From ac90343c054e679f3423d9d2760ae23f22bcce7e Mon Sep 17 00:00:00 2001 From: psudmant Date: Fri, 2 Oct 2020 16:45:30 -0700 Subject: [PATCH 1/3] add R studio support to Biology added R studio support and moved hub to use Dockerfile based on Dockerfile here: https://github.com/utoronto-2i2c/jupyterhub-deploy/tree/staging/deployments/utoronto/image --- .../biology/image/.environment.yml.swp | Bin 0 -> 12288 bytes deployments/biology/image/Dockerfile | 189 ++++++++++++++++++ deployments/biology/image/Rprofile.site | 6 + deployments/biology/image/environment.yml | 5 +- .../biology/image/install-miniforge.bash | 42 ++++ deployments/biology/image/install.R | 47 +++++ .../biology/image/jupyter_notebook_config.py | 12 ++ deployments/biology/image/postBuild | 46 ++--- deployments/biology/image/rsession.conf | 2 + jupyter_notebook_config.py | 12 ++ 10 files changed, 337 insertions(+), 24 deletions(-) create mode 100644 deployments/biology/image/.environment.yml.swp create mode 100644 deployments/biology/image/Dockerfile create mode 100644 deployments/biology/image/Rprofile.site create mode 100644 deployments/biology/image/install-miniforge.bash create mode 100644 deployments/biology/image/install.R create mode 100644 deployments/biology/image/jupyter_notebook_config.py create mode 100644 deployments/biology/image/rsession.conf create mode 100644 jupyter_notebook_config.py diff --git a/deployments/biology/image/.environment.yml.swp b/deployments/biology/image/.environment.yml.swp new file mode 100644 index 0000000000000000000000000000000000000000..999fca0e486eebda0f33d50c570479455df12b26 GIT binary patch literal 12288 zcmeI2zsu7=7{~7wSAT;#o_2eom!vIks}PVPLcy1}Ai9ZMl4}~@K<vo-enWlh0@M?HqMlemDi@qW#l;} z<9Vi2Z!!-0gR5R5ot)Q^m#8u~i`8pUW^$7*ysVI^@|3=tRYo_D#G+W2e$5xr78%$i z14mfD7x+!Zo%84Tsgu_?sd%cD43GgbKnBPF86X2>fDCNB0atFZhp=#{HF36`xBi&h zB~4_243GgbKnBPF86X2>fDDiUGC&5%z<+2!CX8(#W$YPf{{R2^`~Ukf#=d}$;2n4a zUV)e3Id}{nf&0LKn_v%I0v zfDDiUGVr?r&bz!@@k-sPvq~-7zlA$+tjo)+yof1LI;l*#2nS*ywy{yvHqKSp7o+8} zk_SZ|jzkZu4xh?+A3fui&ni=J^pVF#Cz8)h#mAGqV9Xfjoi5UqO1eVYeO2LLUtGY! zvQBI3YKxu{PWhJHl@g%h}9@LopZzSXo&(V{#h?hz>Y*qI)v*#ZUx2{_ihY zb-pvaqD`W1TST`v*h1N1&tH~SF5KMcwo>%R!vwnNGi4hu%fh-SELBbJwo(?)rPeA( F$Pc7mx%~hD literal 0 HcmV?d00001 diff --git a/deployments/biology/image/Dockerfile b/deployments/biology/image/Dockerfile new file mode 100644 index 000000000..e2b1173b5 --- /dev/null +++ b/deployments/biology/image/Dockerfile @@ -0,0 +1,189 @@ +FROM buildpack-deps:focal-scm + +ENV LC_ALL en_US.UTF-8 +ENV LANG en_US.UTF-8 +ENV LANGUAGE en_US.UTF-8 +ENV DEBIAN_FRONTEND=noninteractive +ENV NB_USER jovyan +ENV NB_UID 1000 + +ENV CONDA_DIR /opt/conda +ENV R_LIBS_USER /opt/r + +# Explicitly add littler to PATH +# See https://github.com/conda-forge/r-littler-feedstock/issues/6 +ENV PATH ${CONDA_DIR}/lib/R/library/littler/bin:${CONDA_DIR}/bin:$PATH + +RUN adduser --disabled-password --gecos "Default Jupyter user" ${NB_USER} + +# Create user owned R libs dir +# This lets users temporarily install packages +RUN mkdir -p ${R_LIBS_USER} && chown ${NB_USER}:${NB_USER} ${R_LIBS_USER} + +# Install these without 'recommended' packages to keep image smaller. +# Useful utils that folks sort of take for granted +RUN apt-get update -qq --yes && \ + apt-get install --yes --no-install-recommends -qq \ + htop \ + less \ + man \ + nano \ + screen \ + tar \ + tmux \ + wget \ + vim \ + locales > /dev/null + +RUN echo "${LC_ALL} UTF-8" > /etc/locale.gen && \ + locale-gen + +RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 +RUN echo "deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/" > /etc/apt/sources.list.d/cran.list + +# Install R packages +# Our pre-built R packages from rspm are built against system libs in focal +# rstan takes forever to compile from source, and needs libnodejs +# So we install older (10.x) nodejs from apt rather than newer from conda +RUN apt-get update -qq --yes > /dev/null && \ + apt-get install --yes -qq \ + r-base \ + r-base-dev \ + r-recommended \ + r-cran-littler \ + nodejs + +# Install desktop packages +RUN apt-get update -qq --yes > /dev/null && \ + apt-get install --yes -qq \ + dbus-x11 \ + firefox \ + xfce4 \ + xfce4-panel \ + xfce4-terminal \ + xfce4-session \ + xfce4-settings \ + xorg \ + xubuntu-icon-theme > /dev/null + +# for nbconvert & notebook-to-pdf +RUN apt-get update -qq --yes && \ + apt-get install --yes -qq \ + pandoc \ + texlive-xetex \ + texlive-fonts-recommended \ + libx11-xcb1 \ + libxtst6 \ + libxrandr2 \ + libasound2 \ + libpangocairo-1.0-0 \ + libatk1.0-0 \ + libatk-bridge2.0-0 \ + libgtk-3-0 \ + libnss3 \ + libxss1 \ + > /dev/null + +WORKDIR /home/jovyan + +COPY install-miniforge.bash /tmp/install-miniforge.bash +RUN chmod 777 /tmp/install-miniforge.bash +RUN /tmp/install-miniforge.bash + +# Needed by RStudio +RUN apt-get update -qq --yes && \ + apt-get install --yes --no-install-recommends -qq \ + psmisc \ + sudo \ + libapparmor1 \ + lsb-release \ + libclang-dev > /dev/null + +# Set path where R packages are installed +# Download and install rstudio manually +# Newer one has bug that doesn't work with jupyter-rsession-proxy +ENV RSTUDIO_URL https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.2.5042-amd64.deb +RUN curl --silent --location --fail ${RSTUDIO_URL} > /tmp/rstudio.deb && \ + dpkg -i /tmp/rstudio.deb && \ + rm /tmp/rstudio.deb + +# Needed by many R libraries +# Picked up from https://github.com/rocker-org/rocker/blob/9dc3e458d4e92a8f41ccd75687cd7e316e657cc0/r-rspm/focal/Dockerfile +RUN apt-get update && \ + apt-get install -y --no-install-recommends \ + libgdal26 \ + libgeos-3.8.0 \ + libproj15 \ + libudunits2-0 \ + libxml2 > /dev/null +# R_LIBS_USER is set by default in /etc/R/Renviron, which RStudio loads. +# We uncomment the default, and set what we wanna - so it picks up +# the packages we install. Without this, RStudio doesn't see the packages +# that R does. +# Stolen from https://github.com/jupyterhub/repo2docker/blob/6a07a48b2df48168685bb0f993d2a12bd86e23bf/repo2docker/buildpacks/r.py +RUN sed -i -e '/^R_LIBS_USER=/s/^/#/' /etc/R/Renviron && \ + echo "R_LIBS_USER=${R_LIBS_USER}" >> /etc/R/Renviron + +USER ${NB_USER} + +COPY environment.yml /tmp/ +COPY requirements.txt /tmp/ +COPY infra-requirements.txt /tmp/ + +RUN conda env update -p ${CONDA_DIR} -f /tmp/environment.yml + +# Set CRAN mirror to rspm before we install anything +COPY Rprofile.site /usr/lib/R/etc/Rprofile.site +# RStudio needs its own config +COPY rsession.conf /etc/rstudio/rsession.conf + +#install rsession proxy +RUN pip install --no-cache-dir \ + jupyter-rsession-proxy==1.2 + +# Install IRKernel +RUN r -e "install.packages('IRkernel', version='1.1.1')" && \ + r -e "IRkernel::installspec(prefix='${CONDA_DIR}')" + +# Install R packages, cleanup temp package download location +COPY install.R /tmp/install.R +RUN r /tmp/install.R && \ + rm -rf /tmp/downloaded_packages/ /tmp/*.rds + +# Set bash as shell in terminado. +ADD jupyter_notebook_config.py ${CONDA_PREFIX}/etc/jupyter/ +# Disable history. +ADD ipython_config.py ${CONDA_PREFIX}/etc/ipython/ + +# Install PAUP* for BIO 1B +# https://github.com/berkeley-dsep-infra/datahub/issues/1699 +RUN wget http://phylosolutions.com/paup-test/paup4a168_ubuntu64.gz -O ${CONDA_DIR}/bin/paup.gz +RUN gunzip ${CONDA_DIR}/bin/paup.gz +RUN chmod +x ${CONDA_DIR}/bin/paup + +############################ +# Install packages for IB134L +############################ +#LOCAL_BIN=${REPO_DIR}/.local/bin +#mkdir -p ${LOCAL_BIN} +# +## mitoZ installation +# +#wget https://raw.githubusercontent.com/linzhi2013/MitoZ/master/version_2.4-alpha/release_MitoZ_v2.4-alpha.tar.bz2 -O ${REPO_DIR}/release_MitoZ_v2.4-alpha.tar.bz2 +#pushd ${REPO_DIR} +#tar -jxvf release_MitoZ_v2.4-alpha.tar.bz2 +#rm release_MitoZ_v2.4-alpha.tar.bz2 +#cd release_MitoZ_v2.4-alpha +#wget https://raw.githubusercontent.com/linzhi2013/MitoZ/master/version_2.4-alpha/mitozEnv.yaml +#cd .. +# +### create mitoZ env +#conda env create -n mitozEnv -f release_MitoZ_v2.4-alpha/mitozEnv.yaml # worked after reinstallation of conda +# +### patch ncbiquery.py +#cp patches/ncbiquery.py /srv/conda/envs/mitozEnv/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py +# +### download annotations +##source activate mitozEnv +##python3 mitozEnv_config.py +##source deactivate diff --git a/deployments/biology/image/Rprofile.site b/deployments/biology/image/Rprofile.site new file mode 100644 index 000000000..a96d6ef22 --- /dev/null +++ b/deployments/biology/image/Rprofile.site @@ -0,0 +1,6 @@ +local({ + r <- getOption("repos") + r["CRAN"] <- "https://packagemanager.rstudio.com/all/__linux__/focal/latest" + options(repos = r) + options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version$platform, R.version$arch, R.version$os))) +}) \ No newline at end of file diff --git a/deployments/biology/image/environment.yml b/deployments/biology/image/environment.yml index c8e43846d..d5f91d1ed 100644 --- a/deployments/biology/image/environment.yml +++ b/deployments/biology/image/environment.yml @@ -5,13 +5,16 @@ dependencies: - python=3.8.* - pip=20.* +# nodejs +- nodejs + # Packages from bioconda for IB134L - bwa=0.7.12 - samtools=1.3.1 - mafft=7.471 - emboss=6.6.0 - augustus=3.3.3 -- repeatmasker=4.0.9 + #- repeatmasker=4.0.9 # Packages from bioconda for BIO1B - raxml=8.2.* diff --git a/deployments/biology/image/install-miniforge.bash b/deployments/biology/image/install-miniforge.bash new file mode 100644 index 000000000..7b2441a2b --- /dev/null +++ b/deployments/biology/image/install-miniforge.bash @@ -0,0 +1,42 @@ +#!