cov-lineages/pangolin issues and pull requests

#100 - Pangolin/pangolearn failed, data column mismatch?

Issue - State: closed - Opened by biocyberman about 4 years ago - 8 comments

#100 - Pangolin/pangolearn failed, data column mismatch?

Issue - State: closed - Opened by biocyberman about 4 years ago - 8 comments

#99 - pangoLEARN 0 snakemake not using threads

Issue - State: closed - Opened by tseemann about 4 years ago - 2 comments
Labels: enhancement

#99 - pangoLEARN 0 snakemake not using threads

Issue - State: closed - Opened by tseemann about 4 years ago - 2 comments
Labels: enhancement

#98 - Support PuLP 2.x ?

Issue - State: closed - Opened by tseemann about 4 years ago - 2 comments

#98 - Support PuLP 2.x ?

Issue - State: closed - Opened by tseemann about 4 years ago - 2 comments

#97 - Problem with the path to the data reference

Issue - State: closed - Opened by Gabo-Gonzalez about 4 years ago - 1 comment

#97 - Problem with the path to the data reference

Issue - State: closed - Opened by Gabo-Gonzalez about 4 years ago - 1 comment

#96 - Version control dependencies

Issue - State: closed - Opened by schorlton about 4 years ago - 1 comment

#96 - Version control dependencies

Issue - State: closed - Opened by schorlton about 4 years ago - 1 comment

#95 - Decision tree / Ns?

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

#95 - Decision tree / Ns?

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

#94 - Key error in pangolearn.smk file

Issue - State: closed - Opened by lr5317 about 4 years ago - 2 comments
Labels: question

#94 - Key error in pangolearn.smk file

Issue - State: closed - Opened by lr5317 about 4 years ago - 2 comments
Labels: question

#93 - Error in rule add_failed_seqs:

Issue - State: closed - Opened by dcadam over 4 years ago - 3 comments

#93 - Error in rule add_failed_seqs:

Issue - State: closed - Opened by dcadam over 4 years ago - 3 comments

#92 - Added shebang to pangolearn.py

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

#92 - Added shebang to pangolearn.py

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

#91 - Reduces memory requirements, faster processing

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

#91 - Reduces memory requirements, faster processing

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

#90 - Speed up removeIndices

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

#90 - Speed up removeIndices

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

#89 - Missing joblib module (Ubuntu 18.04.4, pangolin v2.0.4)

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

#89 - Missing joblib module (Ubuntu 18.04.4, pangolin v2.0.4)

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

#88 - fix path for panGUIlin metadata file

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

#88 - fix path for panGUIlin metadata file

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

#87 - default N content to 0.8

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

#87 - default N content to 0.8

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

#86 - fix code block syntax error

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

#86 - fix code block syntax error

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

#85 - parse data dir if specified in the args

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

#85 - parse data dir if specified in the args

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

#84 - uppercase bug fix

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

#84 - uppercase bug fix

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

#83 - pangoLEARN

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

#83 - pangoLEARN

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

#82 - Error in rule assign_lineage

Issue - State: closed - Opened by judyssister over 4 years ago - 6 comments

#82 - Error in rule assign_lineage

Issue - State: closed - Opened by judyssister over 4 years ago - 6 comments

#81 - Installation error (possible permissions issue)

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

#81 - Installation error (possible permissions issue)

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

#80 - Make usage a little bit clearer

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

#80 - Make usage a little bit clearer

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

#79 - snpangolin and safe pangolin

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

#79 - snpangolin and safe pangolin

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

#78 - fatal: not a git repository (or any of the parent directories): .git

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

#78 - fatal: not a git repository (or any of the parent directories): .git

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

#77 - Snpangolin and mod for pangolin prep

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

#77 - Snpangolin and mod for pangolin prep

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

#76 - add sam_2_snps.py

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

#76 - add sam_2_snps.py

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

#75 - Sam 2 csv

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

#75 - Sam 2 csv

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

#74 - Error while installing in Windows

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

#74 - Error while installing in Windows

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

#73 - fixes bug when traversing lineages with long names

Pull Request - State: closed - Opened by jtmccr1 over 4 years ago

#73 - fixes bug when traversing lineages with long names

Pull Request - State: closed - Opened by jtmccr1 over 4 years ago

#72 - Difference reference to nextstrain?

