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Dev #12

Merged
merged 103 commits into from
Apr 26, 2021
Merged

Dev #12

merged 103 commits into from
Apr 26, 2021

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ABignaud
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New version of metaTOR in python3.

js2264 and others added 30 commits September 19, 2020 22:53
@js2264
add encoding=None to genfromtxt
647410e
@js2264
changed hmm databases to essential.hmm from MadsAlbertsen
a79ac48
@js2264
Update metator.sh
c21ad95
@js2264
stop drawing matrices
bd69e3d
@js2264
hamming distance matrix in python
e2e25b7
@js2264
list pigz as dependencies in README
aae949b
@js2264
removed lfs hmm_databases
eee8dc9
@js2264
Add multithread support in hamming.py
a4f4d97
@js2264
specify gawk rather than awk
1596e63
@js2264
added Singularity def file
632a2e2
hamming as separate step of metator pipeline
293b7eb
also create contigs and CC info files when running metator matrix
463eb1d
changed path to assembly to use size_contig_threshold
679fdf4
@js2264
add metaphlan dependency
228e3d5
@js2264
Merge branch 'master' of https://github.com/js2264/metaTOR into master
f7001e1
remove matrix computing when partitioning
2ccea7b
@js2264
do not build metaphlan indices
1eeff47
@js2264
Merge branch 'master' of https://github.com/js2264/metaTOR into master
ff63232
@js2264
cleaned up matrix computing
3191932
fix space when pasting all iterations
097c9b8
Merge with js2264 fork
e2ecff1
@ABignaud
Add sklearn in the requirements and black formatting
713330a
@ABignaud
Change the setup to use python script instead of shell script for the…
b82acf2 
… alignment.
@ABignaud
Add docopt in the requirements
ee2c176
@ABignaud
Add default parameters for the align class
c8e6d0b
@ABignaud
Add default parameters for the network class
9d0585a
@ABignaud
Add the partition class in python
1ea5217
@ABignaud
Remove HMM database.
9a45f98
@ABignaud
Add commentaries for the partition functions
7d0c945
@ABignaud
Add a size threshold of the save community
0e028c1
@ABignaud
Add header in the contigs data file.
3e624a2
@ABignaud
Add a sanity check if fasta folder already existed
9241fe3
@ABignaud
Update pipeline module to work with new modules.
076d8ea
@ABignaud
Update test_command tests and correct minor bugs.
b5f352f
@ABignaud
Add test on the recursif partition and correct minor bugs.
7db50aa
@ABignaud
Add compare bins in validation module test.
0522095
@ABignaud
Remove useless functions in network module.
9e17eac
@ABignaud
Remove slower python implementations of louvain and leiden in partiti…
31d3f79 
…on module.
@ABignaud
Raise Error if Louvain cpp not found as Louvain python has been removed.
fe1f241
@ABignaud
Correct the documentation.
792899b
@ABignaud
Remove RS_length normalization.
7f7c447
@ABignaud
Remove developpment profiler.
94c8098
@ABignaud
Add no clean-up in the validation module.
8bdd928
@ABignaud
Skip index generation if bam start in the network module.
dfc04b0
@ABignaud
Remove compute_contig_coverage function which it's not use anymore.
f855290
@ABignaud
Add the total size of the extractedbins in the information returning …
8f5eba4 
…by the pipeline.
@ABignaud
Update pip requirements.
4fce908
@ABignaud
Remove manual and Singularity file installation.
47fe17f
@ABignaud
Update the Dockerfile for the neversion of metator.
6dc3c34
@ABignaud
Update README.
90bc789
@ABignaud
Add github actions to deploy and build.
f3de151
@ABignaud
Remove tutorial temporarily.
c573fee
@ABignaud
Add test on all branch using github action.
a985578
@ABignaud
Correct typo in the yaml test file.
1bb2060
@ABignaud
Add requests in requirements.txt.
5382bee
@ABignaud
Github action: install with apt and not with conda.
3391e34
@ABignaud
Update alignment files for the github action test and remove travis f…
a78dd8c 
…ile.
@ABignaud ABignaud requested a review from cmdoret April 26, 2021 07:19
@cmdoret cmdoret merged commit e815e72 into master Apr 26, 2021
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@cmdoret cmdoret Awaiting requested review from cmdoret

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3 participants
@ABignaud @cmdoret @js2264