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pegi3s/trinity:2.11.0

Machine learning & AI
Data science
Manifest digest

sha256:d92c5c6ce962a4246254664e9b819b893f053fb4e8136283108c0b36a0a6b2fe

OS/ARCH

linux/amd64

Compressed size

3.47 GB

Last pushed

over 5 years by pegi3s

Type

Image

Manifest digest

sha256:d92c5c6ce962a4246254664e9b819b893f053fb4e8136283108c0b36a0a6b2fe

Image Layers

Image Layers

1ADD file ... in / 25.46 MB
2/bin/sh -c [ -z "$(apt-get34.54 KB
3/bin/sh -c set -xe &&852 B
4/bin/sh -c mkdir -p /run/systemd163 B
5CMD ["/bin/bash"]0 B
6MAINTAINER [email protected]0 B
7ENV DEBIAN_FRONTEND=noninteractive0 B
8/bin/sh -c apt-get update &&510.21 MB
9/bin/sh -c curl -L https://cpanmin.us1.21 MB
10/bin/sh -c cpanm install DB_File792.72 KB
11/bin/sh -c cpanm install URI::Escape697 B
12ENV SRC=/usr/local/src0 B
13ENV BIN=/usr/local/bin0 B
14WORKDIR /usr/local/src0 B
15ENV R_VERSION=R-3.6.30 B
16/bin/sh -c curl https://cran.r-project.org/src/base/R-3/$R_VERSION.tar.gz -o195.8 MB
17/bin/sh -c R -e 'install.packages("BiocManager",95.95 KB
18/bin/sh -c R -e 'BiocManager::install("tidyverse")'80.87 MB
19/bin/sh -c R -e 'BiocManager::install("edgeR")'7.83 MB
20/bin/sh -c R -e 'BiocManager::install("DESeq2")'68.18 MB
21/bin/sh -c R -e 'BiocManager::install("ape")'2.72 MB
22/bin/sh -c R -e 'BiocManager::install("ctc")'548.6 KB
23/bin/sh -c R -e 'BiocManager::install("gplots")'2.27 MB
24/bin/sh -c R -e 'BiocManager::install("Biobase")'2.21 MB
25/bin/sh -c R -e 'BiocManager::install("qvalue")'2.67 MB
26/bin/sh -c R -e 'BiocManager::install("goseq")'160.46 MB
27/bin/sh -c R -e 'BiocManager::install("Glimma")'3.28 MB
28/bin/sh -c R -e 'BiocManager::install("ROTS")'887.05 KB
29/bin/sh -c R -e 'BiocManager::install("GOplot")'2.46 MB
30/bin/sh -c R -e 'BiocManager::install("argparse")'168.11 KB
31/bin/sh -c R -e 'BiocManager::install("fastcluster")'277.8 KB
32/bin/sh -c R -e 'BiocManager::install("DEXSeq")'2.37 MB
33/bin/sh -c R -e 'BiocManager::install("tximport")'339.36 KB
34/bin/sh -c R -e 'BiocManager::install("tximportData")'407.44 MB
35ENV LD_LIBRARY_PATH=/usr/local/lib0 B
36/bin/sh -c apt-get install -y3.9 MB
37/bin/sh -c ln -sf /usr/bin/python3151 B
38/bin/sh -c pip3 install numpy40.77 MB
39/bin/sh -c pip3 install git+https://github.com/ewels/MultiQC.git38.58 MB
40/bin/sh -c pip3 install HTSeq21.19 MB
41WORKDIR /usr/local/src0 B
42/bin/sh -c wget https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.2.1.1/bowtie-1.2.1.1-linux-x86_64.zip/download -O90.34 MB
43/bin/sh -c mkdir /usr/local/lib/site_perl191 B
44WORKDIR /usr/local/src0 B
45/bin/sh -c wget https://github.com/deweylab/RSEM/archive/v1.3.0.tar.gz &&15.08 MB
46WORKDIR /usr/local/src0 B
