Ecosyste.ms: Issues

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GitHub / karel-brinda/miniphy issues and pull requests

#106 - Cluster

Pull Request - State: closed - Opened by karel-brinda 11 months ago

#105 - Add possibility to pass cluster params

Issue - State: closed - Opened by karel-brinda 11 months ago
Labels: enhancement

#104 - Test thoroughly on macos as well

Pull Request - State: closed - Opened by karel-brinda 11 months ago

#103 - Resume jobs

Issue - State: closed - Opened by shenwei356 11 months ago - 3 comments

#102 - Make attotree read the list of input files from a file

Pull Request - State: closed - Opened by karel-brinda 11 months ago

#101 - Tree inference – argument list too long: '/bin/sh

Issue - State: closed - Opened by karel-brinda 11 months ago
Labels: bug

#100 - Extend documentation in the readme

Issue - State: open - Opened by karel-brinda 11 months ago
Labels: enhancement

#100 - Extend documentation in the readme

Issue - State: open - Opened by karel-brinda 11 months ago
Labels: enhancement

#99 - Fix and extend CI testing

Pull Request - State: closed - Opened by karel-brinda 11 months ago

#99 - Fix and extend CI testing

Pull Request - State: closed - Opened by karel-brinda 11 months ago

#98 - Remove ete3 dependency

Issue - State: open - Opened by karel-brinda 11 months ago - 1 comment
Labels: enhancement

#98 - Remove ete3 dependency

Issue - State: open - Opened by karel-brinda 11 months ago - 1 comment
Labels: enhancement

#96 - Fix int conversion

Pull Request - State: closed - Opened by karel-brinda 11 months ago

#96 - Fix int conversion

Pull Request - State: closed - Opened by karel-brinda 11 months ago

#95 - Simplify handling .conda/ in tests

Pull Request - State: closed - Opened by karel-brinda 11 months ago

#95 - Simplify handling .conda/ in tests

Pull Request - State: closed - Opened by karel-brinda 11 months ago

#94 - Missing int conversion by argparse in `create_batches.py`

Issue - State: closed - Opened by shenwei356 11 months ago - 2 comments
Labels: bug

#94 - Missing int conversion by argparse in `create_batches.py`

Issue - State: closed - Opened by shenwei356 11 months ago - 2 comments
Labels: bug

#93 - Suggestion on create_batches.py

Issue - State: open - Opened by shenwei356 11 months ago - 1 comment
Labels: enhancement

#93 - Suggestion on create_batches.py

Issue - State: open - Opened by shenwei356 11 months ago - 1 comment
Labels: enhancement

#91 - Add an -c option for adding comments to batching output

Pull Request - State: closed - Opened by karel-brinda 11 months ago

#91 - Add an -c option for adding comments to batching output

Pull Request - State: closed - Opened by karel-brinda 11 months ago

#90 - Add a param for adding comments to batching output text files

Issue - State: closed - Opened by karel-brinda 11 months ago
Labels: enhancement

#90 - Add a param for adding comments to batching output text files

Issue - State: closed - Opened by karel-brinda 11 months ago
Labels: enhancement

#89 - Dustbin creation – iterate over species in their alphabetical order

Issue - State: closed - Opened by karel-brinda 11 months ago
Labels: enhancement

#89 - Dustbin creation – iterate over species in their alphabetical order

Issue - State: closed - Opened by karel-brinda 11 months ago
Labels: enhancement

#88 - ProPhyle-based compression failing – but only with certain versions of Snakemake

Issue - State: closed - Opened by karel-brinda 11 months ago - 8 comments
Labels: bug

#88 - ProPhyle-based compression failing – but only with certain versions of Snakemake

Issue - State: closed - Opened by karel-brinda 11 months ago - 8 comments
Labels: bug

