pegi3s/trinity:2.15.2

Machine learning & AI

Data science

Manifest digest

sha256:4de00ef0918eef0c619f8c227f999b2c3116410427fc453d2d5ff29d09a6eef5

OS/ARCH

linux/amd64

Compressed size

4.28 GB

Last pushed

23 days by hlfernandez

Type

Image

Manifest digest

sha256:4de00ef0918eef0c619f8c227f999b2c3116410427fc453d2d5ff29d09a6eef5

Image Layers

Image Layers

1ARG RELEASE0 B

2ARG LAUNCHPAD_BUILD_ARCH0 B

3LABEL org.opencontainers.image.ref.name=ubuntu0 B

4LABEL org.opencontainers.image.version=24.040 B

5ADD file ... in / 28.33 MB

6CMD ["/bin/bash"]0 B

7MAINTAINER [email protected]0 B

8ENV DEBIAN_FRONTEND=noninteractive0 B

9/bin/sh -c apt-get -qq update725.92 MB

10/bin/sh -c curl -L https://cpanmin.us1.21 MB

11/bin/sh -c cpanm install DB_File980.52 KB

12/bin/sh -c cpanm install URI::Escape673.56 KB

13ENV SRC=/usr/local/src0 B

14ENV BIN=/usr/local/bin0 B

15WORKDIR /usr/local/src0 B

16WORKDIR /usr/local/src0 B

17/bin/sh -c apt-get install -y170.87 MB

18ENV R_VERSION=R-4.4.00 B

19/bin/sh -c curl https://cran.r-project.org/src/base/R-4/$R_VERSION.tar.gz -o219.94 MB

20/bin/sh -c R -e 'install.packages("BiocManager",491.29 KB

21/bin/sh -c R -e 'BiocManager::install("tidyverse")'84.75 MB

22/bin/sh -c R -e 'BiocManager::install("edgeR")'13.48 MB

23/bin/sh -c R -e 'BiocManager::install("DESeq2")'56.07 MB

24/bin/sh -c R -e 'BiocManager::install("ape")'3.7 MB

25/bin/sh -c R -e 'BiocManager::install("ctc")'441.92 KB

26/bin/sh -c R -e 'BiocManager::install("gplots")'1.19 MB

27/bin/sh -c R -e 'BiocManager::install("Biobase")'92 B

28/bin/sh -c R -e 'BiocManager::install("qvalue")'4.34 MB

29/bin/sh -c R -e 'BiocManager::install("goseq")'179.28 MB

30/bin/sh -c R -e 'BiocManager::install("Glimma")'9.63 MB

31/bin/sh -c R -e 'BiocManager::install("ROTS")'1.01 MB

32/bin/sh -c R -e 'BiocManager::install("GOplot")'3.59 MB

33/bin/sh -c R -e 'BiocManager::install("argparse")'179.69 KB

34/bin/sh -c R -e 'BiocManager::install("fastcluster")'310.27 KB

35/bin/sh -c R -e 'BiocManager::install("DEXSeq")'7.79 MB

36/bin/sh -c R -e 'BiocManager::install("tximport")'362.09 KB

37/bin/sh -c R -e 'BiocManager::install("tximportData")'302.15 MB

38ENV LD_LIBRARY_PATH=/usr/local/lib0 B

39/bin/sh -c apt-get install -y7.55 MB

40/bin/sh -c ln -sf /usr/bin/python3152 B

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 -O

90.34 MB

43/bin/sh -c mkdir /usr/local/lib/site_perl159 B

44WORKDIR /usr/local/src0 B

45/bin/sh -c wget https://github.com/deweylab/RSEM/archive/v1.3.3.tar.gz &&15.79 MB

46WORKDIR /usr/local/src0 B

47/bin/sh -c wget https://github.com/pachterlab/kallisto/releases/download/v0.46.1/kallisto_linux-v0.46.1.tar.gz &&13.94 MB

48ENV FASTQC_VERSION=0.11.90 B

49WORKDIR /usr/local/src0 B

50/bin/sh -c wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v${FASTQC_VERSION}.zip &&19.39 MB

