mgibio/cle:bam_readcount

Machine learning & AI

Data science

Manifest digest

sha256:db9ac62afcc2bfaff1720b68c47a261e2c69cc6cc3c94d959e4c6c8e1e645cb7

OS/ARCH

linux/amd64

Compressed size

2.18 GB

Last pushed

about 8 years by mgibio

Type

Image

Manifest digest

sha256:db9ac62afcc2bfaff1720b68c47a261e2c69cc6cc3c94d959e4c6c8e1e645cb7

Image Layers

Image Layers

1ADD file ... in / 41.12 MB

2/bin/sh -c set -xe &&853 B

3/bin/sh -c rm -rf /var/lib/apt/lists/*619 B

4/bin/sh -c sed -i 's/^#\s*$deb.*universe$$/\1/g'851 B

5/bin/sh -c mkdir -p /run/systemd168 B

6CMD ["/bin/bash"]0 B

7MAINTAINER Susanna Kiwala <[email protected]>0 B

8LABEL description=Image for tools0 B

9/bin/sh -c apt-get update -y581.76 MB

10/bin/sh -c apt-get update -y1.63 MB

11/bin/sh -c pip install --upgrade3.4 MB

12/bin/sh -c ln -s /usr/bin/unzip125 B

13/bin/sh -c cd /tmp/ 11.41 MB

14ENV maven_package_name=apache-maven-3.3.90 B

15ENV gatk_dir_name=gatk-protected0 B

16ENV gatk_version=3.60 B

17/bin/sh -c cd /tmp/ &&8.12 MB

18/bin/sh -c cd /tmp/ 620.61 MB

19/bin/sh -c cd /opt/ &&80.47 MB

20ENV STRELKA_INSTALL_DIR=/opt/strelka/0 B

21/bin/sh -c wget https://github.com/Illumina/strelka/releases/download/v2.7.1/strelka-2.7.1.centos5_x86_64.tar.bz2 51.77 MB

22COPY file:4eb9da6f1e92d57339a950925148278aeb2bc2311f5f6056a8c7354ab6f3fbf6 in /usr/bin/strelka_helper.pl 527 B

23COPY file:4f299ab48bca7664c4ef4eee8079d94dd339361986104ab9297e2c1a6d60f631 in /usr/bin/add_strelka_gt.pl 1.26 KB

24ENV VARSCAN_INSTALL_DIR=/opt/varscan0 B

25WORKDIR /opt/varscan114 B

26/bin/sh -c wget https://github.com/dkoboldt/varscan/releases/download/2.4.2/VarScan.v2.4.2.jar &&111.46 KB

27COPY file:5c2f6d8f8546bfef82dbb9a4d191450f9e4b25fc5a2ed71bb7f6496530f70b13 in /usr/bin/intervals_to_bed.pl 317 B

28COPY file:b7e46791d8dec9de441e5d7e4df7a85ab57a7db2f69d1458d5f50c256d6cf70f in /usr/bin/varscan_helper.sh 606 B

29COPY file:59a94ad94d76c3ab9025a56da68bd4a5f89f1aaae4cceec2b1a9d68fab4f4950 in /usr/bin/varscan_germline_helper.sh 706 B

30ENV HTSLIB_INSTALL_DIR=/opt/htslib0 B

31WORKDIR /tmp0 B

32/bin/sh -c wget https://github.com/samtools/htslib/releases/download/1.3.2/htslib-1.3.2.tar.bz2 &&1.98 MB

33WORKDIR /tmp/htslib-1.3.20 B

34/bin/sh -c ./configure --enable-plugins18.55 MB

35ENV SAMTOOLS_INSTALL_DIR=/opt/samtools0 B

36WORKDIR /tmp0 B

37/bin/sh -c wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 &&8.45 MB

38WORKDIR /tmp/samtools-1.3.10 B

39/bin/sh -c ./configure --with-htslib=$HTSLIB_INSTALL_DIR --prefix=$SAMTOOLS_INSTALL_DIR3.51 MB

