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mgibio/cle:v1.2.0

Machine learning & AI
Data science
Manifest digest

sha256:48b02526c17aa9d81c65cc19df419a7a234e76a5f073284d367dc3c5d6e218ff

OS/ARCH

linux/amd64

Compressed size

1.92 GB

Last pushed

almost 9 years by mgibio

Type

Image

Manifest digest

sha256:48b02526c17aa9d81c65cc19df419a7a234e76a5f073284d367dc3c5d6e218ff

Image Layers

Image Layers

1ADD file ... in / 45.41 MB
2/bin/sh -c set -xe &&850 B
3/bin/sh -c rm -rf /var/lib/apt/lists/*618 B
4/bin/sh -c sed -i 's/^#\s*\(deb.*universe\)$/\1/g'851 B
5/bin/sh -c mkdir -p /run/systemd168 B
6CMD ["/bin/bash"]0 B
7MAINTAINER Susanna Kiwala <[email protected]>0 B
8LABEL description=Image for tools0 B
9/bin/sh -c apt-get update -y514.14 MB
10/bin/sh -c apt-get update -y35.73 MB
11/bin/sh -c pip install --upgrade3.26 MB
12ENV maven_package_name=apache-maven-3.3.90 B
13ENV gatk_dir_name=gatk-protected0 B
14ENV gatk_version=3.60 B
15/bin/sh -c cd /tmp/ &&8.12 MB
16/bin/sh -c cd /tmp/ 620.63 MB
17/bin/sh -c cd /opt/ &&80.5 MB
18ENV STRELKA_INSTALL_DIR=/opt/strelka/0 B
19/bin/sh -c wget https://github.com/Illumina/strelka/releases/download/v2.7.1/strelka-2.7.1.centos5_x86_64.tar.bz2 51.77 MB
20COPY file:3e6f0b526c27fdbae083b918948ab48067e9d262a8942fe55922bde8d5e07589 in /usr/bin/strelka_helper.pl 521 B
21COPY file:588cc83116f0863fcbf8068f2ceb446cb908ac348dc04cc1a26a54875e1f8ca8 in /usr/bin/add_strelka_gt.pl 1.26 KB
22ENV VARSCAN_INSTALL_DIR=/opt/varscan0 B
23WORKDIR /opt/varscan114 B
24/bin/sh -c wget https://github.com/dkoboldt/varscan/releases/download/2.4.2/VarScan.v2.4.2.jar &&111.46 KB
25COPY file:e5b9651f5e58a057a6dcd74a16d1a7c236f295bfce3511af756f20baf5a193b3 in /usr/bin/intervals_to_bed.pl 313 B
26COPY file:c148f785a220405069831d07b824330481dd2e3cba5b68ddb67325595062fe88 in /usr/bin/varscan_helper.sh 601 B
27COPY file:8e55f56124e1a06fe0585a8b8db13efad0a602c8e70f1063eeeee58f509f66fb in /usr/bin/varscan_germline_helper.sh 687 B
28ENV HTSLIB_INSTALL_DIR=/opt/htslib0 B
29WORKDIR /tmp0 B
30/bin/sh -c wget https://github.com/samtools/htslib/releases/download/1.3.2/htslib-1.3.2.tar.bz2 &&1.98 MB
31WORKDIR /tmp/htslib-1.3.20 B
32/bin/sh -c ./configure --enable-plugins18.55 MB
33ENV SAMTOOLS_INSTALL_DIR=/opt/samtools0 B
34WORKDIR /tmp0 B
35/bin/sh -c wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2 &&8.45 MB
36WORKDIR /tmp/samtools-1.3.10 B
37/bin/sh -c ./configure --with-htslib=$HTSLIB_INSTALL_DIR --prefix=$SAMTOOLS_INSTALL_DIR3.51 MB
38WORKDIR /0 B
39/bin/sh -c rm -rf /tmp/samtools-1.3.1136 B
40WORKDIR /opt0 B
41/bin/sh -c wget https://github.com/genome/pindel/archive/v0.2.5b8.tar.gz &&245.33 MB
42WORKDIR /opt/pindel-0.2.5b80 B
43/bin/sh -c ./INSTALL /tmp/htslib-1.3.29.07 MB
44WORKDIR /0 B
45/bin/sh -c rm -rf /tmp/htslib-1.3.2132 B
46/bin/sh -c ln -s /opt/pindel-0.2.5b8/pindel154 B
47/bin/sh -c ln -s /opt/pindel-0.2.5b8/pindel2vcf158 B
48COPY file:39f7530c0141dd6c766f8b08b5cae85700ab6c1284f4a96c4a76bfa9493c76ef in /usr/bin/pindel_helper.pl 418 B
49COPY file:0fb85321f4b1e2e3a7324854099eef686042ad33d4198248b48d62b6c61596ef in /usr/bin/write_pindel_filter_config.pl 485 B
50COPY file:9d933b89f37cf80740d41bfe8ffc3bc496eb3ba0f211d2181ea8d790212b4a94 in /usr/bin/somatic_indelfilter.pl 1.2 KB
