johnegarza/chromoseq:v10

Manifest digest

sha256:9520c81a2ca1732e777bcd3d9c95d8cd6c4e89200676d65ac2e6ab7f3db1bd14

OS/ARCH

linux/amd64

Compressed size

2.8 GB

Last pushed

about 7 years by johnegarza

Type

Image

Manifest digest

sha256:9520c81a2ca1732e777bcd3d9c95d8cd6c4e89200676d65ac2e6ab7f3db1bd14

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 David H. Spencer0 B

7LABEL description=Heavy container for0 B

8/bin/sh -c apt-get update &&23 MB

9/bin/sh -c apt-get update -y285.78 MB

10ENV HTSLIB_INSTALL_DIR=/opt/htslib0 B

11WORKDIR /tmp0 B

12/bin/sh -c wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 &&28.55 MB

13ENV SAMTOOLS_INSTALL_DIR=/opt/samtools0 B

14WORKDIR /tmp0 B

15/bin/sh -c wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 &&5.17 MB

16WORKDIR /usr/local0 B

17/bin/sh -c git clone https://github.com/arq5x/bedtools2.git69.74 MB

18ARG R_VERSION0 B

19ENV R_VERSION=3.6.00 B

20/bin/sh -c cd /tmp/ &&139.52 MB

21ENV CONDA_DIR=/opt/conda0 B

22ENV PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin0 B

23/bin/sh -c cd /tmp &&38.12 MB

24/bin/sh -c conda config --add304.03 MB

25/bin/sh -c cd /tmp &&53.35 MB

26/bin/sh -c conda create --quiet540.23 MB

27ENV manta_version=1.5.00 B

28WORKDIR /opt/0 B

29

/bin/sh -c wget https://github.com/Illumina/manta/releases/download/v${manta_version}/manta-${manta_version}.centos6_x86_64.tar.bz2 &&

41.37 MB

30/bin/sh -c apt-get update &&89.56 MB

31ENV VARSCAN_INSTALL_DIR=/opt/varscan0 B

32WORKDIR /opt/varscan150 B

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

34WORKDIR /opt0 B

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

36WORKDIR /opt/pindel-0.2.5b80 B

37/bin/sh -c ./INSTALL $HTSLIB_INSTALL_DIR9.07 MB

38WORKDIR /0 B

39/bin/sh -c ln -s /opt/pindel-0.2.5b8/pindel200 B

40ENV maven_package_name=apache-maven-3.3.90 B

41ENV gatk_dir_name=gatk-protected0 B

42ENV gatk_version=3.60 B

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

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

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

46WORKDIR /usr/local/bin/0 B

47/bin/sh -c wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat &&2.39 MB

48/bin/sh -c mkdir -p /tmp/ucsc2.03 MB

49/bin/sh -c git clone https://github.com/broadinstitute/ichorCNA.git14.56 MB

50/bin/sh -c Rscript -e "install.packages(c('plyr',60.74 MB

51/bin/sh -c R CMD INSTALL6.11 MB

52/bin/sh -c cd /opt/ &&2.9 MB

53/bin/sh -c cpan install DBI16.85 MB

54/bin/sh -c mkdir /opt/vep/144 B

55WORKDIR /opt/vep0 B

56/bin/sh -c git clone https://github.com/Ensembl/ensembl-vep.git115.04 MB

57WORKDIR /opt/vep/ensembl-vep0 B

58/bin/sh -c git checkout postreleasefix/9015.72 MB

59/bin/sh -c perl INSTALL.pl --NO_UPDATE31.14 MB

60WORKDIR /0 B

61/bin/sh -c ln -s /opt/vep/ensembl-vep/vep183 B

62/bin/sh -c apt-get update &&16.72 MB

63/bin/sh -c curl -fsSL https://download.docker.com/linux/ubuntu/gpg14.33 KB

64/bin/sh -c add-apt-repository 978 B

65/bin/sh -c apt-get update192.72 KB

66/bin/sh -c apt-get install -y73.63 MB

67WORKDIR /opt/0 B

68/bin/sh -c wget https://github.com/broadinstitute/cromwell/releases/download/36/cromwell-36.jar153.24 MB

69/bin/sh -c cd / &&1.04 KB

70/bin/sh -c mkdir /opt/files/145 B

71

COPY file:40fec78ee41405f20943ffdbaff502b8bc7f54ccddf4f18b44dcdfb6b2263144 in /usr/local/bin/add_annotations_to_table_helper.py

1.55 KB

72

COPY file:6d1efb0645ac56c1ef2f15e09a1f25d80ca9e7ae622528f4126d4bd9dfea93aa in /usr/local/bin/docm_and_coding_indel_selection.pl

