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mgibio/cle:v1.0.0

Machine learning & AI
Data science
Manifest digest

sha256:1cb37ebe5656244edb92f875009aa63af2346242df1684c6f206b07d44c48340

OS/ARCH

linux/amd64

Compressed size

2.13 GB

Last pushed

almost 9 years by mgibio

Type

Image

Manifest digest

sha256:1cb37ebe5656244edb92f875009aa63af2346242df1684c6f206b07d44c48340

Image Layers

Image Layers

1ADD file ... in / 45.33 MB
2/bin/sh -c set -xe &&848 B
3/bin/sh -c rm -rf /var/lib/apt/lists/*621 B
4/bin/sh -c sed -i 's/^#\s*\(deb.*universe\)$/\1/g'853 B
5/bin/sh -c mkdir -p /run/systemd169 B
6CMD ["/bin/bash"]0 B
7MAINTAINER Susanna Kiwala <[email protected]>0 B
8LABEL description=Image for tools0 B
9/bin/sh -c apt-get update -y462.22 MB
10/bin/sh -c apt-get update -y37.99 MB
11/bin/sh -c pip install --upgrade3.26 MB
12ENV maven_package_name=apache-maven-3.3.90 B
13ENV gatk_dir_name=gatk-protected0 B
14ENV gatk_version=3.60 B
15/bin/sh -c cd /tmp/ &&8.12 MB
16/bin/sh -c cd /tmp/ 620.63 MB
17/bin/sh -c cd /opt/ &&80.5 MB
18ENV STRELKA_INSTALL_DIR=/opt/strelka/0 B
19/bin/sh -c wget https://github.com/Illumina/strelka/releases/download/v2.7.1/strelka-2.7.1.centos5_x86_64.tar.bz2 51.77 MB
20COPY file:3e6f0b526c27fdbae083b918948ab48067e9d262a8942fe55922bde8d5e07589 in /usr/bin/strelka_helper.pl 519 B
21COPY file:588cc83116f0863fcbf8068f2ceb446cb908ac348dc04cc1a26a54875e1f8ca8 in /usr/bin/add_strelka_gt.pl 1.26 KB
22ENV VARSCAN_INSTALL_DIR=/opt/varscan0 B
23WORKDIR /opt/varscan116 B
24/bin/sh -c wget https://github.com/dkoboldt/varscan/releases/download/2.4.2/VarScan.v2.4.2.jar &&111.46 KB
25COPY file:e5b9651f5e58a057a6dcd74a16d1a7c236f295bfce3511af756f20baf5a193b3 in /usr/bin/intervals_to_bed.pl 313 B
26COPY file:c148f785a220405069831d07b824330481dd2e3cba5b68ddb67325595062fe88 in /usr/bin/varscan_helper.sh 601 B
27ENV HTSLIB_INSTALL_DIR=/opt/htslib0 B
28WORKDIR /tmp0 B
29/bin/sh -c wget https://github.com/samtools/htslib/releases/download/1.3.2/htslib-1.3.2.tar.bz2 &&1.98 MB
30WORKDIR /tmp/htslib-1.3.20 B
31/bin/sh -c ./configure --enable-plugins18.55 MB
32ENV SAMTOOLS_INSTALL_DIR=/opt/samtools0 B
33WORKDIR /tmp0 B
34/bin/sh -c wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 &&8.45 MB
35WORKDIR /tmp/samtools-1.3.10 B
36/bin/sh -c ./configure --with-htslib=$HTSLIB_INSTALL_DIR --prefix=$SAMTOOLS_INSTALL_DIR3.51 MB
37WORKDIR /0 B
38/bin/sh -c rm -rf /tmp/samtools-1.3.1135 B
39WORKDIR /opt0 B
40/bin/sh -c wget https://github.com/genome/pindel/archive/v0.2.5b8.tar.gz &&245.33 MB
41WORKDIR /opt/pindel-0.2.5b80 B
42/bin/sh -c ./INSTALL /tmp/htslib-1.3.29.07 MB
43WORKDIR /0 B
44/bin/sh -c rm -rf /tmp/htslib-1.3.2133 B
45/bin/sh -c ln -s /opt/pindel-0.2.5b8/pindel154 B
46/bin/sh -c ln -s /opt/pindel-0.2.5b8/pindel2vcf158 B
47COPY file:39f7530c0141dd6c766f8b08b5cae85700ab6c1284f4a96c4a76bfa9493c76ef in /usr/bin/pindel_helper.pl 417 B
48COPY file:0fb85321f4b1e2e3a7324854099eef686042ad33d4198248b48d62b6c61596ef in /usr/bin/write_pindel_filter_config.pl 486 B
