tmooney/cle-test:add_umi_alignment_helpers

Manifest digest

sha256:a76d2307a20d356e8f7cff71db15abbc9f0860788519e403f31b6cf450c3bbd5

OS/ARCH

linux/amd64

Compressed size

2.08 GB

Last pushed

over 8 years by tmooney

Type

Image

Manifest digest

sha256:a76d2307a20d356e8f7cff71db15abbc9f0860788519e403f31b6cf450c3bbd5

Image Layers

Image Layers

1ADD file ... in / 41.03 MB

2/bin/sh -c set -xe &&850 B

3/bin/sh -c rm -rf /var/lib/apt/lists/*621 B

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

5/bin/sh -c mkdir -p /run/systemd169 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 -y575.39 MB

10/bin/sh -c apt-get update -y1.49 MB

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

12/bin/sh -c ln -s /usr/bin/unzip128 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/ 620.7 MB

19/bin/sh -c cd /opt/ &&80.5 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:3e6f0b526c27fdbae083b918948ab48067e9d262a8942fe55922bde8d5e07589 in /usr/bin/strelka_helper.pl 520 B

23COPY file:588cc83116f0863fcbf8068f2ceb446cb908ac348dc04cc1a26a54875e1f8ca8 in /usr/bin/add_strelka_gt.pl 1.26 KB

24ENV VARSCAN_INSTALL_DIR=/opt/varscan0 B

25WORKDIR /opt/varscan115 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:e5b9651f5e58a057a6dcd74a16d1a7c236f295bfce3511af756f20baf5a193b3 in /usr/bin/intervals_to_bed.pl 313 B

28COPY file:c148f785a220405069831d07b824330481dd2e3cba5b68ddb67325595062fe88 in /usr/bin/varscan_helper.sh 601 B

29COPY file:42c4ada7cce8eff666be9bc0646ee2a80910f9ea6afc3b1a4f2582662271d26f in /usr/bin/varscan_germline_helper.sh 701 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-1.3.1133 B

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

43ENV BWA_VERSION=0.7.150 B

44/bin/sh -c cd /tmp/ 710.34 KB

45/bin/sh -c cd /tmp/ 19.1 KB

46COPY file:2b6214c1273c601478cc941b40443431e07b50a70bd68ef711fe4f0554dc7cb5 in /usr/bin/alignment_helper.sh 386 B

47COPY file:5ba5e797437ed2aaf494adc0439366248b53d6b3ab2b067a689a89f1bb6118f9 in /usr/bin/markduplicates_helper.sh 467 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-1.3.2132 B

54/bin/sh -c ln -s /opt/pindel-0.2.5b8/pindel154 B

55/bin/sh -c ln -s /opt/pindel-0.2.5b8/pindel2vcf158 B

56COPY file:39f7530c0141dd6c766f8b08b5cae85700ab6c1284f4a96c4a76bfa9493c76ef in /usr/bin/pindel_helper.pl 416 B

57COPY file:0fb85321f4b1e2e3a7324854099eef686042ad33d4198248b48d62b6c61596ef in /usr/bin/write_pindel_filter_config.pl 486 B

58COPY file:9d933b89f37cf80740d41bfe8ffc3bc496eb3ba0f211d2181ea8d790212b4a94 in /usr/bin/somatic_indelfilter.pl 1.19 KB

59/bin/sh -c apt-get update &&8.22 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:217e41b8f8b6be2d27c281ed3359b37c676e6075f5ae7188b347e8e94d7081e5 in /usr/bin/bam_readcount_helper.py 1.25 KB

65

COPY file:e61faa5b0db4339ea60602ae937b83af74d3afafaf6d721320fc4fd8833e6686 in /usr/bin/add_bam_readcount_to_vcf_helper.py

1.73 KB

66/bin/sh -c pip install cyvcf234.45 MB

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

68WORKDIR /opt0 B

69/bin/sh -c wget --no-check-certificate https://raw.githubusercontent.com/genome/fpfilter-tool/v0.1.0/fpfilter.pl7.24 KB