40WORKDIR /0 B

41/bin/sh -c rm -rf /tmp/samtools-1.3.1134 B

42/bin/sh -c mkdir /opt/sambamba/ 2.83 MB

43ENV BWA_VERSION=0.7.150 B

44/bin/sh -c cd /tmp/ 710.37 KB

45/bin/sh -c cd /tmp/ 19.12 KB

46COPY file:d1a461cefa700c72be2fd2dc33361585e69432046a0512a060c8632b60857dce in /usr/bin/alignment_helper.sh 389 B

47COPY file:1121618cddae54d7c42ed86580f1c3834e8fe0057f30479aa4339193b40f346b in /usr/bin/markduplicates_helper.sh 473 B

48WORKDIR /opt0 B

49/bin/sh -c wget https://github.com/genome/pindel/archive/v0.2.5b8.tar.gz &&245.33 MB

50WORKDIR /opt/pindel-0.2.5b80 B

51/bin/sh -c ./INSTALL /tmp/htslib-1.3.29.07 MB

52WORKDIR /0 B

53/bin/sh -c rm -rf /tmp/htslib-1.3.2133 B

54/bin/sh -c ln -s /opt/pindel-0.2.5b8/pindel159 B

55/bin/sh -c ln -s /opt/pindel-0.2.5b8/pindel2vcf164 B

56COPY file:2daeb3d1e17280ccd03efe01959266f2a738c73136a83b6af335d798bbd7cba7 in /usr/bin/pindel_helper.pl 424 B

57COPY file:b567d9bdece74acd19021dde2edcdcce4c6d8ae3fc7c548367ae4e0918e4ec58 in /usr/bin/write_pindel_filter_config.pl 493 B

58COPY file:2350c0457437aef6d08e15479a77657572e267a2b2418a07b0a6e96f3a14953d in /usr/bin/somatic_indelfilter.pl 1.2 KB

59/bin/sh -c apt-get update &&8.37 MB

60ENV SAMTOOLS_ROOT=/opt/samtools0 B

61/bin/sh -c mkdir /opt/bam-readcount121 B

62WORKDIR /opt/bam-readcount0 B

63/bin/sh -c git clone https://github.com/genome/bam-readcount.git10.14 MB

64COPY file:4b6d9ee3f411b0623987bca90a8ee7c2d8255d152d3bd882f9a35614a8cc5572 in /usr/bin/bam_readcount_helper.py 1.25 KB

65

COPY file:a4d14d9bce926109a669ca9037cfe31c9b7fa3ebfa622448949ac0007bc60569 in /usr/bin/add_bam_readcount_to_vcf_helper.py

1.74 KB

66/bin/sh -c pip install cyvcf234.72 MB

67/bin/sh -c pip3 install pysam18.16 MB

68/bin/sh -c pip3 install vcfpy1.08 MB

69/bin/sh -c pip3 install --extra-index-url51.63 MB

70WORKDIR /opt0 B

71/bin/sh -c wget --no-check-certificate https://raw.githubusercontent.com/genome/fpfilter-tool/v0.1.0/fpfilter.pl7.26 KB

72/bin/sh -c ln -s $HTSLIB_INSTALL_DIR/bin/tabix154 B

73COPY file:10c69b2562314cd92fa1533cc24e514edfd0e0ba89e6af125cfdff918fa76afd in /usr/bin/docm_filter.pl 995 B

74COPY file:4d57a807048a846e9360d8f20bdbafd9b9248d8796a67455fd5ec91673f52f99 in /usr/bin/single_sample_docm_filter.pl 598 B

