Namespace
teambraker
Image / Tagbraker3:v.1.0.4.1
Content Digestsha256:2299a6317eef3207372886b3bdcca6afc7735ad4a890eab612c8da4005207281
Details
2023-10-11 08:40:55 UTC
1.62 GB
Labels
-
maintainerJupyter Project <jupyter@googlegroups.com>
-
org.opencontainers.image.ref.nameubuntu
-
org.opencontainers.image.version22.04
Environment
AUGUSTUS_BIN_PATH/usr/bin/
AUGUSTUS_CONFIG_PATH/usr/share/augustus/config/
AUGUSTUS_SCRIPTS_PATH/usr/share/augustus/scripts/
CONDA_DIR/opt/conda
DEBIAN_FRONTENDnoninteractive
GENEMARK_PATH/opt/ETP/bin
HOME/home/jovyan
JUPYTER_PORT8888
LANGen_US.UTF-8
LANGUAGEen_US.UTF-8
LC_ALLen_US.UTF-8
NB_GID100
NB_UID1000
NB_USERjovyan
PATH/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/seqstats:/opt/cdbfasta:/opt/TSEBRA/bin:/opt/MakeHub:/opt/BRAKER/scripts:/opt/ETP/bin:/opt/ETP/tools:/opt/ETP/bin/gmes/ProtHint/bin:/opt/ETP/bin/gmes
SHELL/bin/bash
SUDO_FORCE_REMOVEyes
Layers
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[#002] sha256:7a2b4dd53caccbd374b123296038596c357cf0b9fe9ecd80b9554e4c89a052ff - 0.0% (678 Bytes)
[#003] sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 - 0.0% (32 Bytes)
[#004] sha256:f8cb1d2f7e20229930b7343319f415289630e22a3ccc4d6c0ea599e26f260f58 - 0.0% (1.87 KB)
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[#009] sha256:08234ca7e91faac3145a69aad850139c0a8c05e6cd061969e7299513f7b6c33c - 5.25% (87 MB)
[#010] sha256:35c0c002241e17bc9a93eff727ad7a4c5e6128695c39de1b3f2eda678f417f44 - 0.0% (4.1 KB)
[#011] sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 - 0.0% (32 Bytes)
[#012] sha256:e1519919153b656002b10f5c358c8070eba6cc41a5a4891ee1a72d928abe01d8 - 1.77% (29.3 MB)
[#013] sha256:b866059daba98a2b2023c6ced0c9d9dc2766bd46c9b704d1b0c4f9cf21b834e0 - 6.87% (114 MB)
[#014] sha256:6b626b41cbdd09e248a0dba94ea322c5e58ec87b47b4eaf18aa23eac5c6ff97e - 0.0% (683 Bytes)
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[#016] sha256:e4088845342317ed04fabed3fc6b876d10acbc657f65908565e34b7b06cb15d4 - 0.0% (1.11 KB)
[#017] sha256:788a1778e3caa91a3ad0be0ce410eb507dab62362215eabadfd3d2e76053f3fa - 1.28% (21.2 MB)
[#018] sha256:d2327979cb0785a60c70bce82e873407623cc9b60ee23fe5de9c2077a0877324 - 0.02% (421 KB)
[#019] sha256:d4ba5d386d72a07abacdf50ac7d0c41444b4d9d859d54b9c3e2b772c6f69ebcd - 11.45% (190 MB)
[#020] sha256:326593c72c7e03cb9871c467596fa18fc4b639718a0d9b6401fa9d10c651dfa2 - 9.88% (164 MB)
[#021] sha256:5c0048263e6eb546f9aca8c9de2e27e5f27ab5d0f65b11ec910ec6c425aa89f3 - 0.0% (1.53 KB)
[#022] sha256:179f754036e2ed1733341fa46bb1701649ad0cb671cbb1c27024e82c28a7c739 - 0.0% (437 Bytes)
[#023] sha256:e0f250156230802be0037b5aab71a25983bc15fd6939ddfe860f8ca769aae171 - 16.51% (273 MB)
[#024] sha256:722137bce0015e70b1c769e21a9cee9e2db0dad25023d40b7be5de4f6cd36043 - 0.15% (2.52 MB)
[#025] sha256:afd4f74c025028308b4f876a35509b1c8e66fa6cae794cd7cd756fcf8b9b1538 - 0.08% (1.38 MB)
[#026] sha256:1c44777d0dc4b79af795a0c0e36ff5c06de0ebf44d720d2362b736256cc6608e - 0.05% (924 KB)
[#027] sha256:d1b34f82f8cdd5b8a1a4b02092856245514c8d9a8f4c6967ec3cec874d1b8829 - 3.59% (59.5 MB)
[#028] sha256:7da56a27f920dac47ec7df9eabd6bd4512b38968bfce850ee97ead3a85060fca - 3.49% (57.8 MB)
[#029] sha256:911b3fb18e1c56358fae9bede839bfc53d2f7c23074805b8e50682f3d127f72e - 4.1% (68 MB)