1.13 KB

73COPY file:b360656679ce86debc2b0a196cf85fa8daf9761214f385a93d9be2d4cbce17ce in /usr/local/bin/runIchorCNA.R 6.38 KB

74COPY file:f6ac0c1dca95bf7a449da36b8caa1afb3de96230e79afa6cfc6e064d94ee447a in /usr/local/bin/addReadCountsToVcfCRAM.py 1.88 KB

75COPY file:e60f0794359b41d6559ae222ca4771a938796a6f2a2768f84e9c43ffcc480ae0 in /opt/files/configManta.hg38.py.ini 741 B

76COPY file:2d7336836d1fab33a3840a3f536d853f77c22fb23e7ec611d6fdf09df2d93c8f in /opt/files/ChromoSeq.hg38.bed 6.17 KB

77COPY file:1bbdaa0420fbd656bf7b9a44f9f14b3ad08a19ecf9f4dc4dde566278939723b9 in /opt/files/GeneRegions.bed 6.55 KB

78

COPY file:0ce2474feccbf5046373545847b2174cd3fb0996e5edd1fcb51121e5094021d0 in /opt/files/ChromoSeq.translocations.fixed.v3.sorted.hg38.bedpe

11.62 KB

79COPY file:59c46d2b6fcbbf7122a65b8893d2afe04a664769bdb1461543abaf9ae7391d56 in /usr/local/bin/ChromoSeqReporter.hg38.pl 4.65 KB

80COPY file:50dc96ac25be360915de574b68fb61d83d1d9261cba2d3903c8f906e58f983f9 in /usr/local/bin/BlatContigs.pl 1.68 KB

81COPY file:3057ff0dcec436251dbe334ba09c0a29166c482bf84ea7c3d687b565bac6d564 in /usr/local/bin/pslScore.pl 1.3 KB

82COPY file:b70c5b99d28f9fc81adb8b812277097fe321ca4600059f15d98ac455d1328639 in /opt/files/hg38.blacklist.merged.bed 445 B

83COPY file:ff2271a6fb5b1a401307096005c415d81403f792ab845eef15fcf7b74a0ca040 in /opt/files/B38.callset.public.bedpe.gz 42.32 MB

84

COPY file:b5e79c4b7fcb6a288876ebc71837ffe0db68bacbc90c2c4ddce18bef6c75db3b in /opt/files/all.stranded.filtered.merged.bedpe.gz

31.44 KB

85

COPY file:6b5f56e9a47b480534497eb66a578c562ef512ea4feeedde5f13098fce6c02c3 in /opt/files/all.stranded.filtered.merged.bedpe.gz.tbi

14.03 KB

86COPY file:8c2625684f750e125e86fc3e5d0f036222db65dfc92de262cfc928b0267321b1 in /opt/files/GeneCoverageRegions.bed 4.24 KB

87

COPY file:82a9f4d532d24b754270cb1d6a05386af3702a8f50168990cd0d224d6351ac6a in /opt/files/ChromoSeq.translocations.qc.bed

7.59 KB

88

COPY file:b4d1f3a1dcc5aa03aaae2d62e60fb756989124b816e68fecca3c107f192283b4 in /opt/files/nextera_hg38_500kb_median_normAutosome_median.rds_median.n9.rds

536.66 KB

89COPY file:9742d6bb967cf7f0b0198582bc675d8e2653482976931a5db66e5b08f27a1bfe in /opt/files/basespace_cromwell.config 1.59 KB

90COPY file:c754a7e06c8087931787a7a63c8a9c444ddbe9172baf5db25b6b87bc822b0a6b in /opt/files/all_sequences.dict 86.53 KB

91COPY file:78a2442c2bb94d047e80c8d432c34ab1ae025e7f8cfc381e8a187c3448514fbc in /opt/files/all_sequences.fa.bed.gz 411 B

92COPY file:2f9d97778b11abe0f720eb75a0b814eed0206616b749d90ef146635608f27cca in /opt/files/all_sequences.fa.bed.gz.tbi 1.78 KB

93COPY file:5235189234244d64246efe0cad836b38a9bce11cef122339b5d69068045f7cd1 in /opt/files/all_sequences.fa.fai 33.53 KB

94COPY file:cb846de9480b8a11a88dbb23e38aa851d370653723b3b9d473541e797a4fc172 in /opt/files/driver.py 1.9 KB

95COPY file:1f72d1ec6108c87aad26e7ef4cba4989bd109cdd201d43d496506ff10bf28d40 in /opt/files/Chromoseq_basespace.v10.wdl 5.09 KB

96/bin/sh -c chmod a+wrx /opt/files/*43.05 MB

97/bin/sh -c chmod a+wrx /usr/local/bin/*8.1 MB

Command

ADD file:a65e0467dbedc0992151651c136374c16f65d9905eac9d04d0925039ada64e4c in /