70/bin/sh -c ln -s $HTSLIB_INSTALL_DIR/bin/tabix148 B

71COPY file:ea05705fdc8719a05c07825598bc4b23bb6b092703fe412f59bce9042c603324 in /usr/bin/docm_filter.pl 988 B

72COPY file:76a5345dd64bd8d6db06bae069e8888d6ce794a8f0c62a044e45cccc0ca66aa5 in /usr/bin/single_sample_docm_filter.pl 591 B

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

74WORKDIR /opt/vep0 B

75/bin/sh -c git clone https://github.com/Ensembl/ensembl-vep.git110.48 MB

76WORKDIR /opt/vep/ensembl-vep0 B

77/bin/sh -c git checkout postreleasefix/9014.32 MB

78/bin/sh -c perl INSTALL.pl --NO_UPDATE29.81 MB

79WORKDIR /0 B

80/bin/sh -c ln -s /opt/vep/ensembl-vep/vep178 B

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

82COPY file:679b7ec2c20872befc9dc2a8f09ddc85c27d1c2bc018ec69920f08d68f02ce9e in /opt/lib/perl/VEP/Plugins/Downstream.pm 1.94 KB

83COPY file:e760870dd283b96e29c21a8638c2e57b8c64c70f9a082b68dc7533937ee1f89b in /opt/lib/perl/VEP/Plugins/Wildtype.pm 891 B

84

COPY file:545a545663cee0aea2a5345581dc389695862b7a7c7f679491604ee8ce5ff5e9 in /usr/bin/add_annotations_to_table_helper.py

1.52 KB

85

COPY file:5bcb832a2c8cedbca8303825125149e8b0ccba60e53faaf1cd21d29fb34fcffd in /usr/bin/docm_and_coding_indel_selection.pl

1.09 KB

86ENV BCFTOOLS_INSTALL_DIR=/opt/bcftools0 B

87WORKDIR /tmp0 B

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

89WORKDIR /tmp/bcftools-1.3.10 B

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

91WORKDIR /0 B

92/bin/sh -c rm -rf /tmp/bcftools-1.3.1135 B

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

94COPY file:0d5d9b4ade59782802735558e6d0b074877f3f0a48aff5aa9ba193cd9c333502 in /usr/bin/split_interval_list_helper.pl 389 B

95/bin/sh -c pip install toil[cwl]==3.12.014.08 MB

96/bin/sh -c cd /tmp/ 5.94 KB

97/bin/sh -c sed -i 's/select\[type==X86_644.2 KB

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

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

100/bin/sh -c echo "America/Chicago" >150 B

101/bin/sh -c dpkg-reconfigure --frontend noninteractive350.68 KB

102/bin/sh -c apt-get update &&159.74 KB

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

104/bin/sh -c cd /tmp/libStatGen &&94.57 KB

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

106/bin/sh -c cp /tmp/verifyBamID/bin/verifyBamID /usr/local/bin319.49 KB

107/bin/sh -c rm -rf /tmp/verifyBamID163 B

108/bin/sh -c apt-get update &&69.87 MB

109/bin/sh -c apt-get install -y732.74 KB

110/bin/sh -c Rscript -e 'install.packages("ggplot2",84.61 MB

111COPY file:3f90fa4486a98439610805655524d33734fd5188dd4d16486c5f5568935b060b in /usr/bin/vcf_check.pl 933 B

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

113COPY file:1afca6f2a451ec67c1bcc3797120744569b79b2a5bbcc18a2e2d6cc3fe3f1726 in /usr/bin/umi_alignment.sh 652 B

114COPY file:dc6c53de2402e69ce8292d04c10e8ebc5ad5c67b890de87c70b5af292b4493ee in /usr/bin/umi_realignment.sh 678 B

Command

ADD file:592c2540de1c707636622213ee30ff5b6f8be0a48bb25c97edc7204ea4df1a81 in /