mgibio/cle:v1.4.2

Machine learning & AI

Data science

Manifest digest

sha256:69f53bbc45369352270344a388edc77509fd2fde31bbf266a4fcb2e0eeb1ff19

OS/ARCH

linux/amd64

Compressed size

1.86 GB

Last pushed

over 7 years by mgibio

Type

Image

Manifest digest

sha256:69f53bbc45369352270344a388edc77509fd2fde31bbf266a4fcb2e0eeb1ff19

Image Layers

Image Layers

1ADD file ... in / 41.74 MB

2/bin/sh -c set -xe &&848 B

3/bin/sh -c rm -rf /var/lib/apt/lists/*526 B

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

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

6MAINTAINER Susanna Kiwala <[email protected]>0 B

7LABEL description=Image for tools0 B

8/bin/sh -c apt-get update -y572.02 MB

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

10/bin/sh -c pip install --upgrade3.53 MB

11/bin/sh -c ln -s /usr/bin/unzip127 B

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

13ENV maven_package_name=apache-maven-3.3.90 B

14ENV gatk_dir_name=gatk-protected0 B

15ENV gatk_version=3.60 B

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

17/bin/sh -c cd /tmp/ 260.14 MB

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

19ENV STRELKA_INSTALL_DIR=/opt/strelka/0 B

20/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

21COPY file:4eb9da6f1e92d57339a950925148278aeb2bc2311f5f6056a8c7354ab6f3fbf6 in /usr/bin/strelka_helper.pl 525 B

22COPY file:4f299ab48bca7664c4ef4eee8079d94dd339361986104ab9297e2c1a6d60f631 in /usr/bin/add_strelka_gt.pl 1.26 KB

23ENV VARSCAN_INSTALL_DIR=/opt/varscan0 B

24WORKDIR /opt/varscan114 B

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

26COPY file:5c2f6d8f8546bfef82dbb9a4d191450f9e4b25fc5a2ed71bb7f6496530f70b13 in /usr/bin/intervals_to_bed.pl 319 B

27COPY file:b7e46791d8dec9de441e5d7e4df7a85ab57a7db2f69d1458d5f50c256d6cf70f in /usr/bin/varscan_helper.sh 605 B

28COPY file:59a94ad94d76c3ab9025a56da68bd4a5f89f1aaae4cceec2b1a9d68fab4f4950 in /usr/bin/varscan_germline_helper.sh 706 B

29ENV HTSLIB_INSTALL_DIR=/opt/htslib0 B

30WORKDIR /tmp0 B

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

32WORKDIR /tmp/htslib-1.3.20 B

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

34ENV SAMTOOLS_INSTALL_DIR=/opt/samtools0 B

35WORKDIR /tmp0 B

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

37WORKDIR /tmp/samtools-1.3.10 B

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

39WORKDIR /0 B

40/bin/sh -c rm -rf /tmp/samtools-1.3.1135 B

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

42ENV BWA_VERSION=0.7.150 B

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

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

45COPY file:d1a461cefa700c72be2fd2dc33361585e69432046a0512a060c8632b60857dce in /usr/bin/alignment_helper.sh 391 B

46COPY file:1121618cddae54d7c42ed86580f1c3834e8fe0057f30479aa4339193b40f346b in /usr/bin/markduplicates_helper.sh 473 B

47WORKDIR /opt0 B

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

49WORKDIR /opt/pindel-0.2.5b80 B

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

51WORKDIR /0 B

52/bin/sh -c rm -rf /tmp/htslib-1.3.2134 B

53/bin/sh -c ln -s /opt/pindel-0.2.5b8/pindel158 B

54/bin/sh -c ln -s /opt/pindel-0.2.5b8/pindel2vcf161 B

55COPY file:a888a1a39ad3f38fd12e2e41939142073bcf9a8c0cd9a3e24d66bfccf36a075c in /usr/bin/pindel_helper.pl 428 B