[#030] sha256:a8aaeed7aa6f26e7a85826f0c81a19764c544860568bed2565f89aa5a8eccd91 - 0.88% (14.5 MB)
[#031] sha256:4e55a6c82cf9816efd77f43fda4782801df62d729f37e64cf646c8c830c0202d - 0.0% (43.4 KB)
[#032] sha256:4e8420ef9a6d15a7586ac7a35b91a85cba159711c14b6b3d6c12c60f802749c8 - 0.0% (7.88 KB)
[#033] sha256:d2fcf73697ea247644f6b122f58d8388fbfa87727ef8640485cced96a764a24e - 0.06% (1.06 MB)
[#034] sha256:1079f418230549427d87bfba97ed9f97f16ad8383d036bf380d48674f6ffbd43 - 13.42% (222 MB)
[#035] sha256:a11962292eb461b332f0707b16c946b804f0e9989946797901616640ec359b90 - 11.57% (192 MB)
[#036] sha256:2f5e3f3aa551b6266e636bc67b3fcdaa35003d0f7e98382a8158c886606c2e10 - 7.13% (118 MB)
History
/bin/sh -c #(nop) ARG RELEASE
2023-01-26 04:57:59 UTC/bin/sh -c #(nop) ARG LAUNCHPAD_BUILD_ARCH
2023-01-26 04:58:00 UTC/bin/sh -c #(nop) LABEL org.opencontainers.image.ref.name=ubuntu
2023-01-26 04:58:00 UTC/bin/sh -c #(nop) LABEL org.opencontainers.image.version=22.04
2023-01-26 04:58:02 UTC/bin/sh -c #(nop) ADD file:18e71f049606f6339ce7a995839623f50e6ec6474bfd0a3a7ca799db726f47f6 in /
2023-01-26 04:58:02 UTC/bin/sh -c #(nop) CMD ["/bin/bash"]
2023-02-20 03:08:17 UTC (buildkit.dockerfile.v0)LABEL maintainer=Jupyter Project <jupyter@googlegroups.com>
2023-02-20 03:08:17 UTC (buildkit.dockerfile.v0)ARG NB_USER=jovyan
2023-02-20 03:08:17 UTC (buildkit.dockerfile.v0)ARG NB_UID=1000
2023-02-20 03:08:17 UTC (buildkit.dockerfile.v0)ARG NB_GID=100
2023-02-20 03:08:17 UTC (buildkit.dockerfile.v0)SHELL [/bin/bash -o pipefail -c]
2023-02-20 03:08:17 UTC (buildkit.dockerfile.v0)USER root
2023-02-20 03:08:17 UTC (buildkit.dockerfile.v0)ENV DEBIAN_FRONTEND=noninteractive
2023-02-20 03:08:17 UTC (buildkit.dockerfile.v0)RUN |3 NB_USER=jovyan NB_UID=1000 NB_GID=100 /bin/bash -o pipefail -c apt-get update --yes && apt-get upgrade --yes && apt-get install --yes --no-install-recommends bzip2 ca-certificates locales sudo tini wget && apt-get clean && rm -rf /var/lib/apt/lists/* && echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && locale-gen # buildkit
2023-02-20 03:08:17 UTC (buildkit.dockerfile.v0)ENV CONDA_DIR=/opt/conda SHELL=/bin/bash NB_USER=jovyan NB_UID=1000 NB_GID=100 LC_ALL=en_US.UTF-8 LANG=en_US.UTF-8 LANGUAGE=en_US.UTF-8
2023-02-20 03:08:17 UTC (buildkit.dockerfile.v0)ENV PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin HOME=/home/jovyan
2023-02-20 03:08:17 UTC (buildkit.dockerfile.v0)COPY fix-permissions /usr/local/bin/fix-permissions # buildkit
2023-02-20 03:08:17 UTC (buildkit.dockerfile.v0)RUN |3 NB_USER=jovyan NB_UID=1000 NB_GID=100 /bin/bash -o pipefail -c chmod a+rx /usr/local/bin/fix-permissions # buildkit
2023-02-20 03:08:17 UTC (buildkit.dockerfile.v0)RUN |3 NB_USER=jovyan NB_UID=1000 NB_GID=100 /bin/bash -o pipefail -c sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc && echo 'eval "$(command conda shell.bash hook 2> /dev/null)"' >> /etc/skel/.bashrc # buildkit
2023-02-20 03:08:18 UTC (buildkit.dockerfile.v0)RUN |3 NB_USER=jovyan NB_UID=1000 NB_GID=100 /bin/bash -o pipefail -c echo "auth requisite pam_deny.so" >> /etc/pam.d/su && sed -i.bak -e 's/^%admin/#%admin/' /etc/sudoers && sed -i.bak -e 's/^%sudo/#%sudo/' /etc/sudoers && useradd -l -m -s /bin/bash -N -u "${NB_UID}" "${NB_USER}" && mkdir -p "${CONDA_DIR}" && chown "${NB_USER}:${NB_GID}" "${CONDA_DIR}" && chmod g+w /etc/passwd && fix-permissions "${HOME}" && fix-permissions "${CONDA_DIR}" # buildkit
2023-02-20 03:08:18 UTC (buildkit.dockerfile.v0)USER 1000
2023-02-20 03:08:18 UTC (buildkit.dockerfile.v0)ARG PYTHON_VERSION=3.10
2023-02-20 03:08:18 UTC (buildkit.dockerfile.v0)RUN |4 NB_USER=jovyan NB_UID=1000 NB_GID=100 PYTHON_VERSION=3.10 /bin/bash -o pipefail -c mkdir "/home/${NB_USER}/work" && fix-permissions "/home/${NB_USER}" # buildkit
2023-02-20 03:08:18 UTC (buildkit.dockerfile.v0)COPY initial-condarc /opt/conda/.condarc # buildkit
2023-02-20 03:08:18 UTC (buildkit.dockerfile.v0)WORKDIR /tmp
2023-02-20 03:09:17 UTC (buildkit.dockerfile.v0)RUN |4 NB_USER=jovyan NB_UID=1000 NB_GID=100 PYTHON_VERSION=3.10 /bin/bash -o pipefail -c set -x && arch=$(uname -m) && if [ "${arch}" = "x86_64" ]; then arch="64"; fi && wget -qO /tmp/micromamba.tar.bz2 "https://micromamba.snakepit.net/api/micromamba/linux-${arch}/latest" && tar -xvjf /tmp/micromamba.tar.bz2 --strip-components=1 bin/micromamba && rm /tmp/micromamba.tar.bz2 && PYTHON_SPECIFIER="python=${PYTHON_VERSION}" && if [[ "${PYTHON_VERSION}" == "default" ]]; then PYTHON_SPECIFIER="python"; fi && ./micromamba install --root-prefix="${CONDA_DIR}" --prefix="${CONDA_DIR}" --yes "${PYTHON_SPECIFIER}" 'mamba' 'jupyter_core' && rm micromamba && mamba list python | grep '^python ' | tr -s ' ' | cut -d ' ' -f 1,2 >> "${CONDA_DIR}/conda-meta/pinned" && mamba clean --all -f -y && fix-permissions "${CONDA_DIR}" && fix-permissions "/home/${NB_USER}" # buildkit
2023-02-20 03:09:17 UTC (buildkit.dockerfile.v0)ENTRYPOINT ["tini" "-g" "--"]
2023-02-20 03:09:17 UTC (buildkit.dockerfile.v0)CMD ["start.sh"]
2023-02-20 03:09:17 UTC (buildkit.dockerfile.v0)COPY start.sh /usr/local/bin/ # buildkit
2023-02-20 03:09:17 UTC (buildkit.dockerfile.v0)USER 1000
2023-02-20 03:09:17 UTC (buildkit.dockerfile.v0)WORKDIR /home/jovyan
2023-02-24 14:54:34 UTC/bin/bash -o pipefail -c #(nop) LABEL maintainer=Jupyter Project <jupyter@googlegroups.com>
2023-02-24 14:54:34 UTC/bin/bash -o pipefail -c #(nop) SHELL [/bin/bash -o pipefail -c]
2023-02-24 14:54:34 UTC/bin/bash -o pipefail -c #(nop) USER root
2023-02-24 14:54:45 UTC/bin/bash -o pipefail -c apt-get update --yes && apt-get install --yes --no-install-recommends fonts-liberation pandoc run-one && apt-get clean && rm -rf /var/lib/apt/lists/*
2023-02-24 14:54:46 UTC/bin/bash -o pipefail -c #(nop) USER 1000
2023-02-24 14:54:46 UTC/bin/bash -o pipefail -c #(nop) WORKDIR /tmp
2023-02-24 14:55:37 UTC/bin/bash -o pipefail -c mamba install --quiet --yes 'notebook' 'jupyterhub' 'jupyterlab' && jupyter notebook --generate-config && mamba clean --all -f -y && npm cache clean --force && jupyter lab clean && rm -rf "/home/${NB_USER}/.cache/yarn" && fix-permissions "${CONDA_DIR}" && fix-permissions "/home/${NB_USER}"
2023-02-24 14:55:40 UTC/bin/bash -o pipefail -c #(nop) ENV JUPYTER_PORT=8888
2023-02-24 14:55:40 UTC/bin/bash -o pipefail -c #(nop) EXPOSE 8888
2023-02-24 14:55:40 UTC/bin/bash -o pipefail -c #(nop) CMD ["start-notebook.sh"]
2023-02-24 14:55:40 UTC/bin/bash -o pipefail -c #(nop) COPY multi:8e8d5e74f81a4540b6e1d9d3f417f20299934846dfd40186b6df33296d86cc81 in /usr/local/bin/
