Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / gem-pasteur/Integron_Finder issues and pull requests
#113 - [FEAT] Use the option --prot-file independently of the option --annot-parser
Issue -
State: open - Opened by LCoffion 10 months ago
Labels: enhancement
#112 - [FEAT] improve IF to work with gembase 2
Issue -
State: open - Opened by bneron 12 months ago
Labels: enhancement
#111 - [FEAT] Remove/Relax Matplotlib version requirement
Issue -
State: open - Opened by acarafat 12 months ago
- 5 comments
Labels: enhancement
#110 - [HELP] In silico IntI1 qPCR assay don't match results IntegronFinder
Issue -
State: closed - Opened by LauraVP1994 about 1 year ago
- 10 comments
Labels: help wanted
#109 - [HELP] Different results in hits between multi-gbk and merged gbk on same sample?
Issue -
State: closed - Opened by Svnipni about 1 year ago
- 2 comments
Labels: help wanted
#108 - AttributeError: module 'Bio.Seq' has no attribute 'IUPAC'
Issue -
State: closed - Opened by EllBaum over 1 year ago
- 2 comments
Labels: help wanted
#107 - [BUG] underlay of /etc/localtime required more than 50 (87) bind mounts
Issue -
State: closed - Opened by yegonzalezflores over 1 year ago
- 4 comments
Labels: bug
#106 - How to use --func-annot
Issue -
State: closed - Opened by aslangabriel almost 2 years ago
- 1 comment
Labels: help wanted
#105 - [HELP] How can I get the sequence of whole integron?
Issue -
State: closed - Opened by Galib009 almost 2 years ago
- 3 comments
Labels: help wanted
#104 - [BUG] IF crashes with --gbk option in a specific caase
Issue -
State: open - Opened by eloilit almost 2 years ago
- 3 comments
Labels: bug
#103 - [BUG] IF crashes on a multiple contigs file
Issue -
State: closed - Opened by eloilit about 2 years ago
- 1 comment
Labels: bug
#102 - [HELP] Question: are gene cassettes of a integron all on the same strand?
Issue -
State: closed - Opened by jiarong about 2 years ago
- 4 comments
Labels: help wanted
#101 - [HELP] Question: are the integrase (IntI) always on the opposite strand of gene cassettes?
Issue -
State: closed - Opened by jiarong about 2 years ago
- 3 comments
Labels: help wanted
#100 - [FEAT] genbank or gff as input
Issue -
State: open - Opened by alexweisberg about 2 years ago
Labels: enhancement
#99 - [BUG] IntegronFinder fails when there is a "space" in the path
Issue -
State: closed - Opened by eloilit about 2 years ago
- 1 comment
Labels: bug
#98 - :pencil2: Eloilit patch issue 97 on CPU documentation
Pull Request -
State: closed - Opened by eloilit about 2 years ago
#97 - [FEAT] Add documentation about CPU usage
Issue -
State: closed - Opened by eloilit about 2 years ago
Labels: enhancement
#96 - install Integron_Finder through conda
Issue -
State: closed - Opened by danielarothschild over 2 years ago
#95 - Complete documentation for ARG
Issue -
State: closed - Opened by jeanrjc over 2 years ago
- 1 comment
Labels: enhancement, doc
#94 - IntegronFinder does not pass unitary test "test_main_outdir_exists" (test_merge.TestMain)
Issue -
State: closed - Opened by eloilit almost 3 years ago
#93 - Issue with colorlog logging
Issue -
State: closed - Opened by alexweisberg about 3 years ago
- 1 comment
#92 - ValueError: attempt to get argmin of an empty sequence
Issue -
State: closed - Opened by danyu-uofa about 3 years ago
- 3 comments
#91 - IF give different results depending installation
Issue -
State: closed - Opened by bneron about 3 years ago
- 2 comments
Labels: bug, high priority
#90 - Integron_Finder bogs down server's I/O when ran on metagenomes with ~million contigs
Issue -
State: open - Opened by JuntaoZhong about 3 years ago
- 3 comments
#89 - update hmmsearch command line and profile
Issue -
State: closed - Opened by bneron about 3 years ago
Labels: enhancement
#88 - IntegronFinder should not run twice over the the edge of the replicon
Issue -
State: closed - Opened by jeanrjc over 3 years ago
Labels: bug
#87 - Help me understanding the output of IF with a multi-fasta file
Issue -
State: closed - Opened by bramvandijk88 over 3 years ago
- 2 comments
#86 - Fatal error: Exit code 127 ()
Issue -
State: closed - Opened by IustinBilavschi over 3 years ago
- 1 comment
#85 - End location (191284) must be greater than or equal to start location (271412)
Issue -
State: closed - Opened by erichy91 over 3 years ago
- 6 comments
Labels: bug, high priority
#84 - Keep attC sites even if the evalue change with local_max
Issue -
State: closed - Opened by jeanrjc over 3 years ago
