johnegarza/chromoseq:v9.3

Manifest digest

sha256:e4be9d4a81137dc23e2f43e447b270fc788b87a1537a853b8778c0069cea69af

OS/ARCH

linux/amd64

Compressed size

5.15 GB

Last pushed

over 7 years by johnegarza

Type

Image

Manifest digest

sha256:e4be9d4a81137dc23e2f43e447b270fc788b87a1537a853b8778c0069cea69af

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 Spencer <[email protected]>0 B

7LABEL Image=for basic ad-hoc0 B

8/bin/sh -c apt-get update &&22.87 MB

9/bin/sh -c apt-get update -y769.03 MB

10ENV HTSLIB_INSTALL_DIR=/opt/htslib0 B

11WORKDIR /tmp0 B

12/bin/sh -c wget https://github.com/samtools/htslib/releases/download/1.5/htslib-1.5.tar.bz2 &&25.3 MB

13ENV SAMTOOLS_INSTALL_DIR=/opt/samtools0 B

14WORKDIR /tmp0 B

15/bin/sh -c wget https://github.com/samtools/samtools/releases/download/1.5/samtools-1.5.tar.bz2 &&4.75 MB

16ENV BCFTOOLS_INSTALL_DIR=/opt/bcftools0 B

17WORKDIR /tmp0 B

18/bin/sh -c wget https://github.com/samtools/bcftools/releases/download/1.5/bcftools-1.5.tar.bz2 &&5.58 MB

19ENV picard_version=2.18.90 B

20/bin/sh -c apt-get update &&438.1 MB

21WORKDIR /usr/local0 B

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

23ENV ZIP=vcftools-0.1.14.tar.gz0 B

24ENV URL=https://github.com/vcftools/vcftools/releases/download/v0.1.14/0 B

25ENV FOLDER=vcftools-0.1.140 B

26ENV DST=/tmp0 B

27/bin/sh -c wget $URL/$ZIP -O3.89 MB

28/bin/sh -c mkdir -p /tmp/ucsc12.91 MB

29ARG R_VERSION0 B

30ARG BUILD_DATE0 B

31ENV BUILD_DATE=2017-06-200 B

32ENV R_VERSION=3.6.00 B

33/bin/sh -c cd /tmp/ &&142.09 MB

34ADD file ... in /tmp/ 315 B

35/bin/sh -c R -f /tmp/rpackages.R211.42 MB

36/bin/sh -c cd / &&921 B

37ENV CONDA_DIR=/opt/conda0 B

38ENV PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin0 B

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

40/bin/sh -c conda install --yes268.88 MB

41/bin/sh -c conda create --quiet273.42 MB

42/bin/sh -c git clone --single-branch58.46 MB

43/bin/sh -c apt-get update &&35.42 MB

44/bin/sh -c ln -sf /usr/share/zoneinfo/America/Chicago158 B

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

46/bin/sh -c dpkg-reconfigure --frontend noninteractive380.43 KB

47/bin/sh -c apt-get update &&13.95 MB

48/bin/sh -c cpan install Statistics::Basic13.44 MB

49/bin/sh -c pip install hic2cool102.22 MB

50/bin/sh -c mkdir /tmp/bin150 B

51

ENV PATH=/bin:/usr/bin:/usr/local/bin:/opt/conda/bin/:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

0 B

52MAINTAINER David H. Spencer0 B

53LABEL description=Heavy container for0 B

54ENV manta_version=1.5.00 B

55WORKDIR /opt/0 B

56

/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

57/bin/sh -c apt-get update &&88.03 MB

58ENV VARSCAN_INSTALL_DIR=/opt/varscan0 B

59WORKDIR /opt/varscan150 B

60/bin/sh -c wget https://github.com/dkoboldt/varscan/releases/download/2.4.2/VarScan.v2.4.2.jar &&111.47 KB

61WORKDIR /opt0 B

62/bin/sh -c wget https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2 &&9.36 MB

63WORKDIR /opt/samtools-1.20 B

64/bin/sh -c make10.42 MB

65WORKDIR /opt0 B

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

67WORKDIR /opt/pindel-0.2.5b80 B

68/bin/sh -c ./INSTALL /opt/samtools-1.2/htslib-1.2.19.64 MB

69WORKDIR /0 B

70/bin/sh -c ln -s /opt/pindel-0.2.5b8/pindel199 B

71ENV maven_package_name=apache-maven-3.3.90 B

72ENV gatk_dir_name=gatk-protected0 B

73ENV gatk_version=3.60 B

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

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

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

77/bin/sh -c conda config --add775.68 MB

78WORKDIR /usr/local/bin/0 B

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

80/bin/sh -c cpan install DBI4.2 MB

81/bin/sh -c mkdir /opt/vep/145 B

82WORKDIR /opt/vep0 B

83/bin/sh -c git clone https://github.com/Ensembl/ensembl-vep.git114.92 MB

84WORKDIR /opt/vep/ensembl-vep0 B

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

86/bin/sh -c perl INSTALL.pl --NO_UPDATE30.77 MB

87WORKDIR /0 B

88/bin/sh -c ln -s /opt/vep/ensembl-vep/vep182 B

89/bin/sh -c conda install -y154.4 MB

90/bin/sh -c export PATH=$PATH:/opt/conda/bin/ &&482.99 MB

91/bin/sh -c cd / &&937 B

92/bin/sh -c mkdir -p /opt/lib/perl/VEP/Plugins202 B

93COPY file:40843f9b28716cd6256cfc2b1859c2ee5fe05e5d7a3acfa5af0990b884fbc85c in /opt/lib/perl/VEP/Plugins/Downstream.pm 1.94 KB

