tmooney/cle-test:toil3_12

Manifest digest

sha256:93e7c8d28d316164d6c5b1a4e6ed531531a1b1cfb5f5bef5107f882a0cb397b0

OS/ARCH

linux/amd64

Compressed size

2.22 GB

Last pushed

over 8 years by tmooney

Type

Image

Manifest digest

sha256:93e7c8d28d316164d6c5b1a4e6ed531531a1b1cfb5f5bef5107f882a0cb397b0

Image Layers

Image Layers

1ADD file ... in / 40.86 MB

2/bin/sh -c set -xe &&847 B

3/bin/sh -c rm -rf /var/lib/apt/lists/*620 B

4/bin/sh -c sed -i 's/^#\s*$deb.*universe$$/\1/g'855 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 -y579.32 MB

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

11/bin/sh -c pip install --upgrade3.26 MB

12/bin/sh -c ln -s /usr/bin/unzip128 B

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/ 620.72 MB

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

22COPY file:588cc83116f0863fcbf8068f2ceb446cb908ac348dc04cc1a26a54875e1f8ca8 in /usr/bin/add_strelka_gt.pl 1.26 KB

23ENV VARSCAN_INSTALL_DIR=/opt/varscan0 B

24WORKDIR /opt/varscan115 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:e5b9651f5e58a057a6dcd74a16d1a7c236f295bfce3511af756f20baf5a193b3 in /usr/bin/intervals_to_bed.pl 315 B

27COPY file:c148f785a220405069831d07b824330481dd2e3cba5b68ddb67325595062fe88 in /usr/bin/varscan_helper.sh 602 B

28COPY file:42c4ada7cce8eff666be9bc0646ee2a80910f9ea6afc3b1a4f2582662271d26f in /usr/bin/varscan_germline_helper.sh 702 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-1.3.1134 B

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

42ENV BWA_VERSION=0.7.150 B

43/bin/sh -c cd /tmp/ 710.33 KB

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

45COPY file:2b6214c1273c601478cc941b40443431e07b50a70bd68ef711fe4f0554dc7cb5 in /usr/bin/alignment_helper.sh 385 B

46COPY file:5ba5e797437ed2aaf494adc0439366248b53d6b3ab2b067a689a89f1bb6118f9 in /usr/bin/markduplicates_helper.sh 467 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-1.3.2133 B

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

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

55COPY file:39f7530c0141dd6c766f8b08b5cae85700ab6c1284f4a96c4a76bfa9493c76ef in /usr/bin/pindel_helper.pl 418 B

56COPY file:0fb85321f4b1e2e3a7324854099eef686042ad33d4198248b48d62b6c61596ef in /usr/bin/write_pindel_filter_config.pl 489 B

57COPY file:9d933b89f37cf80740d41bfe8ffc3bc496eb3ba0f211d2181ea8d790212b4a94 in /usr/bin/somatic_indelfilter.pl 1.2 KB

58/bin/sh -c apt-get update &&8.21 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:217e41b8f8b6be2d27c281ed3359b37c676e6075f5ae7188b347e8e94d7081e5 in /usr/bin/bam_readcount_helper.py 1.25 KB

64

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

1.73 KB

65/bin/sh -c pip install cyvcf243.36 MB

66/bin/sh -c pip3 install vcfpy19.1 MB

67WORKDIR /opt0 B

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

69/bin/sh -c ln -s $HTSLIB_INSTALL_DIR/bin/tabix149 B

70COPY file:046c17be2476ccd44133b380b2f372f05b9e574e0348c7d5e163620fb16b3d69 in /usr/bin/docm_filter.pl 658 B

71COPY file:76a5345dd64bd8d6db06bae069e8888d6ce794a8f0c62a044e45cccc0ca66aa5 in /usr/bin/single_sample_docm_filter.pl 593 B

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

73WORKDIR /opt/vep0 B

74/bin/sh -c git clone https://github.com/Ensembl/ensembl-vep.git111.38 MB

75WORKDIR /opt/vep/ensembl-vep0 B

76/bin/sh -c git checkout postreleasefix/90936.78 KB

77/bin/sh -c perl INSTALL.pl --NO_UPDATE29.32 MB

78WORKDIR /0 B

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

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

81COPY file:679b7ec2c20872befc9dc2a8f09ddc85c27d1c2bc018ec69920f08d68f02ce9e in /opt/lib/perl/VEP/Plugins/Downstream.pm 1.94 KB

82COPY file:e760870dd283b96e29c21a8638c2e57b8c64c70f9a082b68dc7533937ee1f89b in /opt/lib/perl/VEP/Plugins/Wildtype.pm 892 B

83

COPY file:ba3c26360c6bb2db0333a6f765d5d7dc694a2e57a22e52adbf523ba83e36e108 in /usr/bin/add_annotations_to_table_helper.py

1.5 KB

84

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

1.09 KB

85ENV BCFTOOLS_INSTALL_DIR=/opt/bcftools0 B

86WORKDIR /tmp0 B

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

88WORKDIR /tmp/bcftools-1.3.10 B

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

90WORKDIR /0 B

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

92ENV picard_version=2.4.10 B

93/bin/sh -c cd /opt/ 242.8 MB

94ENV picard_version=2.14.00 B

95/bin/sh -c mkdir /usr/picard114 B

96WORKDIR /usr/picard0 B

97/bin/sh -c wget https://github.com/broadinstitute/picard/releases/download/${picard_version}/picard.jar10.88 MB

98COPY file:0d5d9b4ade59782802735558e6d0b074877f3f0a48aff5aa9ba193cd9c333502 in /usr/bin/split_interval_list_helper.pl 390 B

99/bin/sh -c pip install toil[cwl]==3.12.014.34 MB

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

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

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

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

104/bin/sh -c echo "America/Chicago" >149 B

105/bin/sh -c dpkg-reconfigure --frontend noninteractive352.55 KB

106/bin/sh -c apt-get update &&156.21 KB

107/bin/sh -c cd /tmp/ &&5.64 MB

108/bin/sh -c cd /tmp/libStatGen &&94.59 KB

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

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

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

112/bin/sh -c apt-get update &&69.84 MB

113/bin/sh -c apt-get install -y732.26 KB

Command

ADD file:affda766655e01cbd66cdf7485f581f22be61d93abadcc9fd22ed34c78069e18 in /