add recipe for EToKi

Open rpetit3 opened this issue 1 year ago • 2 comments

This PR adds EToKi, a toolkit used by Enterobase

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Sep 21 '22 18:09 rpetit3

@BiocondaBot please fetch artifacts

Sep 21 '22 19:09 rpetit3

Package(s) built on Azure are ready for inspection:

Arch	Package	Zip File
noarch	etoki-1.2.2-hdfd78af_0.tar.bz2	LinuxArtifacts

You may also use conda to install these after downloading and extracting the appropriate zip file. From the LinuxArtifacts or OSXArtifacts directories:

conda install -c packages <package name>

Docker image(s) built (images are in the LinuxArtifacts zip file above):

Package	Tag	Install with `docker`
etoki	1.2.2--hdfd78af_0	show `gzip -dc LinuxArtifacts/images/etoki:1.2.2--hdfd78af_0.tar.gz \| docker load`

Sep 21 '22 19:09 BiocondaBot

@BiocondaBot please fetch artifacts

Sep 26 '22 17:09 rpetit3

Package(s) built on Azure are ready for inspection:

Arch	Package	Zip File
noarch	etoki-1.2.2-hdfd78af_0.tar.bz2	LinuxArtifacts

You may also use conda to install these after downloading and extracting the appropriate zip file. From the LinuxArtifacts or OSXArtifacts directories:

conda install -c packages <package name>

Docker image(s) built (images are in the LinuxArtifacts zip file above):

Package	Tag	Install with `docker`
etoki	1.2.2--hdfd78af_0	show `gzip -dc LinuxArtifacts/images/etoki:1.2.2--hdfd78af_0.tar.gz \| docker load`

Sep 26 '22 18:09 BiocondaBot

@BiocondaBot please update

Sep 27 '22 17:09 rpetit3

@BiocondaBot please fetch artifacts

Sep 27 '22 18:09 rpetit3

Package(s) built on Azure are ready for inspection:

Arch	Package	Zip File
noarch	etoki-1.2.2-hdfd78af_0.tar.bz2	LinuxArtifacts

You may also use conda to install these after downloading and extracting the appropriate zip file. From the LinuxArtifacts or OSXArtifacts directories:

conda install -c packages <package name>

Docker image(s) built (images are in the LinuxArtifacts zip file above):

Package	Tag	Install with `docker`
etoki	1.2.2--hdfd78af_0	show `gzip -dc LinuxArtifacts/images/etoki:1.2.2--hdfd78af_0.tar.gz \| docker load`

Sep 27 '22 18:09 BiocondaBot

Testing

Conda

Build env

mamba clean -ay
mamba create -y -n test-etoki -c conda-forge -c bioconda \
    bbmap blast bowtie2 bwa click curl diamond ete3 fasttree flye \
    gatk kraken2 last megahit mmseqs2 nextpolish numba 'numpy==1.21.6' \
    pandas perl-lyve-set piler-cr pilon psutil 'python>=3.6' rapidnj \
    raxml raxml-ng samtools scikit-learn scipy simbac 'spades>=3.15' trf
conda activate test-etoki
unzip LinuxArtifacts.zip
conda install LinuxArtifacts/packages/noarch/etoki-1.2.2-hdfd78af_0.tar.bz2

Basic Usage

EToKi.py
usage: EToKi [-h] {configure,prepare,assemble,MLSTdb,MLSType,MLSTsum,cgMLST,align,phylo,EBEis,uberBlast,clust,isCRISPOL} ...

options:
  -h, --help            show this help message and exit

sub-commands:
  {configure,prepare,assemble,MLSTdb,MLSType,MLSTsum,cgMLST,align,phylo,EBEis,uberBlast,clust,isCRISPOL}
    configure           install and/or configure 3rd party programs
    prepare             trim, collapse, downsize and rename the short reads.
    assemble            de novo or reference-guided assembly for genomic or metagenomic reads
    MLSTdb              Set up exemplar alleles and database for MLST schemes
    MLSType             MLST nomenclature using a local set of references
    MLSTsum             Summarise MLSType results and assign new allele designations
    cgMLST              Select a list of genes for the cgMLST scheme
    align               align multiple queried genomes to a single reference
    phylo               infer phylogeny and ancestral states from genomic alignments
    EBEis               in silico serotype prediction for Escherichia coli and Shigella spp.
    uberBlast           Use Blastn, uBlastp, minimap2 and/or mmseqs to identify similar sequences
    clust               linear-time clustering of short sequences using mmseqs linclust
    isCRISPOL           in silico prediction of CRISPOL array for Salmonella enterica serovar Typhimurium