56COPY file:b567d9bdece74acd19021dde2edcdcce4c6d8ae3fc7c548367ae4e0918e4ec58 in /usr/bin/write_pindel_filter_config.pl 491 B

57COPY file:2350c0457437aef6d08e15479a77657572e267a2b2418a07b0a6e96f3a14953d in /usr/bin/somatic_indelfilter.pl 1.2 KB

58/bin/sh -c apt-get update &&8.38 MB

59ENV SAMTOOLS_ROOT=/opt/samtools0 B

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

61WORKDIR /opt/bam-readcount0 B

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

63COPY file:1d72ddbec2c7f17a05d68da4fe76f1814de13246fc2ddbf5b81a163008f4eb2a in /usr/bin/bam_readcount_helper.py 1.39 KB

64

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

1.74 KB

65/bin/sh -c apt-get update &&4.5 MB

66/bin/sh -c pip install cyvcf242.97 MB

67/bin/sh -c pip3 install pysam18.22 MB

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

69/bin/sh -c pip3 install vcf-annotation-tools59.76 MB

70WORKDIR /opt0 B

71/bin/sh -c wget --no-check-certificate https://raw.githubusercontent.com/genome/fpfilter-tool/v0.1.0/fpfilter.pl7.25 KB

72/bin/sh -c ln -s $HTSLIB_INSTALL_DIR/bin/tabix152 B

73COPY file:ef2f756fa03e1430fe6a337a693109c985a32d7f8a9107aa0d6d3c83132a5a8f in /usr/bin/docm_filter.pl 1.09 KB

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

75/bin/sh -c mkdir /opt/vep/110 B

76WORKDIR /opt/vep0 B

77/bin/sh -c git clone https://github.com/Ensembl/ensembl-vep.git115.02 MB

78WORKDIR /opt/vep/ensembl-vep0 B

79/bin/sh -c git checkout postreleasefix/931.66 MB

80/bin/sh -c perl INSTALL.pl --NO_UPDATE30.55 MB

81WORKDIR /0 B

82/bin/sh -c ln -s /opt/vep/ensembl-vep/vep181 B

83/bin/sh -c mkdir -p /opt/lib/perl/VEP/Plugins170 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 893 B

86

COPY file:c0127f4ae43094a358b6604e0c6c41bfcb236e7185e5472108ee93067c34c5a0 in /usr/bin/add_annotations_to_table_helper.py

1.53 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-1.3.1136 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 390 B

97

COPY file:5d8238c69263a64f2f7f230fa747a4a471b80160b7a6ce399548837b4ccc64ec in /usr/bin/split_interval_list_to_bed_helper.pl

524 B

98/bin/sh -c pip install toil[cwl]==3.12.014.56 MB

99/bin/sh -c cd /tmp/ 5.98 KB

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

101/bin/sh -c apt-get update -y16.88 MB

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

103/bin/sh -c echo "America/Chicago" >155 B

104/bin/sh -c dpkg-reconfigure --frontend noninteractive350.78 KB

105/bin/sh -c apt-get update &&160.22 KB

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

107/bin/sh -c cd /tmp/libStatGen &&97.1 KB

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

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

110/bin/sh -c rm -rf /tmp/verifyBamID154 B

111/bin/sh -c apt-get update &&69.49 MB

112/bin/sh -c apt-get install -y923.74 KB

113/bin/sh -c Rscript -e 'install.packages("ggplot2",129.1 MB

114COPY file:45a10e583d0e9058a005278434871086e8b7865cd478b4245e834a347c35627e in /usr/bin/vcf_check.pl 938 B

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

116COPY file:6ac890fe11d93fe9d1b92b35d0c7cb8cd7d10887641faf56317fead225f8c953 in /usr/bin/umi_alignment.sh 655 B

117COPY file:1e75e4c92587591c6881b360853a7a7182c3b13422cd3455c9c1a99f06512bab in /usr/bin/umi_realignment.sh 684 B

Command

ADD file:a65e0467dbedc0992151651c136374c16f65d9905eac9d04d0925039ada64e4c in /