Issue - State: closed - Opened by biocyberman over 4 years ago - 7 comments

#72 - Difference reference to nextstrain?

Issue - State: closed - Opened by biocyberman over 4 years ago - 7 comments

#71 - Output a single tree file for all queries

Issue - State: closed - Opened by jbv2 over 4 years ago - 1 comment
Labels: enhancement

#71 - Output a single tree file for all queries

Issue - State: closed - Opened by jbv2 over 4 years ago - 1 comment
Labels: enhancement

#70 - Adding more os.path.join to file paths

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

#70 - Adding more os.path.join to file paths

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

#69 - Why pandas==1.0.1 only?

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

#69 - Why pandas==1.0.1 only?

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

#68 - Conda recipe needs to say iqtree < 2

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

#68 - Conda recipe needs to say iqtree < 2

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

#67 - Mismatch reference name between lineage data and pangolin

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

#67 - Mismatch reference name between lineage data and pangolin

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

#66 - syntax error near unexpected token `('

Issue - State: closed - Opened by mdhall272 over 4 years ago - 3 comments

#66 - syntax error near unexpected token `('

Issue - State: closed - Opened by mdhall272 over 4 years ago - 3 comments

#65 - Error: Argument list too long

Issue - State: closed - Opened by HouriiyahT over 4 years ago - 3 comments

#65 - Error: Argument list too long

Issue - State: closed - Opened by HouriiyahT over 4 years ago - 3 comments

#64 - Is lineage_report.csv the only output?

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

#64 - Is lineage_report.csv the only output?

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

#63 - Pangolin assignments are vastly different from the those in Nextstrain

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

#63 - Pangolin assignments are vastly different from the those in Nextstrain

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

#62 - Root gate

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

#62 - Root gate

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

#61 - lineage_report.csv can't be found.

Issue - State: closed - Opened by biocyberman over 4 years ago - 11 comments

#61 - lineage_report.csv can't be found.

Issue - State: closed - Opened by biocyberman over 4 years ago - 11 comments

#60 - Output tree files for queries

Issue - State: closed - Opened by jtmccr1 over 4 years ago - 1 comment
Labels: enhancement

#60 - Output tree files for queries

Issue - State: closed - Opened by jtmccr1 over 4 years ago - 1 comment
Labels: enhancement

#59 - now collapses branches <5e-6

Pull Request - State: closed - Opened by jtmccr1 over 4 years ago

#59 - now collapses branches <5e-6

Pull Request - State: closed - Opened by jtmccr1 over 4 years ago

#58 - pangolin --version should return 0 and go to stdout

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

#58 - pangolin --version should return 0 and go to stdout

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

#57 - Reason for status=fail / Lineage=None

Issue - State: closed - Opened by tseemann over 4 years ago - 6 comments

#57 - Reason for status=fail / Lineage=None

Issue - State: closed - Opened by tseemann over 4 years ago - 6 comments

#56 - mafft-profile will be defunct,use mafft --addprofile

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

#56 - mafft-profile will be defunct,use mafft --addprofile

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

#55 - Error in rule assign_lineages:

Issue - State: closed - Opened by swantan over 4 years ago - 6 comments

#55 - Error in rule assign_lineages:

Issue - State: closed - Opened by swantan over 4 years ago - 6 comments

#54 - test and fixes for issue 52

Pull Request - State: closed - Opened by jtmccr1 over 4 years ago

#54 - test and fixes for issue 52

Pull Request - State: closed - Opened by jtmccr1 over 4 years ago

#53 - Local commits

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

#53 - Local commits

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

#52 - 'NoneType' object has no attribute 'annotations'

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

#52 - 'NoneType' object has no attribute 'annotations'

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

#51 - /tmp and .snakemake clash when running two at once

Issue - State: closed - Opened by tseemann over 4 years ago - 6 comments

#51 - /tmp and .snakemake clash when running two at once

Issue - State: closed - Opened by tseemann over 4 years ago - 6 comments

GitHub / cov-lineages/pangolin issues and pull requests