#87 - Remove dependency on `snakemake.workflow.srcdir`

Pull Request - State: closed - Opened by karel-brinda 11 months ago

#87 - Remove dependency on `snakemake.workflow.srcdir`

Pull Request - State: closed - Opened by karel-brinda 11 months ago

#86 - Simplify testing

Pull Request - State: closed - Opened by karel-brinda 11 months ago

#86 - Simplify testing

Pull Request - State: closed - Opened by karel-brinda 11 months ago

#85 - Simplify test

Pull Request - State: closed - Opened by karel-brinda 11 months ago

#85 - Simplify test

Pull Request - State: closed - Opened by karel-brinda 11 months ago

#84 - Simplify testing

Issue - State: closed - Opened by karel-brinda 11 months ago
Labels: enhancement

#84 - Simplify testing

Issue - State: closed - Opened by karel-brinda 11 months ago
Labels: enhancement

#83 - Always pass the number of threads

Pull Request - State: closed - Opened by karel-brinda 11 months ago

#83 - Always pass the number of threads

Pull Request - State: closed - Opened by karel-brinda 11 months ago

#82 - snakemake.workflow.srcdir discontinued in new versions of Snakemake

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

#82 - snakemake.workflow.srcdir discontinued in new versions of Snakemake

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

#81 - Add number of snakemake threads to config

Issue - State: closed - Opened by karel-brinda 11 months ago
Labels: enhancement

#81 - Add number of snakemake threads to config

Issue - State: closed - Opened by karel-brinda 11 months ago
Labels: enhancement

#80 - Missing dependency: grpc

Issue - State: closed - Opened by shenwei356 11 months ago - 6 comments
Labels: bug

#80 - Missing dependency: grpc

Issue - State: closed - Opened by shenwei356 11 months ago - 6 comments
Labels: bug

#79 - Move attotree to a sep env and use its latest version

Pull Request - State: closed - Opened by karel-brinda about 1 year ago

#79 - Move attotree to a sep env and use its latest version

Pull Request - State: closed - Opened by karel-brinda about 1 year ago

#76 - Rename MOF-Compress to MiniPhy

Pull Request - State: closed - Opened by karel-brinda about 1 year ago

#75 - Add script for batching

Pull Request - State: closed - Opened by karel-brinda about 1 year ago

#74 - Cleanup

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#73 - Add a small version of the logo

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#72 - Fix background

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#71 - Add XZ to essential dependencies

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#70 - Add trees_required config option

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#69 - Remove pandas & numpy as dependencies

Issue - State: open - Opened by karel-brinda over 1 year ago - 1 comment
Labels: enhancement

#68 - Improve Jellyfish configurability

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#67 - Make jellyfish more configurable

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

#66 - Update README.md

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#65 - Update README.md

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#64 - Add .test/ autodetection

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#63 - Tests not runnable by `make` from `.test`

Issue - State: closed - Opened by karel-brinda over 1 year ago
Labels: bug

#62 - Update documentation and make functionality

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#61 - Improve documentation, configuration, and its parsing

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#60 - Config options are parsed only on the top level yaml

Issue - State: closed - Opened by karel-brinda over 1 year ago
Labels: bug

#59 - Add a default script for batching

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

#58 - Add an option for tree post-processing (to switch it off)

Issue - State: open - Opened by karel-brinda over 1 year ago
Labels: enhancement

#57 - Add an option to fail if tree is not provided

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

#56 - Major update of documentation

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#55 - Update documentation

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#54 - Add a make subcommand for just re-compressing the final files

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

#53 - Add the final newick tree to the post output files

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#52 - Raise an error if no input is provided

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#51 - Add possibility to switch off conda

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#51 - Add possibility to switch off conda

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#50 - Add newick to post output

Issue - State: closed - Opened by karel-brinda over 1 year ago

#49 - Add detailed batch stats

Issue - State: closed - Opened by karel-brinda over 1 year ago - 1 comment
Labels: duplicate

#48 - Update docs after the update of the pipeline

Issue - State: closed - Opened by karel-brinda over 1 year ago

#47 - Improve pipeline configurability

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#46 - Make xz configurable

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#46 - Make xz configurable

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#45 - Make xz compression configurable

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

#45 - Make xz compression configurable

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

#44 - Split files between intermediate/ and output/

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#44 - Split files between intermediate/ and output/

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#43 - Update Make help messages

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#42 - Simplify the basic workflow

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#41 - In the default setup, compress only assemblies

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#41 - In the default setup, compress only assemblies

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#40 - Cov

Pull Request - State: closed - Opened by karel-brinda over 1 year ago

#39 - ModuleNotFoundError: No module named 'ete3'

Issue - State: closed - Opened by karel-brinda over 1 year ago
Labels: bug

#38 - merge_global_stats.py: error: the following arguments are required: batch.global.stats

Issue - State: closed - Opened by karel-brinda over 1 year ago - 1 comment
Labels: bug

#38 - merge_global_stats.py: error: the following arguments are required: batch.global.stats

Issue - State: closed - Opened by karel-brinda over 1 year ago - 1 comment
Labels: bug

#37 - Add 'make conda' for just building all conda envs

Issue - State: closed - Opened by karel-brinda over 1 year ago

#37 - Add 'make conda' for just building all conda envs

Issue - State: closed - Opened by karel-brinda over 1 year ago

#36 - Update conda, envs, and directories

Pull Request - State: closed - Opened by karel-brinda over 1 year ago