EToKi.py configure --help
usage: EToKi.py configure [-h] [--install] [--usearch USEARCH] [--download_krakenDB] [--link_krakenDB KRAKEN_DATABASE] [--path PATH]

Install or modify the 3rd party programs.

options:
  -h, --help            show this help message and exit
  --install             install 3rd party programs
  --usearch USEARCH     usearch is required for ortho and MLSType. A 32-bit version of usearch can be downloaded from https://www.drive5.com/usearch/
  --download_krakenDB   When specified, miniKraken2 (8GB) will be downloaded into the EToKi folder. You can also use --link_krakenDB to use a pre-installed kraken2 database.
  --link_krakenDB KRAKEN_DATABASE
                        Kraken is optional in the assemble module. You can specify your own database here
  --path PATH, -p PATH  Specify path to the 3rd party programs manually. Format: <program>=<path>. This parameter can be specified multiple times

Test default `EToKi.py configure`

2022-09-26 18:15:12.122535      bbduk ("/home/robert_petit/miniconda3/envs/test-etoki/bin/bbduk.sh") is present.
2022-09-26 18:15:12.130839      bbmerge ("/home/robert_petit/miniconda3/envs/test-etoki/bin/bbmerge.sh") is present.
2022-09-26 18:15:12.181474      blastn ("/home/robert_petit/miniconda3/envs/test-etoki/bin/blastn") is present.
2022-09-26 18:15:12.230572      blastp ("/home/robert_petit/miniconda3/envs/test-etoki/bin/blastp") is present.
2022-09-26 18:15:12.271949      bowtie2 ("/home/robert_petit/miniconda3/envs/test-etoki/bin/bowtie2") is present.
2022-09-26 18:15:12.318620      bowtie2build ("/home/robert_petit/miniconda3/envs/test-etoki/bin/bowtie2-build") is present.
2022-09-26 18:15:12.319847      bwa ("/home/robert_petit/miniconda3/envs/test-etoki/bin/bwa") is present.
2022-09-26 18:15:12.323165      diamond ("/home/robert_petit/miniconda3/envs/test-etoki/bin/diamond") is present.
2022-09-26 18:15:12.324410      fasttree ("/home/robert_petit/miniconda3/envs/test-etoki/bin/FastTreeMP") is present.
2022-09-26 18:15:12.408020      flye ("/home/robert_petit/miniconda3/envs/test-etoki/bin/flye") is present.
2022-09-26 18:15:12.427521      kraken2 ("/home/robert_petit/miniconda3/envs/test-etoki/bin/kraken2") is present.
2022-09-26 18:15:12.429789      lastal ("/home/robert_petit/miniconda3/envs/test-etoki/bin/lastal") is present.
2022-09-26 18:15:12.431609      lastdb ("/home/robert_petit/miniconda3/envs/test-etoki/bin/lastdb") is present.
2022-09-26 18:15:12.468261      makeblastdb ("/home/robert_petit/miniconda3/envs/test-etoki/bin/makeblastdb") is present.
2022-09-26 18:15:12.523270      megahit ("/home/robert_petit/miniconda3/envs/test-etoki/bin/megahit") is present.
2022-09-26 18:15:12.524415      minimap2 ("/home/robert_petit/miniconda3/envs/test-etoki/bin/minimap2") is present.
2022-09-26 18:15:12.527355      mmseqs ("/home/robert_petit/miniconda3/envs/test-etoki/bin/mmseqs") is present.
2022-09-26 18:15:12.588233      nextpolish ("/home/robert_petit/miniconda3/envs/test-etoki/bin/nextPolish") is present.
2022-09-26 18:15:12.590044      pilercr ("/home/robert_petit/miniconda3/envs/test-etoki/bin/pilercr") is present.
2022-09-26 18:15:12.882437      pilon ("/home/robert_petit/miniconda3/envs/test-etoki/share/pilon-1.24-0/pilon.jar") is present.
2022-09-26 18:15:12.884557      rapidnj ("/home/robert_petit/miniconda3/envs/test-etoki/bin/rapidnj") is present.
2022-09-26 18:15:12.886008      raxml ("/home/robert_petit/miniconda3/envs/test-etoki/bin/raxmlHPC") is present.
2022-09-26 18:15:12.888998      raxml_ng ("/home/robert_petit/miniconda3/envs/test-etoki/bin/raxml-ng") is present.
2022-09-26 18:15:12.896088      repair ("/home/robert_petit/miniconda3/envs/test-etoki/bin/repair.sh") is present.
2022-09-26 18:15:12.899773      samtools ("/home/robert_petit/miniconda3/envs/test-etoki/bin/samtools") is present.
2022-09-26 18:15:13.134708      spades ("/home/robert_petit/miniconda3/envs/test-etoki/bin/spades.py") is present.
2022-09-26 18:15:13.135828      trf ("/home/robert_petit/miniconda3/envs/test-etoki/bin/trf") is present.
2022-09-26 18:15:13.184846      usearch ("/home/robert_petit/miniconda3/envs/test-etoki/bin/blastp") is present.
2022-09-26 18:15:13.184928      WARNING - kraken_database is not present.
You can still use EToKi except the parameter "--kraken" in EToKi assemble will not work.
Alternatively you can download minikraken2 database using --download_krakenDB or pass an pre-installed database into EToKi using --link_krakenDB.
2022-09-26 18:15:13.186703      Configuration complete.

