sanger-pathogens/mlst_check issues and pull requests

#95 - Unable to download database

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

#94 - get_sequence_type -s "Pseudomonas aeruginosa" *.fna Can't locate Bio/Perl.pm in @INC (you may need to install the Bio::Perl module)

Issue - State: open - Opened by neelam19051 almost 3 years ago

#93 - mlst database

Issue - State: open - Opened by buihoangphuc412 almost 4 years ago

#92 - Change paths for farm usage

Pull Request - State: closed - Opened by Lfulcrum about 4 years ago - 1 comment

#91 - No results from get_sequence_type

Issue - State: open - Opened by VoronDM about 4 years ago - 3 comments

#90 - Perl Error while running download_mlst_databases

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

#89 - Docker build fixes & perl locale fix

Pull Request - State: closed - Opened by trstickland almost 5 years ago

#88 - remove path-help email from support

Pull Request - State: closed - Opened by kathryn1995 almost 5 years ago - 1 comment

#87 - readdir() attempted on invalid dirhandle

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

#86 - Added changelog

Pull Request - State: closed - Opened by ssjunnebo about 6 years ago

#85 - Rt574328 readme

Pull Request - State: closed - Opened by ssjunnebo about 6 years ago

#84 - get_sequence_types only writes N for some fasta

Issue - State: open - Opened by ssjunnebo about 6 years ago - 2 comments

#83 - Different order of MLST alleles to Leptospira

Issue - State: open - Opened by ghost over 6 years ago

#82 - add codecov

Pull Request - State: closed - Opened by ssjunnebo over 6 years ago - 1 comment

#81 - fix typo in badge

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

#80 - Add Docker badges to README.md

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

#79 - include bioconda instructions

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

#78 - url not found

Issue - State: open - Opened by bgold04 almost 7 years ago - 2 comments

#77 - download_mlst_databases Could not connect to https://pubmlst.org/data/dbases.xml

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

#76 - 574328 fix readme

Pull Request - State: closed - Opened by ssjunnebo about 7 years ago

#75 - Something went wrong, got a 500 status code at /usr/local/share/perl/5.22.2/Bio/MLST/Download/Downloadable.pm line 24.