49COPY file:9d933b89f37cf80740d41bfe8ffc3bc496eb3ba0f211d2181ea8d790212b4a94 in /usr/bin/somatic_indelfilter.pl 1.2 KB
50/bin/sh -c apt-get update &&8.18 MB
51ENV SAMTOOLS_ROOT=/opt/samtools0 B
52/bin/sh -c mkdir /opt/bam-readcount121 B
53WORKDIR /opt/bam-readcount0 B
54/bin/sh -c git clone https://github.com/genome/bam-readcount.git10.14 MB
55COPY file:d42aab5a702a50ae58f5d7b11bc8aec23cb190c1db5dd055525044b379bcbe93 in /usr/bin/bam_readcount_helper.py 1.23 KB
56/bin/sh -c pip install cyvcf242.18 MB
57WORKDIR /opt0 B
58/bin/sh -c wget --no-check-certificate https://raw.githubusercontent.com/genome/fpfilter-tool/v0.1.0/fpfilter.pl7.24 KB
59/bin/sh -c ln -s $HTSLIB_INSTALL_DIR/bin/tabix149 B
60COPY file:046c17be2476ccd44133b380b2f372f05b9e574e0348c7d5e163620fb16b3d69 in /usr/bin/docm_filter.pl 656 B
61/bin/sh -c mkdir /opt/vep/110 B
62WORKDIR /opt/vep0 B
63/bin/sh -c git clone https://github.com/Ensembl/ensembl-vep.git86.1 MB
64WORKDIR /opt/vep/ensembl-vep0 B
65/bin/sh -c git checkout postreleasefix/872.76 MB
66/bin/sh -c perl INSTALL.pl --NO_UPDATE4.24 MB
67WORKDIR /0 B
68/bin/sh -c ln -s /opt/vep/ensembl-vep/vep.pl178 B
69/bin/sh -c mkdir -p /opt/lib/perl/VEP/Plugins170 B
70COPY file:679b7ec2c20872befc9dc2a8f09ddc85c27d1c2bc018ec69920f08d68f02ce9e in /opt/lib/perl/VEP/Plugins/Downstream.pm 1.94 KB
71COPY file:765f0394e42ebd8b38d2412ee01da3912ef941bda27b4dab453132602796796f in /opt/lib/perl/VEP/Plugins/Wildtype.pm 891 B
72COPY file:48b87ab55e5b63ea61899ddb9b0a644e5b12c3386b03286e91d56684e9d96f1e in /usr/bin/add_annotations_to_table_helper.py 1.47 KB
73ENV BCFTOOLS_INSTALL_DIR=/opt/bcftools0 B
74WORKDIR /tmp0 B
75/bin/sh -c wget https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2 &&3.54 MB
76WORKDIR /tmp/bcftools-1.3.10 B
77/bin/sh -c make prefix=$BCFTOOLS_INSTALL_DIR &&7.07 MB
78WORKDIR /0 B
79/bin/sh -c rm -rf /tmp/bcftools-1.3.1136 B
80ENV picard_version=2.4.10 B
81/bin/sh -c cd /usr/ &&109.85 MB
82WORKDIR /usr/picard0 B
83/bin/sh -c git config --global74.3 MB
84/bin/sh -c ant clean all111.37 MB
85COPY file:0d5d9b4ade59782802735558e6d0b074877f3f0a48aff5aa9ba193cd9c333502 in /usr/bin/split_interval_list_helper.pl 389 B
86/bin/sh -c pip install toil[cwl]==3.6.08.42 MB
87/bin/sh -c sed -i 's/select\[type==X86_643.91 KB
88/bin/sh -c apt-get update -y16.82 MB
89/bin/sh -c ln -sf /usr/share/zoneinfo/America/Chicago157 B
90/bin/sh -c echo "America/Chicago" >149 B
91/bin/sh -c dpkg-reconfigure --frontend noninteractive354.86 KB
92/bin/sh -c apt-get update &&23.16 MB
93/bin/sh -c cd /tmp/ &&5.6 MB
94/bin/sh -c cd /tmp/libStatGen &&93.44 KB
95/bin/sh -c cd /tmp/verifyBamID &&1.58 MB
96/bin/sh -c cp /tmp/verifyBamID/bin/verifyBamID /usr/local/bin319.49 KB
97/bin/sh -c rm -rf /tmp/verifyBamID163 B
98/bin/sh -c apt-get update &&69.8 MB
99/bin/sh -c apt-get install -y705.87 KB

Command

ADD file:5ed435208da6621b45db657dd6549ee132cde58c4b6763920030794c2f31fbc0 in /