jennydaman/trinityrnaseq:2.13.2-grid

Manifest digest

sha256:da812037cf4ff6fd2b59ae9cd1d81db7024244aa9b166e16fcc4251f006bcd74

OS/ARCH

linux/amd64

Compressed size

3.66 GB

Last pushed

almost 5 years by jennydaman

Type

Image

Manifest digest

sha256:da812037cf4ff6fd2b59ae9cd1d81db7024244aa9b166e16fcc4251f006bcd74

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

7ENV DEBIAN_FRONTEND=noninteractive0 B

8/bin/sh -c apt-get -qq update522.88 MB

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

10/bin/sh -c cpanm install DB_File791.47 KB

11/bin/sh -c cpanm install URI::Escape415.27 KB

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 -o195.82 MB

17/bin/sh -c R -e 'install.packages("BiocManager",95.95 KB

18/bin/sh -c R -e 'BiocManager::install("tidyverse")'68.04 MB

19/bin/sh -c R -e 'BiocManager::install("edgeR")'7.8 MB

20/bin/sh -c R -e 'BiocManager::install("DESeq2")'69.19 MB

21/bin/sh -c R -e 'BiocManager::install("ape")'2.74 MB

22/bin/sh -c R -e 'BiocManager::install("ctc")'548.31 KB

23/bin/sh -c R -e 'BiocManager::install("gplots")'1.12 MB

24/bin/sh -c R -e 'BiocManager::install("Biobase")'2.21 MB

25/bin/sh -c R -e 'BiocManager::install("qvalue")'4.18 MB

26/bin/sh -c R -e 'BiocManager::install("goseq")'160.43 MB

27/bin/sh -c R -e 'BiocManager::install("Glimma")'3.28 MB

28/bin/sh -c R -e 'BiocManager::install("ROTS")'882.21 KB

29/bin/sh -c R -e 'BiocManager::install("GOplot")'2.5 MB

30/bin/sh -c R -e 'BiocManager::install("argparse")'168.43 KB

31/bin/sh -c R -e 'BiocManager::install("fastcluster")'277.73 KB

32/bin/sh -c R -e 'BiocManager::install("DEXSeq")'2.37 MB

33/bin/sh -c R -e 'BiocManager::install("tximport")'340.47 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/python3160 B

38/bin/sh -c pip3 install numpy27.85 MB

39/bin/sh -c pip3 install git+https://github.com/ewels/MultiQC.git43.66 MB

40/bin/sh -c pip3 install HTSeq21.42 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 -O

90.34 MB

43/bin/sh -c mkdir /usr/local/lib/site_perl197 B

44WORKDIR /usr/local/src0 B

45/bin/sh -c wget https://github.com/deweylab/RSEM/archive/v1.3.3.tar.gz &&15.08 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 &&

38.17 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 &&

11.45 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" && 127.78 MB

67/bin/sh -c wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat -P2.54 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=1.5.20 B

79

/bin/sh -c wget https://github.com/COMBINE-lab/salmon/releases/download/v${SALMON_VERSION}/Salmon-${SALMON_VERSION}_linux_x86_64.tar.gz &&

102.57 MB

80WORKDIR /usr/local/src0 B

81ENV TRINITY_VERSION=2.13.20 B

82ENV TRINITY_CO=8849ad70be3cad9c5033f54bdf8a3c8801c932290 B

83WORKDIR /usr/local/src0 B

84/bin/sh -c git clone --recursive66.44 MB

85ENV TRINITY_HOME=/usr/local/bin0 B

86ENV PATH=/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin0 B

87WORKDIR /usr/local/src0 B

88/bin/sh -c rm -r ${R_VERSION}466 B

89/bin/sh -c apt-get -qq -y558.16 KB

90COPY file:06d1f7ebd24d4f769550330c71caad9c2feb3e67103dc8947c40098e7a945205 in /usr/local/src/Dockerfile.2.13.2 2.56 KB

91/bin/sh -c apt-get update26 MB

92/bin/sh -c apt-get install -y1.76 MB

93COPY dir:fd79e98c0545d4a811078b95311588188bf13d4d8cbed7a68f87f35b0d1cf046 in /opt/HpcGridRunner 33.77 KB

94COPY file:0d1fec98a861569c38bc20d04b70ae8d9d6bcecb8c5f06909c9a4e571438f280 in /usr/local/bin/chorus.sh 1.54 KB

Command

ADD file:7d9bbf45a5b2510d44d3206a028cf6502757884d49e46d3d2e6356c3a92c4309 in /