TheBrownLab/PhyloFisher issues and pull requests

#123 - added lock

Pull Request - State: closed - Opened by DavidZihala about 2 months ago

#121 - Fix the bug in issue#120 "NameError: name 'metadata' is not defined"

Pull Request - State: closed - Opened by shuiyujinlan 5 months ago

#120 - metadata not defined in forest_local.py

Issue - State: closed - Opened by sipesk 5 months ago - 7 comments

#119 - matrix_constructor.py stops at 55 %

Issue - State: open - Opened by Edouard94 6 months ago - 15 comments

#118 - Integrates nucl matrix contsructor

Pull Request - State: closed - Opened by robert-ervin-jones 8 months ago

#117 - add leaf rename utility

Pull Request - State: closed - Opened by robert-ervin-jones 8 months ago

#116 - heterotachy.py handling of taxon names

Issue - State: open - Opened by atice 8 months ago - 2 comments

#115 - Add .circleci/config.yml

Pull Request - State: closed - Opened by robert-ervin-jones 8 months ago

#114 - fix typo matrix_constructor.smk

Pull Request - State: closed - Opened by giacomomutti 8 months ago

#112 - Duplicate and non-trimmed genes in matrix_constructor.py output

Issue - State: closed - Opened by cha-namoth 9 months ago - 4 comments

#111 - Paralogs added have the exact same name as ortholog

Issue - State: open - Opened by matiasWanntorp 9 months ago - 4 comments

#110 - Running PhyloFisher across multiple nodes

Issue - State: closed - Opened by matiasWanntorp 9 months ago - 2 comments

#109 - Options for amino/nuc and to write fastest sites out

Pull Request - State: open - Opened by aguang 10 months ago - 3 comments

#108 - Including BUSCO's metazoa_odb10 dataset

Issue - State: closed - Opened by dongzhang0725 11 months ago - 2 comments

#107 - fast_site_remover.py with nucleic acid sequences

Issue - State: open - Opened by aguang 11 months ago - 3 comments
Labels: enhancement

#106 - forest.py creates an empty folder

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

#105 - sgt_constructor.py "Could not create conda environment from /opt/anaconda3/envs/fisher/bin/bmge.yaml"

Issue - State: closed - Opened by AlexGalvez 11 months ago - 6 comments

#104 - updates raxml tree path

Pull Request - State: closed - Opened by robert-ervin-jones 11 months ago

#103 - Updates raxml ng

Pull Request - State: closed - Opened by robert-ervin-jones 12 months ago

#102 - No bootstrap values

Issue - State: closed - Opened by mjamy 12 months ago - 16 comments

#101 - Nucleotide alignments

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

#100 - apply_to_db.py does not update metadata.tsv file

Issue - State: closed - Opened by Edouard94 about 1 year ago - 5 comments

#99 - Errors running sgt_constructor.py: `Error in rule prequal`, `Error in rule length_filter_mafft`

Issue - State: closed - Opened by mjamy about 1 year ago - 8 comments

#97 - adds sht_include option to informant

Pull Request - State: closed - Opened by robert-ervin-jones about 1 year ago

#96 - updates matrix_constructor_stats.tsv and adds occupancy.tsv

Pull Request - State: closed - Opened by robert-ervin-jones about 1 year ago

#94 - updates logic behind sanity check

Pull Request - State: closed - Opened by robert-ervin-jones about 1 year ago

#92 - updates forest_local to reflect change to raxml-ng

Pull Request - State: closed - Opened by robert-ervin-jones about 1 year ago

#91 - forest_local.py creates empty output folder

Issue - State: closed - Opened by anoukwillemsen about 1 year ago - 4 comments

#90 - updates raxml command to only use one thread

Pull Request - State: closed - Opened by robert-ervin-jones about 1 year ago

#89 - RAxML within sgt_constructor uses all available resources

Issue - State: closed - Opened by anoukwillemsen about 1 year ago - 2 comments

#88 - Getting error when running apply_to_db.py

Issue - State: closed - Opened by thesamuanels about 1 year ago - 8 comments

#87 - Geeting error when trying to run the select_taxa.py script

Issue - State: closed - Opened by robert-ervin-jones about 1 year ago - 7 comments

