Commit 59bdc9e2 authored by josh's avatar josh
Browse files

Many changes trying to install Eva's requests

major change: update to ubuntu 20.04 and python3
parent 942d947e
Pipeline #192974 failed with stages
in 5 seconds
......@@ -7,7 +7,7 @@ MAINTAINER Mark McCahill "mark.mccahill@duke.edu"
ENV DEBIAN_FRONTEND noninteractive
ENV R_VERSION="3.6.3"
ENV RSTUDIO_VERSION="1.2.1335"
ENV RSTUDIO_VERSION="1.2.5042"
ENV CRAN_REPO="'https://mran.revolutionanalytics.com/snapshot/2020-04-23'"
# get R from a CRAN archive
......@@ -75,13 +75,19 @@ RUN apt-get update && \
# R-Studio
RUN apt-get update && \
apt-get -yq install \
ca-certificates \
wget \
gdebi-core \
libssl1.1 \
libssl-dev \
dpkg-sig \
libapparmor1
python3-ldap3
RUN wget --no-verbose https://download2.rstudio.org/rstudio-server-1.1.383-amd64.deb
RUN gdebi -n rstudio-server-1.1.383-amd64.deb
RUN rm rstudio-server-1.1.383-amd64.deb
# RUN wget --no-verbose https://download2.rstudio.org/rstudio-server-1.1.383-amd64.deb
# RUN gdebi -n rstudio-server-1.1.383-amd64.deb
# RUN rm rstudio-server-1.1.383-amd64.deb
# https://github.com/inversepath/usbarmory-debian-base_image/issues/9
RUN mkdir ~/.gnupg && \
echo "disable-ipv6" >> ~/.gnupg/dirmngr.conf && \
......@@ -162,20 +168,18 @@ RUN apt-get update && \
htop \
libudunits2-dev \
software-properties-common \
sra-toolkit \
libgdal-dev \
build-essential \
python-dev \
python3-pip \
python-numpy \
python-matplotlib \
python-pandas \
ipython \
python3-numpy \
python3-matplotlib \
python3-pandas \
samtools \
rna-star \
bwa \
trimmomatic \
python-igraph \
python3-igraph \
abyss \
bc \
rdp-readseq \
......@@ -184,6 +188,7 @@ RUN apt-get update && \
librdp-taxonomy-tree-java \
clustalw \
fastqc
# sra-toolkit ipython \
# RUN pip install qiime
......@@ -343,20 +348,37 @@ RUN cd /opt && \
# UNDER CONSTRUCTION: Nerd Work Zone <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
# SHOGUN
# https://github.com/knights-lab/BURST/releases
# https://github.com/knights-lab/UTree/releases/tag/v2.0c
RUN curl -L -s https://github.com/knights-lab/UTree/releases/download/v2.0c/utree-v2.0.c-linux-64.tar.gz | \
tar -zx && \
chmod 555 utree-*_gg && \
mv utree-*_gg $MANUAL_BIN
RUN curl -L -s https://github.com/knights-lab/BURST/releases/download/v1.0/burst-v1.0-linux-64.tar.gz | \
tar -zx && \
chmod 555 burst* && \
mv burst* $MANUAL_BIN
RUN curl -L -s -o shogun.tar.gz https://github.com/knights-lab/SHOGUN/archive/v1.0.8.tar.gz && \
pip3 install --no-cache-dir shogun.tar.gz && \
rm shogun.tar.gz
# MetaPhlAn
# https://pypi.org/project/MetaPhlAn/
RUN pip3 install --no-cache-dir MetaPhlAn
# Kraken2
RUN apt-get update && \
apt-get install -yq --no-install-recommends \
kraken2 \
bowtie2
# kaiju
RUN mkdir kaiju && \
curl -L -s kaiju.tar.gz https://github.com/bioinformatics-centre/kaiju/archive/v1.7.4.tar.gz | \
curl -L -s https://github.com/bioinformatics-centre/kaiju/archive/v1.7.4.tar.gz | \
tar -zx -C kaiju --strip-components=1 && \
cd kaiju/src && \
make && \
......
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