Collection of Dockerfiles
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Collection of Dockerfiles
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};"
@byee4 can you try changing this line
to this:
FROM jupyter/datascience-notebook:hub-2.0.2
This will match the JupyterHub version that's running. Thanks
When you've pushed the new image to brianyee/seurat:latest
I'll retest launching it.
Hi Brian, I'm having issues with RUN mamba install -y -c bioconda -c conda-forge --file /tmp/conda-packages.txt
in the docker file. Now I'm just using a copy of deseq2/1.39's files and only added one line in conda-packages.txt
file, bioconductor-ensdb.hsapiens.v79
.
But when I try to build it, I always encounter issues with the error below:
(base) shuhaoxu@Shuhaos-MBP 1.39.3 % docker build -t deseq2/1.39.3 .
[+] Building 617.1s (10/12)
=> [internal] load .dockerignore 0.0s
=> => transferring context: 2B 0.0s
=> [internal] load build definition from Dockerfile 0.0s
=> => transferring dockerfile: 1.62kB 0.0s
=> [internal] load metadata for docker.io/jupyter/datascience-notebook:hub-2.2.2 1.1s
=> [auth] jupyter/datascience-notebook:pull token for registry-1.docker.io 0.0s
=> [1/7] FROM docker.io/jupyter/datascience-notebook:hub-2.2.2@sha256:f5984966ed1024e70369860 0.0s
=> [internal] load build context 0.0s
=> => transferring context: 825B 0.0s
=> CACHED [2/7] COPY apt-packages.txt /tmp/apt-packages.txt 0.0s
=> [3/7] COPY conda-packages.txt /tmp/conda-packages.txt 0.0s
=> [4/7] RUN apt-get update && xargs apt-get install -y < /tmp/apt-packages.txt 231.7s
=> ERROR [5/7] RUN mamba install -y -c bioconda -c conda-forge --file /tmp/conda-packages.t 384.7s
------
> [5/7] RUN mamba install -y -c bioconda -c conda-forge --file /tmp/conda-packages.txt:
------
Dockerfile:26
--------------------
24 |
25 | # Install additional R packages from conda-forge using mamba
26 | >>> RUN mamba install -y -c bioconda -c conda-forge --file /tmp/conda-packages.txt
27 |
28 | RUN Rscript -e 'install.packages("devtools", repos = "https://cran.us.r-project.org")'
--------------------
ERROR: failed to solve: process "/bin/bash -o pipefail -c mamba install -y -c bioconda -c conda-forge --file /tmp/conda-packages.txt" did not complete successfully: exit code: 137
I also tried to just switch using mamda
to conda
, which did not work neither.
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