#85 - 84 forestpy produces an empty directory

Pull Request - State: closed - Opened by robert-ervin-jones about 1 year ago

#84 - forest.py produces an empty directory

Issue - State: closed - Opened by miferg about 1 year ago - 8 comments

#83 - Fix select taxa chimera bug

Pull Request - State: closed - Opened by robert-ervin-jones over 1 year ago

#82 - Non-reproducible baseline example

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

#81 - index out of range error with select_taxa.py --chimera

Issue - State: closed - Opened by cha-namoth over 1 year ago - 5 comments

#80 - updates raxml rule to use raxml-ng

Pull Request - State: closed - Opened by robert-ervin-jones over 1 year ago

#79 - changes raxml threads

Pull Request - State: closed - Opened by robert-ervin-jones over 1 year ago

#77 - add support for singularity

Issue - State: closed - Opened by zhan4429 over 1 year ago - 3 comments

#76 - Nucl matrix utility

Pull Request - State: closed - Opened by robert-ervin-jones over 1 year ago

#75 - adds trimal gt param to matrix_constructor.py

Pull Request - State: closed - Opened by robert-ervin-jones over 1 year ago

#74 - bumps version to 1.2.6

Pull Request - State: closed - Opened by robert-ervin-jones over 1 year ago

#73 - adds path to matrix_constructor.smk to setup.py

Pull Request - State: closed - Opened by robert-ervin-jones over 1 year ago

#72 - matrix_constructor.smk not found

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

#71 - changes sgt to homolog in informant

Pull Request - State: closed - Opened by robert-ervin-jones over 1 year ago

#70 - fixes aa_recoder

Pull Request - State: closed - Opened by robert-ervin-jones over 1 year ago

#69 - aa_encode.py or SR4_class_recoder.py

Issue - State: closed - Opened by robert-ervin-jones over 1 year ago - 1 comment

#67 - reworks backup strategy

Pull Request - State: closed - Opened by robert-ervin-jones over 1 year ago

#66 - fixes paths

Pull Request - State: closed - Opened by robert-ervin-jones over 1 year ago

#64 - fixes conda env paths

Pull Request - State: closed - Opened by robert-ervin-jones almost 2 years ago

#63 - sgt_constructor.py throws 'No module named 'pandas'' error

Issue - State: closed - Opened by cha-namoth almost 2 years ago - 7 comments

#62 - CVE-2007-4559 Patch

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

#61 - updates update_dataframe to reflect addition of long name

Pull Request - State: closed - Opened by robert-ervin-jones almost 2 years ago

#60 - select_taxa.py only recognize short names

Issue - State: closed - Opened by robert-ervin-jones almost 2 years ago

#59 - Error downloading parasorter

Issue - State: closed - Opened by michoug almost 2 years ago - 1 comment

#56 - Matrix construct to smk

Pull Request - State: closed - Opened by robert-ervin-jones almost 2 years ago

#55 - sgt_constructor.py not working, FileNotFoundError: [Errno 2] No such file or directory

Issue - State: closed - Opened by pyongheng almost 2 years ago - 18 comments

#54 - adds recoding classes

Pull Request - State: closed - Opened by lnk1196 almost 2 years ago

#53 - add try excepts to plot generation

Pull Request - State: closed - Opened by robert-ervin-jones almost 2 years ago

#52 - Revert apply to db

Pull Request - State: closed - Opened by robert-ervin-jones almost 2 years ago

#51 - Errors running sgt_constructor.py, Error in rule raxml

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

#50 - removes rogue print

Pull Request - State: closed - Opened by robert-ervin-jones almost 2 years ago

#48 - Bipartition cleanup

Pull Request - State: closed - Opened by robert-ervin-jones almost 2 years ago