/bin/bash +# This downloads and installs a pinned version of miniconda +set -ex + +cd $(dirname $0) +MINIFORGE_VERSION=4.8.3-5 + +URL="https://github.com/conda-forge/miniforge/releases/download/4.8.3-5/Miniforge3-${MINIFORGE_VERSION}-Linux-x86_64.sh" +INSTALLER_PATH=/tmp/miniforge-installer.sh + +# make sure we don't do anything funky with user's $HOME +# since this is run as root +unset HOME + +wget --quiet $URL -O ${INSTALLER_PATH} +chmod +x ${INSTALLER_PATH} + +bash ${INSTALLER_PATH} -b -p ${CONDA_DIR} +export PATH="${CONDA_DIR}/bin:$PATH" + +# Do not attempt to auto update conda or dependencies +conda config --system --set auto_update_conda false +conda config --system --set show_channel_urls true + +# empty conda history file, +# which seems to result in some effective pinning of packages in the initial env, +# which we don't intend. +# this file must not be *removed*, however +echo '' > ${CONDA_DIR}/conda-meta/history + +# Clean things out! +conda clean --all -f -y + +# Remove the big installer so we don't increase docker image size too much +rm ${INSTALLER_PATH} + +# Remove the pip cache created as part of installing miniconda +rm -rf /root/.cache + +chown -R $NB_USER:$NB_USER ${CONDA_DIR} + +conda list -n root diff --git a/deployments/biology/image/install.R b/deployments/biology/image/install.R new file mode 100644 index 000000000..60a3e3930 --- /dev/null +++ b/deployments/biology/image/install.R @@ -0,0 +1,47 @@ +#!/usr/bin/env r + +# Install devtools, so we can install versioned packages +install.packages("devtools") + +# Install a bunch of R packages +# This doesn't do any dependency resolution or anything, +# so refer to `installed.packages()` for authoritative list +cran_packages <- c( + "tidyverse", "1.3.0" + #"learnr", "0.10.1", + #"knitr", "1.29" + #"rmarkdown", "2.3", + #"Rcpp", "1.0.5" + #"reticulate", "1.16", + #"openintro", "2.0.0", + #"gridExtra", "2.3", + #"BHH2", "2016.05.31", + #"nycflights13", "1.0.1", + #"tinytex", "0.25", + #"spdep", "1.1-5", + #"shiny", "1.5.0", + #"rstan", "2.21.2", + #"ggforce", "0.3.2", + #"ggthemes", "4.2.0" +) + +#github_packages <- c( +# # https://github.com/utoronto-2i2c/jupyterhub-deploy/issues/31 +# #"cutterkom/generativeart", "56ce6beed0433748b4372bfffba0e1c9f2740f9b", +# #"djnavarro/flametree", "0999530f758d074c214c068726e68786bb4698f6" +#) +# +for (i in seq(1, length(cran_packages), 2)) { + devtools::install_version( + cran_packages[i], + version = cran_packages[i + 1] + ) +} +# +# +#for (i in seq(1, length(github_packages), 2)) { +# devtools::install_github( +# github_packages[i], +# ref = github_packages[i + 1] +# ) +#} diff --git a/deployments/biology/image/jupyter_notebook_config.py b/deployments/biology/image/jupyter_notebook_config.py new file mode 100644 index 000000000..f14034003 --- /dev/null +++ b/deployments/biology/image/jupyter_notebook_config.py @@ -0,0 +1,12 @@ +# This is sh (dash) by default, not $SHELL +c.NotebookApp.terminado_settings = { "shell_command": ["bash"] } + +c.ServerProxy.servers = { + 'http-server': { + 'command': ['python3', '-m', 'http.server', '{port}'], + 'absolute_url': False, + 'launcher_entry': { + 'title': "HTTP Server" + } + } +} diff --git a/deployments/biology/image/postBuild b/deployments/biology/image/postBuild index 06cf6b9b6..e8c3e250a 100644 --- a/deployments/biology/image/postBuild +++ b/deployments/biology/image/postBuild @@ -15,27 +15,27 @@ chmod +x ${CONDA_DIR}/bin/paup ############################ # Install packages for IB134L ############################ -LOCAL_BIN=${REPO_DIR}/.local/bin -mkdir -p ${LOCAL_BIN} - -# mitoZ installation - -wget https://raw.githubusercontent.com/linzhi2013/MitoZ/master/version_2.4-alpha/release_MitoZ_v2.4-alpha.tar.bz2 -O ${REPO_DIR}/release_MitoZ_v2.4-alpha.tar.bz2 -pushd ${REPO_DIR} -tar -jxvf