75/bin/sh -c mkdir /opt/vep/109 B

76WORKDIR /opt/vep0 B

77/bin/sh -c git clone https://github.com/Ensembl/ensembl-vep.git110.59 MB

78WORKDIR /opt/vep/ensembl-vep0 B

79/bin/sh -c git checkout postreleasefix/9014.31 MB

80/bin/sh -c perl INSTALL.pl --NO_UPDATE30 MB

81WORKDIR /0 B

82/bin/sh -c ln -s /opt/vep/ensembl-vep/vep184 B

83/bin/sh -c mkdir -p /opt/lib/perl/VEP/Plugins169 B

84COPY file:d86db1566ab706075290504b1f5acd82e41bc1ae7e466a28f4b3538a0d1fe1bd in /opt/lib/perl/VEP/Plugins/Downstream.pm 1.94 KB

85COPY file:9220595a7652273ed31cc0c4cbed54c759551232dff12c6fda1376ee6e5cbfa6 in /opt/lib/perl/VEP/Plugins/Wildtype.pm 894 B

86

COPY file:78fde7a92dd8a3dae8640e671cb12ece647e20d1a436e7faf6d1c2fb76909566 in /usr/bin/add_annotations_to_table_helper.py

1.52 KB

87

COPY file:ccddec852ac10c36eb8600a71b6aef3323bb47e46aab6d7b21a68d82de63139d in /usr/bin/docm_and_coding_indel_selection.pl

1.1 KB

88ENV BCFTOOLS_INSTALL_DIR=/opt/bcftools0 B

89WORKDIR /tmp0 B

90/bin/sh -c wget https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2 &&3.54 MB

91WORKDIR /tmp/bcftools-1.3.10 B

92/bin/sh -c make prefix=$BCFTOOLS_INSTALL_DIR &&7.07 MB

93WORKDIR /0 B

94/bin/sh -c rm -rf /tmp/bcftools-1.3.1134 B

95/bin/sh -c mkdir /opt/picard-2.18.1/ 11.69 MB

96COPY file:fff0abd93cca756b3600d5923798a01c713eab29b9e0095564544bcaa43bf269 in /usr/bin/split_interval_list_helper.pl 393 B

97/bin/sh -c pip install toil[cwl]==3.12.014.13 MB

98/bin/sh -c cd /tmp/ 5.99 KB

99/bin/sh -c sed -i 's/select\[type==X86_644.23 KB

100/bin/sh -c apt-get update -y16.86 MB

101/bin/sh -c ln -sf /usr/share/zoneinfo/America/Chicago157 B

102/bin/sh -c echo "America/Chicago" >153 B

103/bin/sh -c dpkg-reconfigure --frontend noninteractive350.76 KB

104/bin/sh -c apt-get update &&159.88 KB

105/bin/sh -c cd /tmp/ &&5.61 MB

106/bin/sh -c cd /tmp/libStatGen &&94.64 KB

107/bin/sh -c cd /tmp/verifyBamID &&1.58 MB

108/bin/sh -c cp /tmp/verifyBamID/bin/verifyBamID /usr/local/bin319.51 KB

109/bin/sh -c rm -rf /tmp/verifyBamID157 B

110/bin/sh -c apt-get update &&69.85 MB

111/bin/sh -c apt-get install -y920.97 KB

112/bin/sh -c Rscript -e 'install.packages("ggplot2",109.9 MB

113COPY file:45a10e583d0e9058a005278434871086e8b7865cd478b4245e834a347c35627e in /usr/bin/vcf_check.pl 939 B

114/bin/sh -c wget --no-check-certificate https://github.com/fulcrumgenomics/fgbio/releases/download/0.5.0/fgbio-0.5.0.jar25.36 MB

115COPY file:6ac890fe11d93fe9d1b92b35d0c7cb8cd7d10887641faf56317fead225f8c953 in /usr/bin/umi_alignment.sh 659 B

116COPY file:1e75e4c92587591c6881b360853a7a7182c3b13422cd3455c9c1a99f06512bab in /usr/bin/umi_realignment.sh 688 B

Command

ADD file:d37ff24540ea7700d0fc053e1996b234428a88f3a324d7fcbd83d8ef95318040 in /