2023-02-24 14:55:40 UTC/bin/bash -o pipefail -c #(nop) COPY file:24e5b986e2679cf2b07a6f65dae1cab812b454b0bfd6bb41a5306f841636d9de in /etc/jupyter/
2023-02-24 14:55:40 UTC/bin/bash -o pipefail -c #(nop) USER root
2023-02-24 14:55:41 UTC/bin/bash -o pipefail -c sed -re "s/c.ServerApp/c.NotebookApp/g" /etc/jupyter/jupyter_server_config.py > /etc/jupyter/jupyter_notebook_config.py && fix-permissions /etc/jupyter/
2023-02-24 14:55:41 UTC/bin/bash -o pipefail -c #(nop) HEALTHCHECK &{["CMD-SHELL" "wget -O- --no-verbose --tries=1 --no-check-certificate http${GEN_CERT:+s}://localhost:${JUPYTER_PORT}${JUPYTERHUB_SERVICE_PREFIX:-/}api || exit 1"] "5s" "3s" "5s" '\x03'}
2023-02-24 14:55:42 UTC/bin/bash -o pipefail -c #(nop) USER 1000
2023-02-24 14:55:42 UTC/bin/bash -o pipefail -c #(nop) WORKDIR /home/jovyan
2023-02-24 15:00:23 UTC/bin/bash -o pipefail -c #(nop) USER root
2023-02-24 15:00:23 UTC/bin/bash -o pipefail -c #(nop) ENV SUDO_FORCE_REMOVE=yes
2023-02-24 15:00:39 UTC/bin/bash -o pipefail -c apt-get -q update && apt-get -y remove sudo && apt-get -y upgrade && apt-get install -yq --no-install-recommends htop openssh-client vim rsync && apt-get clean && rm -rf /var/lib/apt/lists/*
2023-02-24 15:00:40 UTC/bin/bash -o pipefail -c #(nop) USER jovyan
2023-02-24 15:01:04 UTC/bin/bash -o pipefail -c mamba install --quiet --yes 'nbresuse' 'jupyter-starters' && conda clean --all -f -y && fix-permissions $CONDA_DIR && fix-permissions /home/$NB_USER
2023-02-24 15:02:51 UTC/bin/bash -o pipefail -c jupyter labextension install jupyterlab-topbar-extension jupyterlab-system-monitor
2023-02-24 15:05:00 UTC/bin/bash -o pipefail -c #(nop) LABEL maintainer=Jupyter Project <jupyter@googlegroups.com>
2023-02-24 15:05:00 UTC/bin/bash -o pipefail -c #(nop) SHELL [/bin/bash -o pipefail -c]
2023-02-24 15:05:00 UTC/bin/bash -o pipefail -c #(nop) USER root
2023-02-24 15:06:09 UTC/bin/bash -o pipefail -c apt-get update --yes && apt-get install --yes --no-install-recommends git nano-tiny tzdata unzip vim-tiny openssh-client less texlive-xetex texlive-fonts-recommended texlive-plain-generic xclip && apt-get clean && rm -rf /var/lib/apt/lists/*
2023-02-24 15:06:13 UTC/bin/bash -o pipefail -c update-alternatives --install /usr/bin/nano nano /bin/nano-tiny 10
2023-02-24 15:06:13 UTC/bin/bash -o pipefail -c #(nop) USER 1000
2023-02-24 15:06:13 UTC/bin/bash -o pipefail -c #(nop) COPY --chown=1000:100file:418b8119d5a79fec269849d87cd70a165f8a443cd611dfd820642ec476178702 in /opt/conda/lib/R/etc/
2023-08-28 13:54:24 UTC/bin/bash -o pipefail -c #(nop) SHELL [/bin/bash -o pipefail -c]
2023-08-28 13:54:24 UTC/bin/bash -o pipefail -c #(nop) USER root
2023-09-18 17:18:31 UTC/bin/bash -o pipefail -c apt-get update --yes && apt-get install --yes --no-install-recommends build-essential cm-super dvipng ffmpeg time && apt-get clean && rm -rf /var/lib/apt/lists/*
2023-09-18 17:18:39 UTC/bin/bash -o pipefail -c apt update && apt-get install -y --no-install-recommends man-db g++ less zlib1g-dev && apt-get clean && rm -rf /var/lib/apt/lists/*
2023-09-18 17:18:41 UTC/bin/bash -o pipefail -c cd /opt && git clone --recursive https://github.com/clwgg/seqstats && cd seqstats && make