release_MitoZ_v2.4-alpha.tar.bz2 -rm release_MitoZ_v2.4-alpha.tar.bz2 -cd release_MitoZ_v2.4-alpha -wget https://raw.githubusercontent.com/linzhi2013/MitoZ/master/version_2.4-alpha/mitozEnv.yaml -cd .. - -## create mitoZ env -conda env create -n mitozEnv -f release_MitoZ_v2.4-alpha/mitozEnv.yaml # worked after reinstallation of conda - -## patch ncbiquery.py -cp patches/ncbiquery.py /srv/conda/envs/mitozEnv/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py - -## download annotations -#source activate mitozEnv -#python3 mitozEnv_config.py -#source deactivate +#LOCAL_BIN=${REPO_DIR}/.local/bin +#mkdir -p ${LOCAL_BIN} +# +## mitoZ installation +# +#wget https://raw.githubusercontent.com/linzhi2013/MitoZ/master/version_2.4-alpha/release_MitoZ_v2.4-alpha.tar.bz2 -O ${REPO_DIR}/release_MitoZ_v2.4-alpha.tar.bz2 +#pushd ${REPO_DIR} +#tar -jxvf release_MitoZ_v2.4-alpha.tar.bz2 +#rm release_MitoZ_v2.4-alpha.tar.bz2 +#cd release_MitoZ_v2.4-alpha +#wget https://raw.githubusercontent.com/linzhi2013/MitoZ/master/version_2.4-alpha/mitozEnv.yaml +#cd .. +# +### create mitoZ env +#conda env create -n mitozEnv -f release_MitoZ_v2.4-alpha/mitozEnv.yaml # worked after reinstallation of conda +# +### patch ncbiquery.py +#cp patches/ncbiquery.py /srv/conda/envs/mitozEnv/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py +# +### download annotations +##source activate mitozEnv +##python3 mitozEnv_config.py +##source deactivate diff --git a/deployments/biology/image/rsession.conf b/deployments/biology/image/rsession.conf new file mode 100644 index 000000000..a9ab23c21 --- /dev/null +++ b/deployments/biology/image/rsession.conf @@ -0,0 +1,2 @@ +# Use binary packages! +r-cran-repos=https://packagemanager.rstudio.com/all/__linux__/focal/latest diff --git a/jupyter_notebook_config.py b/jupyter_notebook_config.py new file mode 100644 index 000000000..f14034003 --- /dev/null +++ b/jupyter_notebook_config.py @@ -0,0 +1,12 @@ +# This is sh (dash) by default, not $SHELL +c.NotebookApp.terminado_settings = { "shell_command": ["bash"] } + +c.ServerProxy.servers = { + 'http-server': { + 'command': ['python3', '-m', 'http.server', '{port}'], + 'absolute_url': False, + 'launcher_entry': { + 'title': "HTTP Server" + } + } +} From df511196ec9bff4a28a320ad45913bd286b90861 Mon Sep 17 00:00:00 2001 From: psudmant Date: Fri, 2 Oct 2020 19:47:45 -0700 Subject: [PATCH 2/3] add libpython2.7 support for paup --- deployments/biology/image/Dockerfile | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/deployments/biology/image/Dockerfile b/deployments/biology/image/Dockerfile index e2b1173b5..d6733fa7d 100644 --- a/deployments/biology/image/Dockerfile +++ b/deployments/biology/image/Dockerfile @@ -20,6 +20,12 @@ RUN adduser --disabled-password --gecos "Default Jupyter user" ${NB_USER} # This lets users temporarily install packages RUN mkdir -p ${R_LIBS_USER} && chown ${NB_USER}:${NB_USER} ${R_LIBS_USER} +# Required for PAUP* +# Note that this doesn't actually install python2, thankfully +RUN apt-get update -qq --yes > /dev/null && \ + apt-get install --yes -qq \ + libpython2.7 > /dev/null + # Install these without 'recommended' packages to keep image smaller. # Useful utils that folks sort of take for granted RUN apt-get update -qq --yes && \ From 3f9446daf5f458f48e04325b51698fdd8a623b42 Mon Sep 17 00:00:00 2001 