Looks good! Default paths are set

Try with examples from dev repo

Only showing outputs from a few commands

git clone [email protected]:zheminzhou/EToKi.git
cd EToKi/

EToKi.py prepare --pe examples/S_R1.fastq.gz,examples/S_R2.fastq.gz -p examples/prep_out
2022-09-26 18:22:07.954048      Load in 2 read files from 1 libraries
2022-09-26 18:22:09.839308      Obtained 3850621 bases in 21912 reads after Trimming in Lib 0
2022-09-26 18:22:09.948902      Remove potential barcode bases at the beginning 10 bps of reads in examples/prep_out.1.0.s.fastq.gz
--pe examples/prep_out_L1_R1.fastq.gz,examples/prep_out_L1_R2.fastq.gz --se examples/prep_out_L1_SE.fastq.gz

EToKi.py MLSTdb -i examples/Escherichia.Achtman.alleles.fasta -r examples/Escherichia.Achtman.references.fasta -d examples/Escherichia.Achtman.convert.tab
Invalid database read for database data file=./NS_j03nqo1o/seq.db_h, database index=./NS_j03nqo1o/seq.db_h.index
getData: local id (4294967295) >= db size (972)
2022-09-27 18:34:52.581666      Exemplar sequences in ./NS_srhxkr7h/clsFna.clust.exemplar
2022-09-27 18:34:52.581724      Clusters in ./NS_srhxkr7h/clsFna.clust.tab
2022-09-27 18:34:52.607550      Run BLASTn starts
2022-09-27 18:34:52.915525      Run BLASTn finishes. Got 970 alignments
2022-09-27 18:34:52.915681      Run diamond starts
2022-09-27 18:34:53.843997      Run diamond finishes. Got 967 alignments
2022-09-27 18:34:54.022393      removed 0 paralogous sites.
2022-09-27 18:34:54.022473      obtained 5530 alleles and 38 references alleles
2022-09-27 18:34:54.024636      A file of reference alleles has been generated:  examples/Escherichia.Achtman.references.fasta
2022-09-27 18:34:54.062641      A lookup table of all alleles has been generated:  examples/Escherichia.Achtman.convert.tab

EToKi.py clust -p examples/Escherichia.Achtman.alleles_clust -i examples/Escherichia.Achtman.alleles.fasta -d 0.95 -c 0.95
2022-09-27 18:36:07.622716      Exemplar sequences in examples/Escherichia.Achtman.alleles_clust.clust.exemplar
2022-09-27 18:36:07.622781      Clusters in examples/Escherichia.Achtman.alleles_clust.clust.tab