Labels: bug
#83 - program not work for Staphylococcus aureus
Issue -
State: closed - Opened by WMBio over 3 years ago
- 1 comment
#82 - Problem installing integron_finder via bioconda
Issue -
State: closed - Opened by evolarjun over 3 years ago
- 5 comments
#81 - some major and common problems
Issue -
State: closed - Opened by hongyuan-zheng almost 4 years ago
- 2 comments
#80 - error on calling --gembases option
Issue -
State: closed - Opened by cachapuz2001 almost 4 years ago
- 1 comment
#79 - Error related to prodigal: RuntimeError("{0} failed returncode = {1}".format(prodigal_cmd, returncode))
Issue -
State: closed - Opened by sasonbol almost 4 years ago
- 16 comments
#78 - AttributeError: module 'Bio.Seq' has no attribute 'IUPAC'
Issue -
State: closed - Opened by deoliveiralab about 4 years ago
- 4 comments
#77 - conda install causes pandas.io.common ImportError
Issue -
State: closed - Opened by nebfield about 4 years ago
- 2 comments
#76 - Error running Singularity
Issue -
State: closed - Opened by ramadatta over 4 years ago
- 4 comments
#75 - Integron classes 1,2,3
Issue -
State: closed - Opened by koopkaup over 4 years ago
- 1 comment
#74 - Installing from pip not working
Issue -
State: closed - Opened by leaemiliepradier almost 5 years ago
- 3 comments
#73 - go_left = (full_element[full_element.type_elt == "attC"].pos_beg.values[0] - df_max.pos_end.values[0]: index 0 is out of bounds for axis 0 with size 0
Issue -
State: closed - Opened by vbrover almost 5 years ago
- 6 comments
Labels: bug, high priority
#72 - "integron_finder --local_max --func_annot mysequences.fst" should be "integron_finder --local-max --func-annot mysequences.fst"
Issue -
State: closed - Opened by vbrover almost 5 years ago
#71 - IndexError attc.py
Issue -
State: closed - Opened by jfourquet2 almost 5 years ago
- 4 comments
#70 - Topology issues
Issue -
State: closed - Opened by jeanrjc almost 5 years ago
- 2 comments
Labels: bug, high priority, easyfix
#69 - problem with overlapping/near identical attC sites
Issue -
State: closed - Opened by jeanrjc almost 5 years ago
- 6 comments
Labels: bug, easyfix
#68 - in summary output, add the size of contig
Issue -
State: closed - Opened by jeanrjc almost 5 years ago
Labels: enhancement, easyfix
#67 - ID_integron should not be in .summary file
Issue -
State: closed - Opened by jeanrjc almost 5 years ago
- 1 comment
Labels: bug, easyfix
#66 - summary files should be created when no integron is found
Issue -
State: closed - Opened by jeanrjc almost 5 years ago
- 2 comments
Labels: enhancement, easyfix
#65 - bug in .integrons output
Issue -
State: closed - Opened by jeanrjc almost 5 years ago
Labels: bug, easyfix
#64 - Cannot install
Issue -
State: closed - Opened by vbrover almost 5 years ago
- 3 comments
#63 - Trouble installing integron_finder using pip install
Issue -
State: closed - Opened by aaron-bio about 5 years ago
- 1 comment
#62 - errors
Issue -
State: closed - Opened by mdtorohernando about 5 years ago
- 2 comments
#61 - I cannot find intergron_Finder in bioconda
Issue -
State: closed - Opened by glichtenstein over 5 years ago
- 4 comments
#60 - preparation problems
Issue -
State: closed - Opened by aslangabriel over 5 years ago
- 11 comments
#59 - Added newlines
Pull Request -
State: closed - Opened by g1o almost 6 years ago
- 2 comments
#58 - Runtime error on draft assemblies
Issue -
State: closed - Opened by lowandrew almost 6 years ago
- 1 comment
#57 - installing Integron_Finderv2 on conda
Issue -
State: closed - Opened by mhyleung almost 6 years ago
- 2 comments
#56 - Invalid characters
Issue -
State: closed - Opened by pbravakos almost 6 years ago
- 4 comments
#55 - Prediction over sequence start with --linear
Issue -
State: closed - Opened by johrollin about 6 years ago
- 4 comments
Labels: bug
#54 - add github page for khillion
Pull Request -
State: closed - Opened by khillion about 6 years ago
- 1 comment
#53 - Small change to keep it up with the matplot version
Pull Request -
State: closed - Opened by g1o over 6 years ago
- 1 comment
#52 - -vv does not work
Issue -
State: closed - Opened by bneron over 6 years ago
Labels: bug, high priority
#51 - Small change to check pipeline
Pull Request -
State: closed - Opened by aperrin almost 7 years ago
#50 - Complete Documentation with all new options and changes
Issue -
State: closed - Opened by jeanrjc almost 7 years ago
Labels: doc, high priority
#49 - log file
Issue -
