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Modernize conda environment: channels
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- Do not rely on 'defaults' anymore but only 'conda-forge' as per
  bioconda recommendations
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@DrYak
DrYak committed May 27, 2024
1 parent 1652c89 commit 0938ef1
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Showing 31 changed files with 0 additions and 31 deletions.
1 change: 0 additions & 1 deletion workflow/envs/bcftools.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- bcftools = 1.13
- cyvcf2 = 0.30.11
1 change: 0 additions & 1 deletion workflow/envs/bowtie_align.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- bowtie2=2.4.1
- samtools=1.10
1 change: 0 additions & 1 deletion workflow/envs/bwa_QA.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- bwa=0.7.17
- mafft=7.458
1 change: 0 additions & 1 deletion workflow/envs/bwa_align.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- bwa=0.7.17
- samtools=1.10
1 change: 0 additions & 1 deletion workflow/envs/cojac.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- cojac =0.9.1
1 change: 0 additions & 1 deletion workflow/envs/consseq_qa.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- emboss
1 change: 0 additions & 1 deletion workflow/envs/dehuman.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- bwa=0.7.17
- samtools>1.11
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1 change: 0 additions & 1 deletion workflow/envs/diversity_measures.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- python>=3.6
- pyvcf=0.6.8
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1 change: 0 additions & 1 deletion workflow/envs/fastqc.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- fastqc=0.11.9
1 change: 0 additions & 1 deletion workflow/envs/haploclique.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- haploclique=1.3.1
1 change: 0 additions & 1 deletion workflow/envs/hmm_align.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- mafft=7.305
- ngshmmalign=0.1.1
1 change: 0 additions & 1 deletion workflow/envs/initial_vicuna.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- bwa=0.7.17
- samtools=1.10
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1 change: 0 additions & 1 deletion workflow/envs/initial_vicuna_msa.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- mafft=7.458
- smallgenomeutilities=0.3.1
1 change: 0 additions & 1 deletion workflow/envs/lofreq.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- lofreq=2.1.3
- samtools=1.9
1 change: 0 additions & 1 deletion workflow/envs/lollipop.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- lollipop =0.3.0
1 change: 0 additions & 1 deletion workflow/envs/minimap_align.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- minimap2=2.26
- samtools=1.19
1 change: 0 additions & 1 deletion workflow/envs/msa.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- mafft=7.458
1 change: 0 additions & 1 deletion workflow/envs/predicthaplo.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- predicthaplo=2.1.4
- samtools=1.10
1 change: 0 additions & 1 deletion workflow/envs/preprocessing.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- prinseq=0.20.4
1 change: 0 additions & 1 deletion workflow/envs/primerstrim.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- ivar=1.3.1
- samtools>=1.15
1 change: 0 additions & 1 deletion workflow/envs/sam2bam.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- samtools=1.15.1
1 change: 0 additions & 1 deletion workflow/envs/savage.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- picard=2.22.3
- savage=0.4.2
1 change: 0 additions & 1 deletion workflow/envs/simbench.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- art
- python>=3.6
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1 change: 0 additions & 1 deletion workflow/envs/smallgenomeutilities.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- smallgenomeutilities=0.3.9
1 change: 0 additions & 1 deletion workflow/envs/snv.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- shorah=1.99.2
- bcftools=1.10.2
1 change: 0 additions & 1 deletion workflow/envs/sratools.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- sra-tools
- bioawk
1 change: 0 additions & 1 deletion workflow/envs/testbench.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- python>=3.6
- numpy
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1 change: 0 additions & 1 deletion workflow/envs/timeline.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- python
- numpy
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1 change: 0 additions & 1 deletion workflow/envs/upload.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- xxhash
- coreutils # [not linux]
1 change: 0 additions & 1 deletion workflow/envs/visualization.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- pyvcf
- bcbio-gff
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1 change: 0 additions & 1 deletion workflow/envs/xsv.yaml
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channels:
- conda-forge
- bioconda
- defaults
dependencies:
- xsv
- zstd

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