encodedcc/dnase-seq-pipeline:PIP-1482-1483-optional-metrics_dee25dd1-42bc-4262-a47c-a0555d067a81

Manifest digest

sha256:5d3983130a2b6d6b7b47ab9c0c4a0644a74b69dd556863e7ce7fbe6514a2ca3b

OS/ARCH

linux/amd64

Compressed size

1.19 GB

Last pushed

over 5 years by encoderobot

Type

Image

Manifest digest

sha256:5d3983130a2b6d6b7b47ab9c0c4a0644a74b69dd556863e7ce7fbe6514a2ca3b

Image Layers

Image Layers

1ADD file ... in / 25.45 MB

2/bin/sh -c [ -z "$(apt-get34.53 KB

3/bin/sh -c set -xe &&854 B

4/bin/sh -c mkdir -p /run/systemd163 B

5CMD ["/bin/bash"]0 B

6MAINTAINER Otto Jolanki0 B

7ENV DEBIAN_FRONTEND=noninteractive0 B

8/bin/sh -c apt-get update &&451.24 MB

9/bin/sh -c mkdir /software137 B

10WORKDIR /software0 B

11ENV PATH=/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin0 B

12/bin/sh -c wget --quiet https://github.com/samtools/htslib/releases/download/1.10.2/htslib-1.10.2.tar.bz232.76 MB

13/bin/sh -c wget --quiet https://github.com/smithlabcode/preseq/releases/download/v2.0.3/preseq_v2.0.3.tar.bz215.73 MB

14ENV PATH=/software/preseq:/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin0 B

15/bin/sh -c wget --quiet https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz224.65 MB

16/bin/sh -c git clone https://github.com/lh3/bwa.git3.38 MB

17ENV PATH=/software/bwa:/software/preseq:/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin0 B

18/bin/sh -c wget --quiet https://github.com/broadinstitute/picard/releases/download/2.8.1/picard.jar28.68 MB

19/bin/sh -c chmod 755 picard.jar28.68 MB

20/bin/sh -c git clone https://github.com/bedops/bedops.git135.46 MB

21

ENV PATH=/software/bedops/bin:/software/bwa:/software/preseq:/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

0 B

22/bin/sh -c wget --quiet https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz39.47 MB

23

ENV PATH=/software/bedtools2/bin/:/software/bedops/bin:/software/bwa:/software/preseq:/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

0 B

24/bin/sh -c git clone https://github.com/StamLab/hotspot.git28.23 MB

25

ENV PATH=/software/hotspot/hotspot-distr/ScriptTokenizer/src:/software/bedtools2/bin/:/software/bedops/bin:/software/bwa:/software/preseq:/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

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26

ENV PATH=/software/hotspot/hotspot-distr/hotspot-deploy/bin:/software/hotspot/hotspot-distr/ScriptTokenizer/src:/software/bedtools2/bin/:/software/bedops/bin:/software/bwa:/software/preseq:/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

0 B

27ENV HOTSPOT_DIRECTORY=/software/hotspot/hotspot-distr0 B

28/bin/sh -c git clone https://github.com/ENCODE-DCC/kentUtils_bin_v381.git30.69 MB

29

ENV PATH=/software/kentUtils_bin_v381/bin:/software/hotspot/hotspot-distr/hotspot-deploy/bin:/software/hotspot/hotspot-distr/ScriptTokenizer/src:/software/bedtools2/bin/:/software/bedops/bin:/software/bwa:/software/preseq:/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

0 B

30/bin/sh -c git clone https://github.com/StamLab/modwt.git1.04 MB

31

ENV PATH=/software/modwt/bin:/software/kentUtils_bin_v381/bin:/software/hotspot/hotspot-distr/hotspot-deploy/bin:/software/hotspot/hotspot-distr/ScriptTokenizer/src:/software/bedtools2/bin/:/software/bedops/bin:/software/bwa:/software/preseq:/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

0 B

32/bin/sh -c git clone 3.38 MB

33

ENV PATH=/software/hotspot2/bin:/software/modwt/bin:/software/kentUtils_bin_v381/bin:/software/hotspot/hotspot-distr/hotspot-deploy/bin:/software/hotspot/hotspot-distr/ScriptTokenizer/src:/software/bedtools2/bin/:/software/bedops/bin:/software/bwa:/software/preseq:/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

0 B

34

ENV PATH=/software/hotspot2/scripts:/software/hotspot2/bin:/software/modwt/bin:/software/kentUtils_bin_v381/bin:/software/hotspot/hotspot-distr/hotspot-deploy/bin:/software/hotspot/hotspot-distr/ScriptTokenizer/src:/software/bedtools2/bin/:/software/bedops/bin:/software/bwa:/software/preseq:/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

0 B

35/bin/sh -c git clone 724.12 KB

36ENV STAMPIPES=/software/stampipes0 B

37/bin/sh -c pip install 89.5 MB

38/bin/sh -c pip3 install 134.67 MB

39/bin/sh -c pip install 143 MB

40/bin/sh -c apt-get install -y3.55 MB

41/bin/sh -c chmod 755 /software/stampipes/scripts/bwa/bamcounts.py2.36 KB

42/bin/sh -c chmod 755 /software/stampipes/scripts/bwa/aggregate/basic/cutfragments.awk497 B

43/bin/sh -c chmod 755 /software/stampipes/scripts/bam/random_sample.sh676 B

44/bin/sh -c chmod 755 /software/stampipes/scripts/bam/random_sample_read1.sh533 B