Issue - State: closed - Opened by bastian-wur over 7 years ago - 1 comment

#74 - update email address

Pull Request - State: closed - Opened by ssjunnebo almost 8 years ago

#73 - download from https

Pull Request - State: closed - Opened by andrewjpage almost 8 years ago

#72 - Update lustre directory in bin scripts

Pull Request - State: closed - Opened by vaofford about 8 years ago

#71 - update 108 to 118

Pull Request - State: closed - Opened by andrewjpage about 8 years ago

#70 - Test descriptions

Pull Request - State: closed - Opened by andrewjpage about 8 years ago

#69 - updates from review

Pull Request - State: closed - Opened by andrewjpage about 8 years ago

#68 - Licence

Issue - State: closed - Opened by happykhan about 8 years ago - 1 comment

#67 - Update mlst to latest perl

Pull Request - State: closed - Opened by andrewjpage over 8 years ago

#66 - Docker

Pull Request - State: closed - Opened by andrewjpage over 8 years ago

#65 - Issue with running get_sequence_type

Issue - State: closed - Opened by BioMEC over 8 years ago - 1 comment

#64 - nds change to dist zilla starter bundle

Pull Request - State: closed - Opened by nds over 8 years ago

#63 - BUG: missing semicolon in get_emm_sequence_type script

Pull Request - State: closed - Opened by aslett1 about 9 years ago

#62 - Order alleles consistently when concatonating

Pull Request - State: closed - Opened by bewt85 about 9 years ago

#61 - Ignore metadata column headings in profiles

Pull Request - State: closed - Opened by bewt85 about 9 years ago

#60 - [468141,463456]: Cope better with small changes to alleles

Pull Request - State: closed - Opened by bewt85 over 9 years ago

#59 - Travis badge should just report master

Pull Request - State: closed - Opened by bewt85 over 9 years ago

#58 - Added AUTHORS with ap13 and bt5 as authors

Pull Request - State: closed - Opened by aslett1 over 9 years ago

#57 - BUG: Missing semicolon in get_sequence_type script

Pull Request - State: closed - Opened by bewt85 over 9 years ago

#56 - Ticket 463462: dodgy default arguments for blast_exec and makeblastdb_exec

Pull Request - State: closed - Opened by bewt85 over 9 years ago

#55 - Fix perl version in .travis.yml

Pull Request - State: closed - Opened by bewt85 over 9 years ago

#54 - Hopefully adds Travis CI support

Pull Request - State: closed - Opened by bewt85 over 9 years ago

#53 - Ticket 463083 Update versioning

Pull Request - State: closed - Opened by bewt85 almost 10 years ago - 1 comment

#52 - Ticket 452414 Fix false contamination

Pull Request - State: closed - Opened by bewt85 almost 10 years ago

#51 - Ticket 453529 Fix MLST spreadsheet output

Pull Request - State: closed - Opened by bewt85 almost 10 years ago - 3 comments

#50 - Ticket 442599 Fix database updated

Pull Request - State: closed - Opened by bewt85 almost 10 years ago - 1 comment

#49 - Fixes tests

Pull Request - State: closed - Opened by bewt85 almost 10 years ago

#48 - Deal with cases where allele name contains a - or _

Pull Request - State: closed - Opened by carlacummins about 10 years ago

#47 - Prevented splitting of allele names in header

Pull Request - State: closed - Opened by carlacummins about 10 years ago

#46 - pass in number of parallel processes

Pull Request - State: closed - Opened by andrewjpage over 10 years ago

#45 - Added AUTHORS file

Pull Request - State: closed - Opened by aslett1 over 10 years ago

#44 - changes in main bin file due to addition of -md5 option in the lib

Pull Request - State: closed - Opened by jyothishnt over 10 years ago

#43 - Changes in get_emm_sequence_type due to addition of -md5 option

Pull Request - State: closed - Opened by jyothishnt over 10 years ago

#42 - Fixed error when using -a option

Pull Request - State: closed - Opened by carlacummins over 10 years ago

#41 - Tests modified and passed successfully

Pull Request - State: closed - Opened by jyothishnt over 10 years ago

#40 - New -md5 option

Pull Request - State: closed - Opened by jyothishnt over 10 years ago

#39 - Improved error handling for unknown species

Pull Request - State: closed - Opened by carlacummins almost 11 years ago

#38 - Skip corrupt database

Pull Request - State: closed - Opened by andrewjpage about 11 years ago

#37 - Updated sequence type choosing

Pull Request - State: closed - Opened by carlacummins about 11 years ago

#36 - Edits to sequence type choosing

Pull Request - State: closed - Opened by carlacummins about 11 years ago

#35 - output concat sequence where all are unknown

Pull Request - State: closed - Opened by andrewjpage over 11 years ago

#34 - renamed LICENSE

Pull Request - State: closed - Opened by CraigPorter over 11 years ago

#33 - GPL

Pull Request - State: closed - Opened by andrewjpage over 11 years ago

#32 - filter out main allele

Pull Request - State: closed - Opened by andrewjpage almost 12 years ago

#31 - use new st

Pull Request - State: closed - Opened by andrewjpage almost 12 years ago

#30 - use st instead of gene id

Pull Request - State: closed - Opened by andrewjpage almost 12 years ago

#29 - When theres contamination allow for the alternative matches to be displayed in the results

Pull Request - State: closed - Opened by andrewjpage almost 12 years ago

#28 - make scripts executable

Pull Request - State: closed - Opened by andrewjpage about 12 years ago

#27 - Emm st

Pull Request - State: closed - Opened by andrewjpage about 12 years ago

#26 - added unit test for matching alleles with underscore eg S.pyogenes

Pull Request - State: closed - Opened by CraigPorter about 12 years ago

#25 - ignore mlst clade for cdiff

Pull Request - State: closed - Opened by andrewjpage about 12 years ago

#24 - filter underscores in header name

Pull Request - State: closed - Opened by andrewjpage about 12 years ago

#23 - tests

Pull Request - State: closed - Opened by andrewjpage about 12 years ago

#22 - Update documentation to work better with CPAN

Pull Request - State: closed - Opened by andrewjpage about 12 years ago

#21 - Absent locus

Pull Request - State: closed - Opened by CraigPorter about 12 years ago

#20 - Corrected bug in results filter for multiple species

Pull Request - State: closed - Opened by CraigPorter about 12 years ago

#19 - Search multiple mlst

Pull Request - State: closed - Opened by CraigPorter about 12 years ago