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tmooney/starfusion:pre-1.11.c-fefaf71

Manifest digest

sha256:27a269c995e507deb6679adb3ab858c128cd204fd0f02f2c02a427486b45bb5e

OS/ARCH

linux/amd64

Compressed size

2.25 GB

Last pushed

almost 4 years by tmooney

Type

Image

Manifest digest

sha256:27a269c995e507deb6679adb3ab858c128cd204fd0f02f2c02a427486b45bb5e

Image Layers

Image Layers

1ADD file ... in / 25.46 MB
2/bin/sh -c [ -z "$(apt-get34.54 KB
3/bin/sh -c set -xe &&848 B
4/bin/sh -c mkdir -p /run/systemd161 B
5CMD ["/bin/bash"]0 B
6MAINTAINER [email protected]0 B
7/bin/sh -c apt-get update &&333.54 MB
8/bin/sh -c ln -sf /usr/bin/python3152 B
9/bin/sh -c apt-get install -y376 B
10/bin/sh -c curl https://bootstrap.pypa.io/get-pip.py -o5.62 MB
11/bin/sh -c pip install numpy50.94 MB
12ENV SRC=/usr/local/src0 B
13ENV BIN=/usr/local/bin0 B
14ENV DATA=/usr/local/data0 B
15/bin/sh -c mkdir $DATA170 B
16/bin/sh -c curl -L https://cpanmin.us1.21 MB
17/bin/sh -c cpanm install PerlIO::gzip212.48 KB
18/bin/sh -c cpanm install Set::IntervalTree2.2 MB
19/bin/sh -c cpanm install DB_File778.06 KB
20/bin/sh -c cpanm install URI::Escape419.33 KB
21/bin/sh -c cpanm install Carp::Assert48.15 KB
22/bin/sh -c cpanm install JSON::XS.pm716.33 KB
23ENV SAMTOOLS_VERSION=1.90 B
24/bin/sh -c SAMTOOLS_URL="https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2" && 46.33 MB
25/bin/sh -c apt-get install -y10.65 MB
26ENV TRINITY_VERSION=2.8.50 B
27/bin/sh -c TRINITY_URL="https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v${TRINITY_VERSION}.tar.gz" && 44.93 MB
28ENV TRINITY_HOME=/usr/local/src/trinityrnaseq-Trinity-v2.8.50 B
29WORKDIR /usr/local/src0 B
30/bin/sh -c wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.3.1/bowtie2-2.3.3.1-linux-x86_64.zip/download -O41.15 MB
31WORKDIR /usr/local/src0 B
32/bin/sh -c wget https://github.com/gmarcais/Jellyfish/releases/download/v2.2.7/jellyfish-2.2.7.tar.gz &&4.29 MB
33WORKDIR /usr/local/src0 B
34/bin/sh -c wget https://github.com/COMBINE-lab/salmon/releases/download/v0.9.1/Salmon-0.9.1_linux_x86_64.tar.gz &&11.73 MB
35ENV GMAP_VERSION=2017-11-150 B
36WORKDIR /usr/local/src0 B
37/bin/sh -c GMAP_URL="http://research-pub.gene.com/gmap/src/gmap-gsnap-$GMAP_VERSION.tar.gz" && 177.04 MB
38WORKDIR /usr/local/src0 B
39/bin/sh -c wget https://github.com/broadinstitute/picard/releases/download/2.20.3/picard.jar14.54 MB
40ENV PICARD_HOME=/usr/local/src0 B
41WORKDIR /usr/local/src0 B
42ENV R_VERSION=R-3.6.30 B
43/bin/sh -c curl https://cran.r-project.org/src/base/R-3/$R_VERSION.tar.gz -o195.64 MB
44/bin/sh -c R -e 'install.packages("BiocManager",322.59 KB
45/bin/sh -c R -e 'BiocManager::install("argparse")'754.56 KB
46/bin/sh -c R -e 'BiocManager::install("tidyverse")'68.7 MB
47/bin/sh -c R -e 'BiocManager::install("cowplot")'1.32 MB
48/bin/sh -c R -e 'BiocManager::install("ranger")'9.39 MB
49ENV STAR_VERSION=2.7.8a0 B
50/bin/sh -c STAR_URL="https://github.com/alexdobin/STAR/archive/${STAR_VERSION}.tar.gz" && 19.08 MB
51/bin/sh -c apt-get install -y17.51 MB
52ENV FI_HASH=afbcda7726c6b39a7c5d8719245f6b5b8604cdf70 B
53/bin/sh -c git clone --recursive74 MB
54COPY file:af5f5c5a52da0e5c82dd8c42cfcfc65a19db2b7604e7a56de0a746c39a8567e1 in /usr/local/bin/ 983 B
55MAINTAINER [email protected]0 B
56/bin/sh -c apt-get clean &&10.36 MB
57/bin/sh -c locale-gen en_US.UTF-8416.54 KB
58WORKDIR /usr/local/src0 B
59ENV BLAST_VERSION=2.9.00 B
60/bin/sh -c wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${BLAST_VERSION}/ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz &&710.62 MB
61WORKDIR /usr/local/src0 B
62/bin/sh -c wget http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz &&55.75 MB
63WORKDIR /usr/local/src0 B
64/bin/sh -c wget https://dfam.org/releases/Dfam_3.1/infrastructure/dfamscan.pl.gz &&5.58 KB
65WORKDIR /usr/local/src0 B
66/bin/sh -c wget https://github.com/broadinstitute/picard/releases/download/2.20.3/picard.jar14.54 MB
67ENV PICARD_HOME=/usr/local/src0 B
68WORKDIR /usr/local/src0 B
69ENV STAR_FUSION_VERSION=pre-1.11.c0 B
70ENV STARF_CHECKOUT=3414829b37b8a669b55b556856741bdd3e56fc1f0 B
71/bin/sh -c apt-get update &&26.63 MB
72/bin/sh -c git clone https://github.com/STAR-Fusion/STAR-Fusion.git332.29 MB
73ENV STAR_FUSION_HOME=/usr/local/src/STAR-Fusion0 B
74ENV PATH=/usr/local/src/STAR-Fusion:/usr/local/src/STAR-Fusion/FusionInspector:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin0 B
75COPY STAR-Fusion.patch /usr/local/src/STAR-Fusion/ # buildkit418 B
76RUN /bin/sh -c patch -u10.98 KB

Command

ADD file:7d9bbf45a5b2510d44d3206a028cf6502757884d49e46d3d2e6356c3a92c4309 in /