From: psudmant Date: Fri, 2 Oct 2020 19:48:46 -0700 Subject: [PATCH 3/3] remove apt.txt and postBuild --- .../biology/image/.environment.yml.swp | Bin 12288 -> 0 bytes deployments/biology/image/apt.txt | 14 ------ deployments/biology/image/postBuild | 41 ------------------ 3 files changed, 55 deletions(-) delete mode 100644 deployments/biology/image/.environment.yml.swp delete mode 100644 deployments/biology/image/apt.txt delete mode 100644 deployments/biology/image/postBuild diff --git a/deployments/biology/image/.environment.yml.swp b/deployments/biology/image/.environment.yml.swp deleted file mode 100644 index 999fca0e486eebda0f33d50c570479455df12b26..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 12288 zcmeI2zsu7=7{~7wSAT;#o_2eom!vIks}PVPLcy1}Ai9ZMl4}~@K<vo-enWlh0@M?HqMlemDi@qW#l;} z<9Vi2Z!!-0gR5R5ot)Q^m#8u~i`8pUW^$7*ysVI^@|3=tRYo_D#G+W2e$5xr78%$i z14mfD7x+!Zo%84Tsgu_?sd%cD43GgbKnBPF86X2>fDCNB0atFZhp=#{HF36`xBi&h zB~4_243GgbKnBPF86X2>fDDiUGC&5%z<+2!CX8(#W$YPf{{R2^`~Ukf#=d}$;2n4a zUV)e3Id}{nf&0LKn_v%I0v zfDDiUGVr?r&bz!@@k-sPvq~-7zlA$+tjo)+yof1LI;l*#2nS*ywy{yvHqKSp7o+8} zk_SZ|jzkZu4xh?+A3fui&ni=J^pVF#Cz8)h#mAGqV9Xfjoi5UqO1eVYeO2LLUtGY! zvQBI3YKxu{PWhJHl@g%h}9@LopZzSXo&(V{#h?hz>Y*qI)v*#ZUx2{_ihY zb-pvaqD`W1TST`v*h1N1&tH~SF5KMcwo>%R!vwnNGi4hu%fh-SELBbJwo(?)rPeA( F$Pc7mx%~hD diff --git a/deployments/biology/image/apt.txt b/deployments/biology/image/apt.txt deleted file mode 100644 index 6a0d08bfb..000000000 --- a/deployments/biology/image/apt.txt +++ /dev/null @@ -1,14 +0,0 @@ -# Required for PAUP* -# Note that this doesn't actually install python2, thankfully -libpython2.7 - -# utils -vim -less -tmux -man - -# nbconvert -texlive-xetex -texlive-fonts-recommended -texlive-generic-recommended diff --git a/deployments/biology/image/postBuild b/deployments/biology/image/postBuild deleted file mode 100644 index e8c3e250a..000000000 --- a/deployments/biology/image/postBuild +++ /dev/null @@ -1,41 +0,0 @@ -#!/bin/bash -set -euo pipefail - -# Create ipython config directory if it doesn't exist -mkdir -p ${CONDA_DIR}/etc/ipython -cp ipython_config.py ${CONDA_DIR}/etc/ipython/ipython_config.py - -# Install PAUP* for BIO 1B -# https://github.com/berkeley-dsep-infra/datahub/issues/1699 - -wget http://phylosolutions.com/paup-test/paup4a168_ubuntu64.gz -O ${CONDA_DIR}/bin/paup.gz -gunzip ${CONDA_DIR}/bin/paup.gz -chmod +x ${CONDA_DIR}/bin/paup - -############################ -# Install packages for IB134L -############################ -#LOCAL_BIN=${REPO_DIR}/.local/bin -#mkdir -p ${LOCAL_BIN} -# -## mitoZ installation -# -#wget https://raw.githubusercontent.com/linzhi2013/MitoZ/master/version_2.4-alpha/release_MitoZ_v2.4-alpha.tar.bz2 -O ${REPO_DIR}/release_MitoZ_v2.4-alpha.tar.bz2 -#pushd ${REPO_DIR} -#tar -jxvf release_MitoZ_v2.4-alpha.tar.bz2 -#rm release_MitoZ_v2.4-alpha.tar.bz2 -#cd release_MitoZ_v2.4-alpha -#wget https://raw.githubusercontent.com/linzhi2013/MitoZ/master/version_2.4-alpha/mitozEnv.yaml -#cd .. -# -### create mitoZ env -#conda env create -n mitozEnv -f release_MitoZ_v2.4-alpha/mitozEnv.yaml # worked after reinstallation of conda -# -### patch ncbiquery.py -#cp patches/ncbiquery.py /srv/conda/envs/mitozEnv/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py -# -### download annotations -##source activate mitozEnv -##python3 mitozEnv_config.py -##source deactivate -