johnegarza/chromoseq:latest

Manifest digest

sha256:9f74f646ced69d16eaff1f03cf47a8d38003cb3ebcd11940d096d52966b40b91

OS/ARCH

linux/amd64

Compressed size

7.15 GB

Last pushed

over 7 years by johnegarza

Type

Image

Manifest digest

sha256:9f74f646ced69d16eaff1f03cf47a8d38003cb3ebcd11940d096d52966b40b91

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 David Spencer <[email protected]>0 B

8LABEL Image=for basic ad-hoc0 B

9/bin/sh -c apt-get update &&33.75 MB

10/bin/sh -c apt-get update -y768.14 MB

11ENV HTSLIB_INSTALL_DIR=/opt/htslib0 B

12WORKDIR /tmp0 B

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

14ENV SAMTOOLS_INSTALL_DIR=/opt/samtools0 B

15WORKDIR /tmp0 B

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

17ENV BCFTOOLS_INSTALL_DIR=/opt/bcftools0 B

18WORKDIR /tmp0 B

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

20ENV picard_version=2.18.90 B

21/bin/sh -c apt-get update &&424.11 MB

22WORKDIR /usr/local0 B

23/bin/sh -c git clone https://github.com/arq5x/bedtools2.git62.27 MB

24ENV ZIP=vcftools-0.1.14.tar.gz0 B

25ENV URL=https://github.com/vcftools/vcftools/releases/download/v0.1.14/0 B

26ENV FOLDER=vcftools-0.1.140 B

27ENV DST=/tmp0 B

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

29/bin/sh -c mkdir -p /tmp/ucsc10.58 MB

30ARG R_VERSION0 B

31ARG BUILD_DATE0 B

32ENV BUILD_DATE=2017-06-200 B

33ENV R_VERSION=3.5.00 B

34/bin/sh -c cd /tmp/ &&143.69 MB

35ADD file ... in /tmp/ 296 B

36/bin/sh -c R -f /tmp/rpackages.R301.46 MB

37/bin/sh -c cd / &&1.15 KB

38ENV CONDA_DIR=/opt/conda0 B

39ENV PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin0 B

40/bin/sh -c cd /tmp &&38.14 MB

41/bin/sh -c conda install --yes329.45 MB

42/bin/sh -c conda create --quiet336.94 MB

43/bin/sh -c apt-get update &&46.26 MB

44/bin/sh -c ln -sf /usr/share/zoneinfo/America/Chicago156 B

45/bin/sh -c echo "America/Chicago" >154 B

46/bin/sh -c dpkg-reconfigure --frontend noninteractive380.41 KB

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

48/bin/sh -c cpan install Statistics::Basic12.3 MB

49/bin/sh -c mkdir /tmp/bin117 B

50ENV PATH=/bin:/usr/bin:/usr/local/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin0 B

51MAINTAINER David H. Spencer0 B

52LABEL description=Heavy container for0 B

53ENV manta_version=1.5.00 B

54WORKDIR /opt/0 B

55

/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

56/bin/sh -c apt-get update &&170.11 MB

57/bin/sh -c cd /opt/ &&34.81 MB

58/bin/sh -c Rscript -e "source('https://bioconductor.org/biocLite.R');12.1 MB

59/bin/sh -c Rscript --default-packages=devtools -e10.42 MB

60/bin/sh -c cd /opt/ &&7.52 KB

61ENV VARSCAN_INSTALL_DIR=/opt/varscan0 B

62WORKDIR /opt/varscan115 B

63/bin/sh -c wget https://github.com/dkoboldt/varscan/releases/download/2.4.2/VarScan.v2.4.2.jar &&111.49 KB

64WORKDIR /opt0 B

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

66WORKDIR /opt/samtools-1.20 B

67/bin/sh -c make10.42 MB

68WORKDIR /opt0 B

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

70WORKDIR /opt/pindel-0.2.5b80 B

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

72WORKDIR /0 B

73/bin/sh -c ln -s /opt/pindel-0.2.5b8/pindel205 B

74ENV maven_package_name=apache-maven-3.3.90 B

75ENV gatk_dir_name=gatk-protected0 B

76ENV gatk_version=3.60 B

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

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

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

80/bin/sh -c conda config --add714.19 MB

81WORKDIR /usr/local/bin/0 B

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

83/bin/sh -c cpan install DBI15.65 MB

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

85WORKDIR /opt/vep0 B

86/bin/sh -c git clone https://github.com/Ensembl/ensembl-vep.git113.37 MB

87WORKDIR /opt/vep/ensembl-vep0 B

88/bin/sh -c git checkout postreleasefix/9015.71 MB

89/bin/sh -c perl INSTALL.pl --NO_UPDATE30.59 MB

90WORKDIR /0 B

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

92/bin/sh -c conda install -y313.95 MB

93/bin/sh -c export PATH=$PATH:/opt/conda/bin/ &&484.47 MB

94/bin/sh -c cd / &&982 B

95/bin/sh -c mkdir -p /opt/lib/perl/VEP/Plugins174 B

96COPY file:40843f9b28716cd6256cfc2b1859c2ee5fe05e5d7a3acfa5af0990b884fbc85c in /opt/lib/perl/VEP/Plugins/Downstream.pm 1.94 KB