94COPY file:6f62a0cc524a85b5e5c055eb0996ed226a9a8ef9311f0cacc4007caebb16d426 in /opt/lib/perl/VEP/Plugins/Wildtype.pm 897 B

95/bin/sh -c apt-get update &&28.84 MB

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

97/bin/sh -c add-apt-repository 979 B

98/bin/sh -c apt-get update191.86 KB

99/bin/sh -c apt-get install -y70.42 MB

100WORKDIR /opt/0 B

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

102/bin/sh -c mkdir /opt/files/148 B

103

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

1.55 KB

104

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

1.13 KB

105COPY file:b360656679ce86debc2b0a196cf85fa8daf9761214f385a93d9be2d4cbce17ce in /usr/local/bin/runIchorCNA.R 6.39 KB

106COPY file:f6ac0c1dca95bf7a449da36b8caa1afb3de96230e79afa6cfc6e064d94ee447a in /usr/local/bin/addReadCountsToVcfCRAM.py 1.89 KB

107COPY file:e60f0794359b41d6559ae222ca4771a938796a6f2a2768f84e9c43ffcc480ae0 in /opt/files/configManta.hg38.py.ini 744 B

108COPY file:2d7336836d1fab33a3840a3f536d853f77c22fb23e7ec611d6fdf09df2d93c8f in /opt/files/ChromoSeq.hg38.bed 6.16 KB

109COPY file:1bbdaa0420fbd656bf7b9a44f9f14b3ad08a19ecf9f4dc4dde566278939723b9 in /opt/files/GeneRegions.bed 6.55 KB

110

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

11.62 KB

111COPY file:59c46d2b6fcbbf7122a65b8893d2afe04a664769bdb1461543abaf9ae7391d56 in /usr/local/bin/ChromoSeqReporter.hg38.pl 4.66 KB

112COPY file:50dc96ac25be360915de574b68fb61d83d1d9261cba2d3903c8f906e58f983f9 in /usr/local/bin/BlatContigs.pl 1.68 KB

113COPY file:3057ff0dcec436251dbe334ba09c0a29166c482bf84ea7c3d687b565bac6d564 in /usr/local/bin/pslScore.pl 1.31 KB

114COPY file:b70c5b99d28f9fc81adb8b812277097fe321ca4600059f15d98ac455d1328639 in /opt/files/hg38.blacklist.merged.bed 446 B

115COPY file:ff2271a6fb5b1a401307096005c415d81403f792ab845eef15fcf7b74a0ca040 in /opt/files/B38.callset.public.bedpe.gz 42.32 MB

116

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

31.44 KB

117

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

14.03 KB

118COPY file:8c2625684f750e125e86fc3e5d0f036222db65dfc92de262cfc928b0267321b1 in /opt/files/GeneCoverageRegions.bed 4.24 KB

119

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

7.59 KB

120

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

536.66 KB

121COPY file:9742d6bb967cf7f0b0198582bc675d8e2653482976931a5db66e5b08f27a1bfe in /opt/files/basespace_cromwell.config 1.59 KB

122COPY file:58e29e0780e2c6e54c3bb3bf5f001b7eaca4e721f93ed172de6cafad4df69c20 in /opt/files/Chromoseq_basespace.v9.wdl 5.14 KB

123COPY file:c754a7e06c8087931787a7a63c8a9c444ddbe9172baf5db25b6b87bc822b0a6b in /opt/files/all_sequences.dict 86.53 KB

124COPY file:78a2442c2bb94d047e80c8d432c34ab1ae025e7f8cfc381e8a187c3448514fbc in /opt/files/all_sequences.fa.bed.gz 412 B

125COPY file:2f9d97778b11abe0f720eb75a0b814eed0206616b749d90ef146635608f27cca in /opt/files/all_sequences.fa.bed.gz.tbi 1.78 KB

126COPY file:5235189234244d64246efe0cad836b38a9bce11cef122339b5d69068045f7cd1 in /opt/files/all_sequences.fa.fai 33.53 KB

127COPY file:6647cca8dd423e0351d020b9affb040c768e598140d339f30d244aec5eb0c884 in /opt/files/driver.py 1.9 KB

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

129/bin/sh -c Rscript -e "install.packages(c('plyr',12.79 MB

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

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

132/bin/sh -c chmod a+wrx /usr/local/bin/*14.18 MB

Command

ADD file:a65e0467dbedc0992151651c136374c16f65d9905eac9d04d0925039ada64e4c in /