EToKi.py align -r GCF_000010485:examples/GCF_000010485.1_ASM1048v1_genomic.fna.gz -p examples/phylo_out \
> GCF_000005845:examples/GCF_000005845.2_ASM584v2_genomic.fna.gz \
> GCF_000214765:examples/GCF_000214765.2_ASM21476v3_genomic.fna.gz \
> GCF_001566635:examples/GCF_001566635.1_ASM156663v1_genomic.fna.gz
## Repetitive 99095
## 1 114832
## 2 149633
## 3 631841
# 4 3844282
{
  "low_qual_map": {},
  "mappings": {
    "GCF_000005845": "examples/phylo_out.GCF_000005845.1.gff.gz",
    "GCF_000010485": "examples/phylo_out.GCF_000010485.0.gff.gz",
    "GCF_000214765": "examples/phylo_out.GCF_000214765.2.gff.gz",
    "GCF_001566635": "examples/phylo_out.GCF_001566635.3.gff.gz"
  },
  "matrix": "examples/phylo_out.matrix.gz"
}

Everything looks good, now try with Docker

Docker

gzip -dc LinuxArtifacts/images/etoki:1.2.2--hdfd78af_0.tar.gz | docker load

Basic Usage

docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data quay.io/biocontainers/etoki:1.2.2--hdfd78af_0 EToKi.py
usage: EToKi [-h]
             {configure,prepare,assemble,MLSTdb,MLSType,MLSTsum,cgMLST,align,phylo,EBEis,uberBlast,clust,isCRISPOL}
             ...

options:
  -h, --help            show this help message and exit

sub-commands:
  {configure,prepare,assemble,MLSTdb,MLSType,MLSTsum,cgMLST,align,phylo,EBEis,uberBlast,clust,isCRISPOL}
    configure           install and/or configure 3rd party programs
    prepare             trim, collapse, downsize and rename the short reads.
    assemble            de novo or reference-guided assembly for genomic or
                        metagenomic reads
    MLSTdb              Set up exemplar alleles and database for MLST schemes
    MLSType             MLST nomenclature using a local set of references
    MLSTsum             Summarise MLSType results and assign new allele
                        designations
    cgMLST              Select a list of genes for the cgMLST scheme
    align               align multiple queried genomes to a single reference
    phylo               infer phylogeny and ancestral states from genomic
                        alignments
    EBEis               in silico serotype prediction for Escherichia coli and
                        Shigella spp.
    uberBlast           Use Blastn, uBlastp, minimap2 and/or mmseqs to
                        identify similar sequences
    clust               linear-time clustering of short sequences using mmseqs
                        linclust
    isCRISPOL           in silico prediction of CRISPOL array for Salmonella
                        enterica serovar Typhimurium

docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data quay.io/biocontainers/etoki:1.2.2--hdfd78af_0 EToKi.py configure
2022-09-27 18:40:08.875129      bbduk ("/usr/local/bin/bbduk.sh") is present.
2022-09-27 18:40:08.883779      bbmerge ("/usr/local/bin/bbmerge.sh") is present.
2022-09-27 18:40:08.936761      blastn ("/usr/local/bin/blastn") is present.
2022-09-27 18:40:08.982669      blastp ("/usr/local/bin/blastp") is present.
2022-09-27 18:40:09.029808      bowtie2 ("/usr/local/bin/bowtie2") is present.
2022-09-27 18:40:09.081023      bowtie2build ("/usr/local/bin/bowtie2-build") is present.
2022-09-27 18:40:09.082426      bwa ("/usr/local/bin/bwa") is present.
2022-09-27 18:40:09.086746      diamond ("/usr/local/bin/diamond") is present.
2022-09-27 18:40:09.088070      fasttree ("/usr/local/bin/FastTreeMP") is present.
2022-09-27 18:40:09.176993      flye ("/usr/local/bin/flye") is present.
2022-09-27 18:40:09.197672      kraken2 ("/usr/local/bin/kraken2") is present.
2022-09-27 18:40:09.200008      lastal ("/usr/local/bin/lastal") is present.
2022-09-27 18:40:09.202053      lastdb ("/usr/local/bin/lastdb") is present.
2022-09-27 18:40:09.236770      makeblastdb ("/usr/local/bin/makeblastdb") is present.
2022-09-27 18:40:09.296714      megahit ("/usr/local/bin/megahit") is present.
2022-09-27 18:40:09.298093      minimap2 ("/usr/local/bin/minimap2") is present.
2022-09-27 18:40:09.301458      mmseqs ("/usr/local/bin/mmseqs") is present.
2022-09-27 18:40:09.369408      nextpolish ("/usr/local/bin/nextPolish") is present.
2022-09-27 18:40:09.371536      pilercr ("/usr/local/bin/pilercr") is present.
2022-09-27 18:40:09.375018      ERROR - pilon ("/usr/local/share/pilon-1.24-0/pilon.jar") is not present.
2022-09-27 18:40:09.377006      rapidnj ("/usr/local/bin/rapidnj") is present.
2022-09-27 18:40:09.378588      raxml ("/usr/local/bin/raxmlHPC") is present.
2022-09-27 18:40:09.382549      raxml_ng ("/usr/local/bin/raxml-ng") is present.
2022-09-27 18:40:09.390484      repair ("/usr/local/bin/repair.sh") is present.
2022-09-27 18:40:09.392758      samtools ("/usr/local/bin/samtools") is present.
2022-09-27 18:40:09.665679      spades ("/usr/local/bin/spades.py") is present.
2022-09-27 18:40:09.666908      trf ("/usr/local/bin/trf") is present.
2022-09-27 18:40:09.714822      usearch ("/usr/local/bin/blastp") is present.
2022-09-27 18:40:09.714931      WARNING - kraken_database is not present.
You can still use EToKi except the parameter "--kraken" in EToKi assemble will not work.
Alternatively you can download minikraken2 database using --download_krakenDB or pass an pre-installed database into EToKi using --link_krakenDB.
Traceback (most recent call last):
  File "/usr/local/bin/EToKi.py", line 49, in <module>
    etoki()
  File "/usr/local/bin/EToKi.py", line 43, in etoki
    eval(arg.cmd)(sys.argv[2:])
  File "/usr/local/share/etoki-1.2.2/modules/configure.py", line 424, in configure
    write_configure(configs)
  File "/usr/local/share/etoki-1.2.2/modules/configure.py", line 460, in write_configure
    pd.DataFrame(configs).to_csv(EnConf_file, sep='=', index=False, header=False)
  File "/usr/local/lib/python3.10/site-packages/pandas/util/_decorators.py", line 211, in wrapper
    return func(*args, **kwargs)
  File "/usr/local/lib/python3.10/site-packages/pandas/core/generic.py", line 3721, in to_csv
    return DataFrameRenderer(formatter).to_csv(
  File "/usr/local/lib/python3.10/site-packages/pandas/util/_decorators.py", line 211, in wrapper
    return func(*args, **kwargs)
  File "/usr/local/lib/python3.10/site-packages/pandas/io/formats/format.py", line 1189, in to_csv
    csv_formatter.save()
  File "/usr/local/lib/python3.10/site-packages/pandas/io/formats/csvs.py", line 241, in save
    with get_handle(
  File "/usr/local/lib/python3.10/site-packages/pandas/io/common.py", line 857, in get_handle
    handle = open(
PermissionError: [Errno 13] Permission denied: '/usr/local/share/etoki-1.2.2/modules/configure.ini'

This error is ok, since the dependencies are already set.

Try with examples from dev repo

Only showing outputs from a few commands

git clone [email protected]:zheminzhou/EToKi.git
cd EToKi/

docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data quay.io/biocontainers/etoki:1.2.2--hdfd78af_0 EToKi.py prepare --pe /data/examples/S_R1.fastq.gz,/data/examples/S_R2.fastq.gz -p /data/examples/prep_out
2022-09-27 18:50:08.661691      Load in 2 read files from 1 libraries
2022-09-27 18:50:08.874634      Obtained 3868631 bases in 22002 reads after Trimming in Lib 0
--pe /data/examples/prep_out_L1_R1.fastq.gz,/data/examples/prep_out_L1_R2.fastq.gz

docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data quay.io/biocontainers/etoki:1.2.2--hdfd78af_0 EToKi.py MLSTdb -i /data/examples/Escherichia.Achtman.alleles.fasta -r /data/examples/Escherichia.Achtman.references.fasta -d /data/examples/Escherichia.Achtman.convert.tab
Traceback (most recent call last):
  File "/usr/local/bin/EToKi.py", line 49, in <module>
    etoki()
  File "/usr/local/bin/EToKi.py", line 43, in etoki
    eval(arg.cmd)(sys.argv[2:])
  File "/usr/local/share/etoki-1.2.2/modules/MLSTdb.py", line 177, in MLSTdb
    allele_text, refAlleles = buildReference(alleles, references, max_iden, min_iden, coverage, paralog, relaxEnd)
  File "/usr/local/share/etoki-1.2.2/modules/MLSTdb.py", line 55, in buildReference
    with tempfile.TemporaryDirectory(prefix='NS_', dir='.') as dirPath :
  File "/usr/local/lib/python3.10/tempfile.py", line 819, in __init__
    self.name = mkdtemp(suffix, prefix, dir)
  File "/usr/local/lib/python3.10/tempfile.py", line 368, in mkdtemp
    _os.mkdir(file, 0o700)
PermissionError: [Errno 13] Permission denied: './NS__njmbfw5'

So close, will need to patch it.

