by saphia almost 9 years ago
Labels: enhancement

#4 - update gembase format

Issue - State: closed - Opened by bneron almost 9 years ago
Labels: enhancement

#3 - Feature version

Pull Request - State: closed - Opened by freeh4cker over 9 years ago

#2 - Portability fixes for Windows

Pull Request - State: closed - Opened by fjossandon about 10 years ago - 7 comments

#1 - setup.py install tests failed on MacOSX

Issue - State: closed - Opened by bawee about 10 years ago - 1 comment