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https://github.com/YeoLab/containers/blob/88f550d6756fa2c99bfd166d65c3d5e26219147e/images/skipper/bedtools_2.31.0/Dockerfile#L25C33-L25C34
Can we add samtools to this Dockerfile and rebuild the container? We'll need it for this Skipper rule:
rule make_scaled_bigwig: input: CHROM_SIZES, bam = lambda wildcards: replicate_label_to_bams[wildcards.replicate_label], output: bg_plus = temp("output/bedgraphs/scaled/plus/{replicate_label}.scaled.plus.bg"), bg_minus = temp("output/bedgraphs/scaled/minus/{replicate_label}.scaled.minus.bg"), bw_plus = "output/bigwigs/scaled/plus/{replicate_label}.scaled.plus.bw", bw_minus = "output/bigwigs/scaled/minus/{replicate_label}.scaled.minus.bw", params: error_file = "stderr/{replicate_label}.make_bigwig.err", out_file = "stdout/{replicate_label}.make_bigwig.out", run_time = "40:00", memory = "1000", job_name = "make_bigwig" benchmark: "benchmarks/bigwigs/unassigned_experiment.{replicate_label}.make_bigwig.txt" container: "docker://howardxu520/skipper:bedtools_2.31.0" shell: "factor=$(samtools idxstats {input.bam} | awk '{{sum += $3}} END {{print 10**6 / sum}}');" "bedtools genomecov -scale $factor -split -strand + -bg -ibam {input.bam} | sort -k1,1 -k2,2n | grep -v EBV > {output.bg_plus};" "bedtools genomecov -scale $factor -split -strand - -bg -ibam {input.bam} | sort -k1,1 -k2,2n | grep -v EBV > {output.bg_minus};" "{TOOL_DIR}/bedGraphToBigWig {output.bg_plus} {CHROM_SIZES} {output.bw_plus};" "{TOOL_DIR}/bedGraphToBigWig {output.bg_minus} {CHROM_SIZES} {output.bw_minus};"
The text was updated successfully, but these errors were encountered:
howardxu520
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https://github.com/YeoLab/containers/blob/88f550d6756fa2c99bfd166d65c3d5e26219147e/images/skipper/bedtools_2.31.0/Dockerfile#L25C33-L25C34
Can we add samtools to this Dockerfile and rebuild the container? We'll need it for this Skipper rule:
The text was updated successfully, but these errors were encountered: