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mgibio/vep_helper-cwl:1.0.3

Machine learning & AI
Data science
Manifest digest

sha256:e42f448f28e3c6386e938aa09ee1f692106c98db5eb6396c39348417c41f1161

OS/ARCH

linux/amd64

Compressed size

611.39 MB

Last pushed

over 7 years by mgibio

Type

Image

Manifest digest

sha256:e42f448f28e3c6386e938aa09ee1f692106c98db5eb6396c39348417c41f1161

Image Layers

Image Layers

1ADD file ... in / 41.51 MB
2/bin/sh -c set -xe &&847 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
6/bin/sh -c apt-get update &&173.99 MB
7/bin/sh -c cpanm DBI DBD::mysql4.52 MB
8/bin/sh -c useradd -r -m4.39 KB
9/bin/sh -c usermod -a -G1.34 KB
10USER vep0 B
11ENV OPT=/opt/vep0 B
12WORKDIR /opt/vep0 B
13/bin/sh -c mkdir -p src137 B
14WORKDIR /opt/vep/src0 B
15/bin/sh -c git clone -b11.88 MB
16/bin/sh -c git clone https://github.com/ens-lgil/ensembl-vep.git112.8 MB
17WORKDIR /opt/vep/src/ensembl-vep0 B
18/bin/sh -c git remote update172.8 KB
19WORKDIR /opt/vep/src0 B
20/bin/sh -c ensembl-vep/travisci/get_dependencies.sh185.37 MB
21ENV PERL5LIB=:/opt/vep/src/bioperl-live-release-1-6-9240 B
22ENV KENT_SRC=/opt/vep/src/kent-335_base/src0 B
23ENV HTSLIB_DIR=/opt/vep/src/htslib0 B
24ENV MACHTYPE=x86_640 B
25ENV CFLAGS=-fPIC0 B
26ENV DEPS=/opt/vep/src0 B
27USER root0 B
28/bin/sh -c ensembl-vep/travisci/build_c.sh17.69 MB
29WORKDIR /opt/vep/src/htslib0 B
30/bin/sh -c make install4.27 MB
31WORKDIR /opt/vep/src0 B
32/bin/sh -c git clone --depth1.02 MB
33WORKDIR /opt/vep/src/bioperl-ext/Bio/Ext/Align0 B
34/bin/sh -c perl -pi -e"s|(cd714 B
35/bin/sh -c perl Makefile.PL8.59 KB
36/bin/sh -c make804.5 KB
37/bin/sh -c make install322.11 KB
38WORKDIR /opt/vep/src0 B
39/bin/sh -c wget https://github.com/Ensembl/ensembl-xs/archive/2.3.2.zip -O96.58 KB
40/bin/sh -c unzip -q ensembl-xs.zip75.59 KB
41/bin/sh -c mv ensembl-xs-2.3.2 ensembl-xs75.61 KB
42/bin/sh -c rm ensembl-xs.zip186 B
43WORKDIR /opt/vep/src/ensembl-xs0 B
44/bin/sh -c perl Makefile.PL18.99 KB
45/bin/sh -c make313.89 KB
46/bin/sh -c make install83.17 KB
47WORKDIR /opt/vep/src0 B
48/bin/sh -c cpanm --installdeps --with-recommends13.99 MB
49/bin/sh -c cpanm --installdeps --with-recommends22.15 MB
50/bin/sh -c echo "en_US.UTF-8 UTF-8"414.64 KB
51ENV LC_ALL=en_US.UTF-80 B
52ENV LANG=en_US.UTF-80 B
53USER vep0 B
54/bin/sh -c echo >> $OPT/.profile567 B
55ENV PATH=/opt/vep/src/ensembl-vep:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin0 B
56WORKDIR /opt/vep/src/ensembl-vep0 B
57/bin/sh -c chmod u+x *.pl19.97 KB
58/bin/sh -c ./INSTALL.pl -l14.92 MB
59MAINTAINER John Garza <[email protected]>0 B
60LABEL description=Vep helper image0 B
61USER root0 B
62/bin/sh -c apt-get update -y4.63 MB
63WORKDIR /0 B
64/bin/sh -c ln -s /opt/vep/src/ensembl-vep/vep186 B
65WORKDIR /opt/vep/src/ensembl-vep0 B
66/bin/sh -c perl INSTALL.pl --NO_UPDATE172 B
67/bin/sh -c mkdir -p /opt/lib/perl/VEP/Plugins170 B
68WORKDIR /opt/lib/perl/VEP/Plugins0 B
69/bin/sh -c wget https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/93/Downstream.pm https://raw.githubusercontent.com/griffithlab/pVACtools/master/tools/pvacseq/VEP_plugins/Wildtype.pm316.15 KB
70COPY file:78fde7a92dd8a3dae8640e671cb12ece647e20d1a436e7faf6d1c2fb76909566 in /usr/bin/add_annotations_to_table_helper.py 1.53 KB
71COPY file:ccddec852ac10c36eb8600a71b6aef3323bb47e46aab6d7b21a68d82de63139d in /usr/bin/docm_and_coding_indel_selection.pl 1.1 KB
72COPY file:45a10e583d0e9058a005278434871086e8b7865cd478b4245e834a347c35627e in /usr/bin/vcf_check.pl 941 B
73COPY file:5c2f6d8f8546bfef82dbb9a4d191450f9e4b25fc5a2ed71bb7f6496530f70b13 in /usr/bin/intervals_to_bed.pl 320 B
74COPY file:4d57a807048a846e9360d8f20bdbafd9b9248d8796a67455fd5ec91673f52f99 in /usr/bin/single_sample_docm_filter.pl 602 B
75USER vep0 B

Command

ADD file:916a45030dee881bbc8bbabf8bcfcc8828c29ce1c318000950bbe84c57f9df73 in /