51/bin/sh -c apt-get update &&8.18 MB
52ENV SAMTOOLS_ROOT=/opt/samtools0 B
53/bin/sh -c mkdir /opt/bam-readcount118 B
54WORKDIR /opt/bam-readcount0 B
55/bin/sh -c git clone https://github.com/genome/bam-readcount.git10.14 MB
56COPY file:217e41b8f8b6be2d27c281ed3359b37c676e6075f5ae7188b347e8e94d7081e5 in /usr/bin/bam_readcount_helper.py 1.25 KB
57COPY file:39a28f79e77322ed615e30cddf0d1ec57e008c1fdbf47dea91e1e122a09de73c in /usr/bin/add_bam_readcount_to_vcf_helper.py 1.73 KB
58/bin/sh -c pip install cyvcf242.77 MB
59/bin/sh -c pip3 install vcfpy17.84 MB
60WORKDIR /opt0 B
61/bin/sh -c wget --no-check-certificate https://raw.githubusercontent.com/genome/fpfilter-tool/v0.1.0/fpfilter.pl7.25 KB
62/bin/sh -c ln -s $HTSLIB_INSTALL_DIR/bin/tabix148 B
63COPY file:046c17be2476ccd44133b380b2f372f05b9e574e0348c7d5e163620fb16b3d69 in /usr/bin/docm_filter.pl 659 B
64/bin/sh -c mkdir /opt/vep/110 B
65WORKDIR /opt/vep0 B
66/bin/sh -c git clone https://github.com/Ensembl/ensembl-vep.git86.16 MB
67WORKDIR /opt/vep/ensembl-vep0 B
68/bin/sh -c git checkout postreleasefix/872.83 MB
69/bin/sh -c perl INSTALL.pl --NO_UPDATE4.24 MB
70WORKDIR /0 B
71/bin/sh -c ln -s /opt/vep/ensembl-vep/vep.pl177 B
72/bin/sh -c mkdir -p /opt/lib/perl/VEP/Plugins169 B
73COPY file:679b7ec2c20872befc9dc2a8f09ddc85c27d1c2bc018ec69920f08d68f02ce9e in /opt/lib/perl/VEP/Plugins/Downstream.pm 1.94 KB
74COPY file:765f0394e42ebd8b38d2412ee01da3912ef941bda27b4dab453132602796796f in /opt/lib/perl/VEP/Plugins/Wildtype.pm 892 B
75COPY file:ba3c26360c6bb2db0333a6f765d5d7dc694a2e57a22e52adbf523ba83e36e108 in /usr/bin/add_annotations_to_table_helper.py 1.51 KB
76COPY file:5bcb832a2c8cedbca8303825125149e8b0ccba60e53faaf1cd21d29fb34fcffd in /usr/bin/docm_and_coding_indel_selection.pl 1.09 KB
77ENV BCFTOOLS_INSTALL_DIR=/opt/bcftools0 B
78WORKDIR /tmp0 B
79/bin/sh -c wget https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2 &&3.54 MB
80WORKDIR /tmp/bcftools-1.3.10 B
81/bin/sh -c make prefix=$BCFTOOLS_INSTALL_DIR &&7.07 MB
82WORKDIR /0 B
83/bin/sh -c rm -rf /tmp/bcftools-1.3.1139 B
84ENV picard_version=2.14.00 B
85/bin/sh -c mkdir /usr/picard112 B
86WORKDIR /usr/picard0 B
87/bin/sh -c wget https://github.com/broadinstitute/picard/releases/download/${picard_version}/picard.jar10.88 MB
88COPY file:0d5d9b4ade59782802735558e6d0b074877f3f0a48aff5aa9ba193cd9c333502 in /usr/bin/split_interval_list_helper.pl 389 B
89/bin/sh -c pip install toil[cwl]==3.6.010.6 MB
90/bin/sh -c sed -i 's/select\[type==X86_643.91 KB
91/bin/sh -c apt-get update -y16.83 MB
92/bin/sh -c ln -sf /usr/share/zoneinfo/America/Chicago158 B
93/bin/sh -c echo "America/Chicago" >150 B
94/bin/sh -c dpkg-reconfigure --frontend noninteractive355.34 KB
95/bin/sh -c apt-get update &&23.17 MB
96/bin/sh -c cd /tmp/ &&5.6 MB
97/bin/sh -c cd /tmp/libStatGen &&94.57 KB
98/bin/sh -c cd /tmp/verifyBamID &&1.58 MB
99/bin/sh -c cp /tmp/verifyBamID/bin/verifyBamID /usr/local/bin319.49 KB
100/bin/sh -c rm -rf /tmp/verifyBamID165 B
101/bin/sh -c apt-get update &&69.82 MB
102/bin/sh -c apt-get install -y713.53 KB

Command

ADD file:5b334adf9d9a2256add2a801b49d4b23c93b0973ec22bb798973d571c948f102 in /