State: closed - Opened by asetGem almost 7 years ago
Labels: enhancement, high priority
#48 - Add function parsing attC sites
Issue -
State: closed - Opened by asetGem almost 7 years ago
- 1 comment
Labels: enhancement, low priority
#47 - stdout/stderr management
Issue -
State: closed - Opened by asetGem almost 7 years ago
- 3 comments
Labels: enhancement, medium priority
#46 - Diversify installation
Issue -
State: closed - Opened by asetGem almost 7 years ago
Labels: installation, medium priority
#45 - Add threshold of number of attC to keep a CALIN
Issue -
State: closed - Opened by asetGem almost 7 years ago
- 1 comment
Labels: enhancement, low priority
#44 - Parallelisation
Issue -
State: closed - Opened by asetGem almost 7 years ago
- 1 comment
Labels: enhancement, medium priority
#43 - Circularity with multi-fasta input
Issue -
State: closed - Opened by asetGem almost 7 years ago
- 3 comments
Labels: enhancement, high priority
#42 - Improve error handling
Issue -
State: closed - Opened by asetGem almost 7 years ago
- 4 comments
Labels: enhancement, medium priority
#41 - Handle multi-fasta input files
Issue -
State: closed - Opened by asetGem almost 7 years ago
- 1 comment
Labels: enhancement, high priority
#40 - Modify default outputs
Issue -
State: closed - Opened by asetGem almost 7 years ago
- 1 comment
Labels: enhancement, high priority
#39 - Add information on running tests in doc
Issue -
State: closed - Opened by asetGem almost 7 years ago
- 1 comment
Labels: doc, high priority
#38 - add unit test for all Integron methods
Issue -
State: closed - Opened by bneron over 7 years ago
Labels: testing
#37 - remove accent for XML compatibility
Pull Request -
State: closed - Opened by khillion over 7 years ago
#36 - Find integrons in a multiple sequence fasta file
Issue -
State: closed - Opened by koopkaup over 7 years ago
- 2 comments
#35 - help --gembase
Issue -
State: closed - Opened by johrollin over 7 years ago
- 5 comments
#34 - error python-pandas-0.19
Issue -
State: closed - Opened by johrollin over 7 years ago
- 2 comments
#33 - add unit test for get_version_message
Issue -
State: closed - Opened by bneron almost 8 years ago
Labels: testing
#32 - add unit test for scan_hmm_bank
Issue -
State: closed - Opened by bneron almost 8 years ago
Labels: testing
#31 - find unit test to to_gbk
Issue -
State: closed - Opened by bneron almost 8 years ago
Labels: testing
#30 - add unit test for read_infernal
Issue -
State: closed - Opened by bneron almost 8 years ago
#29 - add unit test for read_hmm
Issue -
State: closed - Opened by bneron almost 8 years ago
Labels: testing
#28 - add unit test for func_annot
Issue -
State: closed - Opened by bneron almost 8 years ago
Labels: testing
#27 - add unit test for func_annot
Issue -
State: closed - Opened by bneron almost 8 years ago
- 1 comment
Labels: testing
#26 - add unit test for find_integrase
Issue -
State: closed - Opened by bneron almost 8 years ago
Labels: testing
#25 - add unit test for find_attc
Issue -
State: closed - Opened by bneron almost 8 years ago
Labels: testing
#24 - add unit test for local_max
Issue -
State: closed - Opened by bneron almost 8 years ago
Labels: testing
#23 - add unit test for expand
Issue -
State: closed - Opened by bneron almost 8 years ago
Labels: testing
#22 - add unit test for find_attc_max
Issue -
State: closed - Opened by bneron almost 8 years ago
Labels: testing
#21 - add unit test for find_integron
Issue -
State: closed - Opened by bneron almost 8 years ago
Labels: testing
#20 - add unit test for search_attc
Issue -
State: closed - Opened by bneron almost 8 years ago
Labels: testing
#19 - Add documentation for Galaxy
Pull Request -
State: closed - Opened by khillion almost 8 years ago
- 3 comments
#18 - fillna="na" error if pandas version 0.19.0, solved by downgrading pandas to 0.18.0
Issue -
State: closed - Opened by SwapnilDoijad almost 8 years ago
- 2 comments
Labels: bug
#17 - Accept multiple fasta file
Issue -
State: closed - Opened by jeanrjc over 8 years ago
- 3 comments
Labels: enhancement
#16 - ValueError: Cannot set a frame with no defined index and a value that cannot be converted to a Series
Issue -
State: closed - Opened by hcdenbakker over 8 years ago
- 3 comments
#15 - read_infernal() does not re-adjust position for truncated but significant hits
Issue -
State: closed - Opened by jeanrjc over 8 years ago
#14 - --gembase option not working on v1.3
Issue -
State: closed - Opened by jeanrjc almost 9 years ago
- 1 comment