2023-09-18 17:18:42 UTC/bin/bash -o pipefail -c #(nop) ENV PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/seqstats
2023-09-18 17:18:47 UTC/bin/bash -o pipefail -c cd /opt && git clone https://github.com/gpertea/cdbfasta.git && cd cdbfasta && make
2023-09-18 17:18:47 UTC/bin/bash -o pipefail -c #(nop) ENV PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/seqstats:/opt/cdbfasta
2023-10-11 08:33:20 UTC/bin/bash -o pipefail -c cd /opt && git clone https://github.com/Gaius-Augustus/TSEBRA
2023-10-11 08:33:20 UTC/bin/bash -o pipefail -c #(nop) ENV PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/seqstats:/opt/cdbfasta:/opt/TSEBRA/bin
2023-10-11 08:33:57 UTC/bin/bash -o pipefail -c cd /opt && git clone https://github.com/Gaius-Augustus/MakeHub.git && cd MakeHub && git checkout braker3 && wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/bedToBigBed && wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/genePredCheck && wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/faToTwoBit && wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/gtfToGenePred && wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/hgGcPercent && wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/ixIxx && wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/twoBitInfo && wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/wigToBigWig && wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/genePredToBed && wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64.v369/genePredToBigGenePred && chmod u+x bedToBigBed genePredCheck faToTwoBit gtfToGenePred hgGcPercent ixIxx twoBitInfo wigToBigWig genePredToBed genePredToBigGenePred make_hub.py
2023-10-11 08:33:57 UTC/bin/bash -o pipefail -c #(nop) ENV PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/seqstats:/opt/cdbfasta:/opt/TSEBRA/bin:/opt/MakeHub
2023-10-11 08:33:57 UTC/bin/bash -o pipefail -c #(nop) ENV AUGUSTUS_CONFIG_PATH=/usr/share/augustus/config/
2023-10-11 08:33:57 UTC/bin/bash -o pipefail -c #(nop) ENV AUGUSTUS_BIN_PATH=/usr/bin/
2023-10-11 08:33:57 UTC/bin/bash -o pipefail -c #(nop) ENV AUGUSTUS_SCRIPTS_PATH=/usr/share/augustus/scripts/
2023-10-11 08:34:12 UTC/bin/bash -o pipefail -c apt update && apt install -yq augustus augustus-data augustus-doc && apt clean all && fix-permissions "${AUGUSTUS_CONFIG_PATH}"
2023-10-11 08:34:36 UTC/bin/bash -o pipefail -c apt update && apt install -yq libyaml-perl libhash-merge-perl libparallel-forkmanager-perl libscalar-util-numeric-perl libclass-data-inheritable-perl libexception-class-perl libtest-pod-perl libfile-which-perl libmce-perl libthread-queue-perl libmath-utils-perl libscalar-list-utils-perl && apt clean all
2023-10-11 08:34:41 UTC/bin/bash -o pipefail -c cd /usr/share/augustus/scripts && rm optimize_augustus.pl && wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/optimize_augustus.pl && rm aa2nonred.pl && wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/aa2nonred.pl && rm gff2gbSmallDNA.pl && wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/gff2gbSmallDNA.pl && rm new_species.pl && wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/new_species.pl && rm filterGenesIn.pl && wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/filterGenesIn.pl && rm filterGenesIn_mRNAname.pl && wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/filterGenesIn_mRNAname.pl && rm filterGenes.pl && wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/filterGenes.pl && rm join_mult_hints.pl && wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/join_mult_hints.pl && rm randomSplit.pl && wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/randomSplit.pl && rm join_aug_pred.pl && wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/join_aug_pred.pl && rm getAnnoFastaFromJoingenes.py && wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/getAnnoFastaFromJoingenes.py && rm gtf2gff.pl && wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/gtf2gff.pl && rm splitMfasta.pl && wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/splitMfasta.pl && rm createAugustusJoblist.pl && wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/scripts/createAugustusJoblist.pl && chmod a+x optimize_augustus.pl aa2nonred.pl gff2gbSmallDNA.pl new_species.pl filterGenesIn_mRNAname.pl filterGenes.pl filterGenesIn.pl join_mult_hints.pl randomSplit.pl join_aug_pred.pl getAnnoFastaFromJoingenes.py gtf2gff.pl splitMfasta.pl createAugustusJoblist.pl
2023-10-11 08:34:42 UTC/bin/bash -o pipefail -c cd /usr/share/augustus/config && mkdir parameters && cd parameters && wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/config/parameters/AUG_CMDLN_PARAMETERS.md && wget https://raw.githubusercontent.com/Gaius-Augustus/Augustus/master/config/parameters/aug_cmdln_parameters.json && chmod a+r AUG_CMDLN_PARAMETERS.md aug_cmdln_parameters.json && cd .. && chmod a+r parameters && chmod a+x parameters
2023-10-11 08:34:46 UTC/bin/bash -o pipefail -c apt update && apt install -yq bamtools && apt clean all
2023-10-11 08:34:46 UTC/bin/bash -o pipefail -c #(nop) USER 1000
2023-10-11 08:40:28 UTC/bin/bash -o pipefail -c mamba install --quiet -c bioconda -c anaconda --yes biopython && mamba clean --all -f -y && fix-permissions "${CONDA_DIR}" && fix-permissions "/home/${NB_USER}"
2023-10-11 08:40:32 UTC/bin/bash -o pipefail -c #(nop) WORKDIR /home/jovyan
2023-10-11 08:40:32 UTC/bin/bash -o pipefail -c #(nop) USER root
2023-10-11 08:40:41 UTC/bin/bash -o pipefail -c cd /opt && git clone --depth=1 https://github.com/Gaius-Augustus/BRAKER.git && cd BRAKER && cd example && wget http://bioinf.uni-greifswald.de/augustus/datasets/RNAseq.bam
2023-10-11 08:40:41 UTC/bin/bash -o pipefail -c #(nop) ENV PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/seqstats:/opt/cdbfasta:/opt/TSEBRA/bin:/opt/MakeHub:/opt/BRAKER/scripts
2023-10-11 08:40:54 UTC/bin/bash -o pipefail -c cd /opt && wget http://topaz.gatech.edu/GeneMark/etp.for_braker.tar.gz && tar -xzf etp.for_braker.tar.gz && mv etp.for_braker ETP && chmod a+x /opt/ETP/bin/*py /opt/ETP/bin/*pl /opt/ETP/tools/*
2023-10-11 08:40:55 UTC/bin/bash -o pipefail -c #(nop) ENV GENEMARK_PATH=/opt/ETP/bin
2023-10-11 08:40:55 UTC/bin/bash -o pipefail -c #(nop) ENV PATH=/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/seqstats:/opt/cdbfasta:/opt/TSEBRA/bin:/opt/MakeHub:/opt/BRAKER/scripts:/opt/ETP/bin:/opt/ETP/tools:/opt/ETP/bin/gmes/ProtHint/bin:/opt/ETP/bin/gmes
2023-10-11 08:40:55 UTC/bin/bash -o pipefail -c #(nop) USER 1000
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