51WORKDIR /usr/local/src0 B

52ENV BLASTPLUS_VERSION=2.12.00 B

53

/bin/sh -c wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${BLASTPLUS_VERSION}/ncbi-blast-${BLASTPLUS_VERSION}+-x64-linux.tar.gz &&

478.64 MB

54WORKDIR /usr/local/src0 B

55ENV BOWTIE2_VERSION=2.4.40 B

56

/bin/sh -c wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/${BOWTIE2_VERSION}/bowtie2-${BOWTIE2_VERSION}-linux-x86_64.zip/download -O

61.22 MB

57ENV SAMTOOLS_VERSION=1.130 B

58

/bin/sh -c wget https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 &&

41.33 MB

59ENV JELLYFISH_VERSION=2.3.00 B

60

/bin/sh -c wget https://github.com/gmarcais/Jellyfish/releases/download/v${JELLYFISH_VERSION}/jellyfish-${JELLYFISH_VERSION}.tar.gz &&

13.21 MB

61ENV SUBREAD_VERSION=2.0.20 B

62

/bin/sh -c wget https://sourceforge.net/projects/subread/files/subread-${SUBREAD_VERSION}/subread-${SUBREAD_VERSION}-Linux-x86_64.tar.gz/download -O

78.28 MB

63/bin/sh -c wget https://cloud.biohpc.swmed.edu/index.php/s/oTtGWbWjaxsQ2Ho/download -O99.08 MB

64ENV GSNAP_VER=2021-07-230 B

65WORKDIR /usr/local/src0 B

66/bin/sh -c GMAP_URL="http://research-pub.gene.com/gmap/src/gmap-gsnap-$GSNAP_VER.tar.gz" && 127.87 MB

67/bin/sh -c wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat -P2.53 MB

68WORKDIR /usr/local/src0 B

69/bin/sh -c wget https://github.com/broadinstitute/picard/releases/download/2.25.7/picard.jar16 MB

70ENV PICARD_HOME=/usr/local/src0 B

71WORKDIR /usr/local/src0 B

72ENV GATK_VERSION=4.2.1.00 B

73/bin/sh -c wget https://github.com/broadinstitute/gatk/releases/download/${GATK_VERSION}/gatk-${GATK_VERSION}.zip &&905.57 MB

74ENV GATK_HOME=/usr/local/src/gatk-4.2.1.00 B

75ENV STAR_VERSION=2.7.8a0 B

76/bin/sh -c STAR_URL="https://github.com/alexdobin/STAR/archive/${STAR_VERSION}.tar.gz" && 19.08 MB

77WORKDIR /usr/local/src0 B

78ENV SALMON_VERSION=1.10.00 B

79/bin/sh -c wget https://github.com/COMBINE-lab/salmon/releases/download/v1.10.0/salmon-1.10.0_linux_x86_64.tar.gz -O179.39 MB

80WORKDIR /usr/local/src0 B

81/bin/sh -c wget http://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.gz &&4.77 MB

82/bin/sh -c apt-get install -y13.55 MB

83/bin/sh -c pip3 install git+https://github.com/ewels/MultiQC.git226.09 MB

84/bin/sh -c pip3 install HTSeq52.04 MB

85WORKDIR /usr/local/src0 B

86ENV TRINITY_VERSION=2.15.20 B

87ENV TRINITY_CO=4be803497fd22ce8461a9637eff46bc3b75a594a0 B

88WORKDIR /usr/local/src0 B

89/bin/sh -c git clone --recursive95 MB

90ENV TRINITY_HOME=/usr/local/bin0 B

91ENV PATH=/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin0 B

92WORKDIR /usr/local/src0 B

93/bin/sh -c rm -r ${R_VERSION}496 B

94/bin/sh -c apt-get -qq -y666.12 KB

95COPY file:04bfda4b6403243c263aa0766a5c3a30e3eb592e4a6611c577ef4cf791c89e87 in /usr/local/src/Dockerfile.2.15.2 2.67 KB

Command

 ARG RELEASE