47/bin/sh -c wget https://github.com/pachterlab/kallisto/releases/download/v0.43.1/kallisto_linux-v0.43.1.tar.gz &&11.14 MB
48WORKDIR /usr/local/src0 B
49/bin/sh -c wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip &&18.99 MB
50WORKDIR /usr/local/src0 B
51/bin/sh -c wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.5.0/ncbi-blast-2.5.0+-x64-linux.tar.gz &&427.48 MB
52WORKDIR /usr/local/src0 B
53/bin/sh -c wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.1/bowtie2-2.3.4.1-linux-x86_64.zip/download -O47.92 MB
54/bin/sh -c wget https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2 &&28.7 MB
55/bin/sh -c wget https://github.com/gmarcais/Jellyfish/releases/download/v2.2.7/jellyfish-2.2.7.tar.gz &&4.26 MB
56WORKDIR /usr/local/src0 B
57/bin/sh -c wget https://github.com/deweylab/RSEM/archive/v1.3.0.tar.gz &&15.08 MB
58WORKDIR /usr/local/src0 B
59ENV SALMON_VERSION=1.0.00 B
60/bin/sh -c wget https://github.com/COMBINE-lab/salmon/releases/download/v${SALMON_VERSION}/Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz &&81.43 MB
61ENV STAR_VERSION=2.7.2b0 B
62/bin/sh -c STAR_URL="https://github.com/alexdobin/STAR/archive/${STAR_VERSION}.tar.gz" && 15.62 MB
63/bin/sh -c wget https://sourceforge.net/projects/subread/files/subread-2.0.0/subread-2.0.0-Linux-x86_64.tar.gz/download -O119.52 MB
64/bin/sh -c wget ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.1.0-Linux_x86_64.zip &&75.96 MB
65ENV GMAP_VERSION=2017-11-150 B
66WORKDIR /usr/local/src0 B
67/bin/sh -c GMAP_URL="http://research-pub.gene.com/gmap/src/gmap-gsnap-$GMAP_VERSION.tar.gz" && 177.04 MB
68WORKDIR /usr/local/src0 B
69/bin/sh -c wget https://github.com/broadinstitute/picard/releases/download/2.20.3/picard.jar14.54 MB
70ENV PICARD_HOME=/usr/local/src0 B
71WORKDIR /usr/local/src0 B
72ENV GATK_VERSION=4.1.4.00 B
73/bin/sh -c wget https://github.com/broadinstitute/gatk/releases/download/${GATK_VERSION}/gatk-${GATK_VERSION}.zip &&761.95 MB
74ENV GATK_HOME=/usr/local/src/gatk-4.1.4.00 B
75WORKDIR /usr/local/src0 B
76/bin/sh -c ln -sf /usr/local/src/salmon-latest_linux_x86_64/bin/salmon189 B
77/bin/sh -c wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat -P2.41 MB
78WORKDIR /usr/local/src0 B
79ENV TRINITY_VERSION=2.11.00 B
80ENV TRINITY_CO=e903e224e2df93f1fabafb1abe02d7db05255a5e0 B
81WORKDIR /usr/local/src0 B
82/bin/sh -c git clone --recursive67.98 MB
83ENV TRINITY_HOME=/usr/local/bin/trinityrnaseq0 B
84ENV PATH=/usr/local/bin/trinityrnaseq:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin0 B
85WORKDIR /usr/local/src0 B
86/bin/sh -c rm -r ${R_VERSION}466 B
87/bin/sh -c apt-get clean332 B
88COPY file:76f4e0bcb545f3e4c31e030c6b2a7c3a2521aeb1fc9583301cba3978c8a40fac in /usr/local/src/Dockerfile.2.11.0 2.49 KB

Command

ADD file:91a750fb184711fde03c9172f41e8a907ccbb1bfb904c2c3f4ef595fcddbc3a9 in /