Sep 27 '22 18:09 rpetit3

@BiocondaBot please fetch artifacts

Sep 27 '22 19:09 rpetit3

Package(s) built on Azure are ready for inspection:

Arch	Package	Zip File
noarch	etoki-1.2.3-hdfd78af_0.tar.bz2	LinuxArtifacts

You may also use conda to install these after downloading and extracting the appropriate zip file. From the LinuxArtifacts or OSXArtifacts directories:

conda install -c packages <package name>

Docker image(s) built (images are in the LinuxArtifacts zip file above):

Package	Tag	Install with `docker`
etoki	1.2.3--hdfd78af_0	show `gzip -dc LinuxArtifacts/images/etoki:1.2.3--hdfd78af_0.tar.gz \| docker load`

Sep 27 '22 19:09 BiocondaBot

@BiocondaBot please fetch artifacts

Sep 27 '22 21:09 rpetit3

Package(s) built on Azure are ready for inspection:

Arch	Package	Zip File
noarch	etoki-1.2.3-hdfd78af_0.tar.bz2	LinuxArtifacts

You may also use conda to install these after downloading and extracting the appropriate zip file. From the LinuxArtifacts or OSXArtifacts directories:

conda install -c packages <package name>

Docker image(s) built (images are in the LinuxArtifacts zip file above):

Package	Tag	Install with `docker`
etoki	1.2.3--hdfd78af_0	show `gzip -dc LinuxArtifacts/images/etoki:1.2.3--hdfd78af_0.tar.gz \| docker load`

Sep 27 '22 21:09 BiocondaBot

docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data quay.io/biocontainers/etoki:1.2.3--hdfd78af_0 EToKi.py MLSTdb -i /data/examples/Escherichia.Achtman.alleles.fasta -r /data/examples/Escherichia.Achtman.references.fasta -d /data/examples/Escherichia.Achtman.convert.tab
Invalid database read for database data file=/tmp/NS_t90lh45n/seq.db_h, database index=/tmp/NS_t90lh45n/seq.db_h.index
getData: local id (4294967295) >= db size (972)
2022-09-27 21:33:29.741924      Exemplar sequences in /tmp/NS_o696dkdz/clsFna.clust.exemplar
2022-09-27 21:33:29.741994      Clusters in /tmp/NS_o696dkdz/clsFna.clust.tab
2022-09-27 21:33:29.773625      Run BLASTn starts
2022-09-27 21:33:30.044658      Run BLASTn finishes. Got 970 alignments
2022-09-27 21:33:30.044811      Run diamond starts
2022-09-27 21:33:30.968038      Run diamond finishes. Got 967 alignments
2022-09-27 21:33:31.149411      removed 0 paralogous sites.
2022-09-27 21:33:31.149483      obtained 5530 alleles and 38 references alleles
2022-09-27 21:33:31.151609      A file of reference alleles has been generated:  /data/examples/Escherichia.Achtman.references.fasta
2022-09-27 21:33:31.190645      A lookup table of all alleles has been generated:  /data/examples/Escherichia.Achtman.convert.tab

We are good to go now

Sep 27 '22 21:09 rpetit3

@BiocondaBot please add label

Sep 27 '22 21:09 rpetit3

@BiocondaBot please merge

Sep 27 '22 21:09 dpryan79

I will attempt to upload artifacts and merge this PR. This may take some time, please have patience.

Sep 27 '22 21:09 BiocondaBot

Thank you!

Sep 27 '22 21:09 rpetit3

bioconda-recipes bioconda-recipes copied to clipboard

add recipe for EToKi

Testing

Conda

Build env

Basic Usage

Test default EToKi.py configure

Try with examples from dev repo

Docker

Basic Usage

Try with examples from dev repo

bioconda-recipes
bioconda-recipes copied to clipboard

Test default `EToKi.py configure`