44 lines
907 B
YAML
44 lines
907 B
YAML
name: epi2melabs-wf-transcriptomes
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channels:
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- epi2melabs
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- conda-forge
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- bioconda
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- defaults
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dependencies:
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- python==3.8.*
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- bokeh==2.4.3
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- aplanat>=0.6.15
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- epi2melabs
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- minimap2==2.24
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- samtools==1.14
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- bedtools==2.30.0
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- pychopper>=2.7.0
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- pandas==1.3.5
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- gffread==0.12.7
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- gffcompare==0.11.2
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- gffutils==0.10.1
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- seqkit==2.2.0
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- stringtie==2.1.1
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- curl
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- pysam==0.17.0
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- racon==1.4.20
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- spoa==3.4.0
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- fastcat==0.4.10
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- isonclust2==2.3
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- parallel
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- scikit-learn==1.0.2
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- natsort
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# Fusion detection dependencies
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# - bpipe=0.9.9.2
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- java-jdk
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- r-base
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- gxx
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# Differential expression dependencies
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- bioconductor-genomicfeatures
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- bioconductor-drimseq
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- bioconductor-edger
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- bioconductor-dexseq
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- bioconductor-stager
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- r-dplyr
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- r-tidyr
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- salmon==1.9.0 |