45/bin/sh -c chmod 755 /software/stampipes/scripts/SPOT/runhotspot.bash2.09 KB

46/bin/sh -c chmod 755 /software/stampipes/scripts/utility/picard_inserts_process.py1.64 KB

47/bin/sh -c chmod 755 /software/stampipes/scripts/utility/preseq_targets.sh469 B

48/bin/sh -c chmod 755 /software/stampipes/awk/*.awk950 B

49/bin/sh -c chmod 755 /software/stampipes/makefiles/densities/chrombuckets.mk673 B

50

ENV PATH=/software/stampipes/scripts/umi:/software/hotspot2/scripts:/software/hotspot2/bin:/software/modwt/bin:/software/kentUtils_bin_v381/bin:/software/hotspot/hotspot-distr/hotspot-deploy/bin:/software/hotspot/hotspot-distr/ScriptTokenizer/src:/software/bedtools2/bin/:/software/bedops/bin:/software/bwa:/software/preseq:/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

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51

ENV PATH=/software/stampipes/scripts/bwa:/software/stampipes/scripts/umi:/software/hotspot2/scripts:/software/hotspot2/bin:/software/modwt/bin:/software/kentUtils_bin_v381/bin:/software/hotspot/hotspot-distr/hotspot-deploy/bin:/software/hotspot/hotspot-distr/ScriptTokenizer/src:/software/bedtools2/bin/:/software/bedops/bin:/software/bwa:/software/preseq:/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

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52

ENV PATH=/software/stampipes/scripts/bam:/software/stampipes/scripts/bwa:/software/stampipes/scripts/umi:/software/hotspot2/scripts:/software/hotspot2/bin:/software/modwt/bin:/software/kentUtils_bin_v381/bin:/software/hotspot/hotspot-distr/hotspot-deploy/bin:/software/hotspot/hotspot-distr/ScriptTokenizer/src:/software/bedtools2/bin/:/software/bedops/bin:/software/bwa:/software/preseq:/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

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53

ENV PATH=/software/stampipes/scripts/SPOT:/software/stampipes/scripts/bam:/software/stampipes/scripts/bwa:/software/stampipes/scripts/umi:/software/hotspot2/scripts:/software/hotspot2/bin:/software/modwt/bin:/software/kentUtils_bin_v381/bin:/software/hotspot/hotspot-distr/hotspot-deploy/bin:/software/hotspot/hotspot-distr/ScriptTokenizer/src:/software/bedtools2/bin/:/software/bedops/bin:/software/bwa:/software/preseq:/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

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54

ENV PATH=/software/stampipes/scripts/bwa/aggregate/basic:/software/stampipes/scripts/SPOT:/software/stampipes/scripts/bam:/software/stampipes/scripts/bwa:/software/stampipes/scripts/umi:/software/hotspot2/scripts:/software/hotspot2/bin:/software/modwt/bin:/software/kentUtils_bin_v381/bin:/software/hotspot/hotspot-distr/hotspot-deploy/bin:/software/hotspot/hotspot-distr/ScriptTokenizer/src:/software/bedtools2/bin/:/software/bedops/bin:/software/bwa:/software/preseq:/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

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55

ENV PATH=/software/stampipes/scripts/utility:/software/stampipes/scripts/bwa/aggregate/basic:/software/stampipes/scripts/SPOT:/software/stampipes/scripts/bam:/software/stampipes/scripts/bwa:/software/stampipes/scripts/umi:/software/hotspot2/scripts:/software/hotspot2/bin:/software/modwt/bin:/software/kentUtils_bin_v381/bin:/software/hotspot/hotspot-distr/hotspot-deploy/bin:/software/hotspot/hotspot-distr/ScriptTokenizer/src:/software/bedtools2/bin/:/software/bedops/bin:/software/bwa:/software/preseq:/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

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56

ENV PATH=/software/stampipes/awk:/software/stampipes/scripts/utility:/software/stampipes/scripts/bwa/aggregate/basic:/software/stampipes/scripts/SPOT:/software/stampipes/scripts/bam:/software/stampipes/scripts/bwa:/software/stampipes/scripts/umi:/software/hotspot2/scripts:/software/hotspot2/bin:/software/modwt/bin:/software/kentUtils_bin_v381/bin:/software/hotspot/hotspot-distr/hotspot-deploy/bin:/software/hotspot/hotspot-distr/ScriptTokenizer/src:/software/bedtools2/bin/:/software/bedops/bin:/software/bwa:/software/preseq:/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

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57

ENV PATH=/software/stampipes/makefiles/densities:/software/stampipes/awk:/software/stampipes/scripts/utility:/software/stampipes/scripts/bwa/aggregate/basic:/software/stampipes/scripts/SPOT:/software/stampipes/scripts/bam:/software/stampipes/scripts/bwa:/software/stampipes/scripts/umi:/software/hotspot2/scripts:/software/hotspot2/bin:/software/modwt/bin:/software/kentUtils_bin_v381/bin:/software/hotspot/hotspot-distr/hotspot-deploy/bin:/software/hotspot/hotspot-distr/ScriptTokenizer/src:/software/bedtools2/bin/:/software/bedops/bin:/software/bwa:/software/preseq:/software:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

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Command

ADD file:53f100793e6c0adfca99977a42bb65cb7971c26e4d6e4499d1c30a1f51f06854 in /