97COPY file:6f62a0cc524a85b5e5c055eb0996ed226a9a8ef9311f0cacc4007caebb16d426 in /opt/lib/perl/VEP/Plugins/Wildtype.pm 896 B

98/bin/sh -c apt-get update &&43.64 MB

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

100/bin/sh -c add-apt-repository 6.16 KB

101/bin/sh -c apt-get update190.88 KB

102/bin/sh -c apt-get install -y70.4 MB

103WORKDIR /opt/0 B

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

105/bin/sh -c mkdir /opt/files/114 B

106

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

1.56 KB

107

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

1.13 KB

108COPY file:b360656679ce86debc2b0a196cf85fa8daf9761214f385a93d9be2d4cbce17ce in /usr/local/bin/runIchorCNA.R 6.39 KB

109COPY file:05384e546ea4f82cb5dc6708547fee8a5ff3591f64d70baa8e602d7265a812f2 in /usr/local/bin/addReadCountsToVcfCRAM.py 1.86 KB

110COPY file:e60f0794359b41d6559ae222ca4771a938796a6f2a2768f84e9c43ffcc480ae0 in /opt/files/configManta.hg38.py.ini 743 B

111COPY file:2d7336836d1fab33a3840a3f536d853f77c22fb23e7ec611d6fdf09df2d93c8f in /opt/files/ChromoSeq.hg38.bed 6.16 KB

112COPY file:1bbdaa0420fbd656bf7b9a44f9f14b3ad08a19ecf9f4dc4dde566278939723b9 in /opt/files/GeneRegions.bed 6.55 KB

113

COPY file:badfa5eae8679b6729eb4724e81d61c352fa29a8560ee8aeb24f397199f7a41c in /opt/files/ChromoSeq.translocations.fixed.v2.sorted.hg38.bedpe

12.8 KB

114COPY file:1cd5186adb79283506f773cfb54c6e4d24dc91e4cc042b19e813959de1b221b3 in /usr/local/bin/ChromoSeqReporter.hg38.pl 4.1 KB

115COPY file:5ad3058ef908512584c9b306500f46494332041c5a604cd972aa822991d3a133 in /usr/local/bin/BlatContigs.pl 1.67 KB

116COPY file:3057ff0dcec436251dbe334ba09c0a29166c482bf84ea7c3d687b565bac6d564 in /usr/local/bin/pslScore.pl 1.31 KB

117COPY file:b70c5b99d28f9fc81adb8b812277097fe321ca4600059f15d98ac455d1328639 in /opt/files/hg38.blacklist.merged.bed 444 B

118COPY file:ff2271a6fb5b1a401307096005c415d81403f792ab845eef15fcf7b74a0ca040 in /opt/files/B38.callset.public.bedpe.gz 42.32 MB

119COPY file:8c2625684f750e125e86fc3e5d0f036222db65dfc92de262cfc928b0267321b1 in /opt/files/GeneCoverageRegions.bed 4.24 KB

120

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

7.59 KB

121

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

536.66 KB

122COPY file:5862ba597d809cb9d3d3572469016060d8f520f3813550607cfe903a34fc7a8c in /opt/files/basespace_cromwell.config 1.42 KB

123

COPY file:4a697d3c4a75c96ad8b8f8cec52f1fea42677d60fce61bccf4fe3d34fba7c8cf in /opt/files/Chromoseq.v8.cromwell34.hg38.wdl

4.96 KB

124COPY file:c754a7e06c8087931787a7a63c8a9c444ddbe9172baf5db25b6b87bc822b0a6b in /opt/files/all_sequences.dict 86.53 KB

125COPY file:78a2442c2bb94d047e80c8d432c34ab1ae025e7f8cfc381e8a187c3448514fbc in /opt/files/all_sequences.fa.bed.gz 421 B

126COPY file:2f9d97778b11abe0f720eb75a0b814eed0206616b749d90ef146635608f27cca in /opt/files/all_sequences.fa.bed.gz.tbi 1.79 KB

127COPY file:5235189234244d64246efe0cad836b38a9bce11cef122339b5d69068045f7cd1 in /opt/files/all_sequences.fa.fai 33.54 KB

128COPY file:b585babd1a74d5a1bbe2d8990eab88916d3fee817be283619c56fc668bce7fbc in /opt/files/all_sequences.fa.gz 882.76 MB

129COPY file:09f4e4019d911a6c8b0217048c6d091e7fc4b5455b926b781156fd2bf2c43ed0 in /opt/files/driver.py 1.78 KB

130/bin/sh -c chmod a+wrx /opt/files/*925.77 MB

131/bin/sh -c chmod a+wrx /usr/local/bin/*14.47 MB

Command

ADD file:592c2540de1c707636622213ee30ff5b6f8be0a48bb25c97edc7204ea4df1a81 in /