Namespace
teambraker
Image / Tagbraker3:isoseq
Content Digestsha256:e2d0bd1f4cc721198136cec50177076263e3f502b9ea64d728813e32c80bbeb8
Details
2024-05-10 10:44:00 UTC
3.6 GB
Labels
-
maintainerJupyter Project <jupyter@googlegroups.com>
-
org.opencontainers.image.ref.nameubuntu
-
org.opencontainers.image.version22.04
Environment
AUGUSTUS_BIN_PATH/opt/Augustus/bin/
AUGUSTUS_CONFIG_PATH/opt/Augustus/config/
AUGUSTUS_SCRIPTS_PATH/opt/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/MakeHub:/opt/Augustus/scripts/:/opt/Augustus/bin/:/opt/TSEBRA/bin:/opt/MakeHub:/opt/BRAKER/scripts:/opt/ETP/bin:/opt/ETP/tools:/opt/ETP/bin/gmes/ProtHint/bin:/opt/ETP/bin/gmes:/opt/compleasm_kit:/opt/EukSpecies-BRAKER2/bin
SHELL/bin/bash
SUDO_FORCE_REMOVEyes
Layers
[#000] sha256:10ac4908093d4325f2c94b2c9a571fa1071a17a72dd9c21c1ffb2c86f68ca028 - 0.79% (29 MB)
[#001] sha256:7708118be96360b9f60a83c941be5403b6e7ba774bc48efcf7ebcef5080890df - 0.3% (10.9 MB)
[#002] sha256:7a2b4dd53caccbd374b123296038596c357cf0b9fe9ecd80b9554e4c89a052ff - 0.0% (678 Bytes)
[#003] sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 - 0.0% (32 Bytes)
[#004] sha256:f8cb1d2f7e20229930b7343319f415289630e22a3ccc4d6c0ea599e26f260f58 - 0.0% (1.87 KB)
[#005] sha256:f258ff22d3c5551f1084a74074f421c004d50ba9d55513aaa0041ce58ac60d6a - 0.0% (4.81 KB)
[#006] sha256:57a3a23e6ced7ad69923a9cc27e78ecf85df9b77e41a2aa06f34811277e8bd19 - 0.0% (151 Bytes)
[#007] sha256:9db1b1a7829fb51eb7cbab0240e6aecadc54adafca7ab733ab1073ce43a777b8 - 0.0% (273 Bytes)
[#008] sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 - 0.0% (32 Bytes)
[#009] sha256:08234ca7e91faac3145a69aad850139c0a8c05e6cd061969e7299513f7b6c33c - 2.36% (87 MB)
[#010] sha256:35c0c002241e17bc9a93eff727ad7a4c5e6128695c39de1b3f2eda678f417f44 - 0.0% (4.1 KB)
[#011] sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 - 0.0% (32 Bytes)
[#012] sha256:e1519919153b656002b10f5c358c8070eba6cc41a5a4891ee1a72d928abe01d8 - 0.79% (29.3 MB)
[#013] sha256:b866059daba98a2b2023c6ced0c9d9dc2766bd46c9b704d1b0c4f9cf21b834e0 - 3.09% (114 MB)
[#014] sha256:6b626b41cbdd09e248a0dba94ea322c5e58ec87b47b4eaf18aa23eac5c6ff97e - 0.0% (683 Bytes)
[#015] sha256:5eb1983a9f441a358006913b3a8d3a7c96ff306025965d6aba4e4d79380ea331 - 0.0% (1.04 KB)
[#016] sha256:e4088845342317ed04fabed3fc6b876d10acbc657f65908565e34b7b06cb15d4 - 0.0% (1.11 KB)
[#017] sha256:788a1778e3caa91a3ad0be0ce410eb507dab62362215eabadfd3d2e76053f3fa - 0.58% (21.2 MB)
[#018] sha256:d2327979cb0785a60c70bce82e873407623cc9b60ee23fe5de9c2077a0877324 - 0.01% (421 KB)
[#019] sha256:d4ba5d386d72a07abacdf50ac7d0c41444b4d9d859d54b9c3e2b772c6f69ebcd - 5.15% (190 MB)
[#020] sha256:326593c72c7e03cb9871c467596fa18fc4b639718a0d9b6401fa9d10c651dfa2 - 4.44% (164 MB)
[#021] sha256:5c0048263e6eb546f9aca8c9de2e27e5f27ab5d0f65b11ec910ec6c425aa89f3 - 0.0% (1.53 KB)
[#022] sha256:179f754036e2ed1733341fa46bb1701649ad0cb671cbb1c27024e82c28a7c739 - 0.0% (437 Bytes)
[#023] sha256:0036aa004abd8d0b18648a176c35ceaa6cf27390d19708689f0a00459445d98b - 28.25% (1.02 GB)
[#024] sha256:b262b6a9d014f6a4900ff82be2b9185c4589291e44fface36e85b116a42b0d34 - 5.77% (213 MB)
[#025] sha256:5415ba5bc966db69b8a2d70483f52bf6ba6a2ad9e96c7923c0c56011ee61c4eb - 8.49% (313 MB)
[#026] sha256:ffd1f9eff95a1479d1605f47ecc6b93d6ba0cdeabada8b2c3b7b2c69885c1dc7 - 0.4% (14.6 MB)
[#027] sha256:9db4a708b8ef0d092ed75a39ec2f0c7016ff0801098ed89c0e040b1778fde273 - 6.03% (222 MB)
[#028] sha256:aa7f2ec93a89d868341048bb4ad5e36dd49b3ad459b7e53d044f315b9d18965b - 0.02% (692 KB)
[#029] sha256:6a710c21b919a1a4df61486f5ef4f58dc9f34e71f73206566f0c644744c165f3 - 1.62% (59.5 MB)
[#030] sha256:aea936765c5c75cbc241bb8afc603bc9c19835c6244272aca2591ca623b4c4c0 - 1.57% (57.9 MB)
[#031] sha256:9fff005985c942fe79e0a2c75951ac7ac61af142942f1095a3f8c670541c73e8 - 0.0% (170 KB)
[#032] sha256:c6b79c596fd7002538391a70d57831a5297f7e54ba2c6e015f97f6e6da68889c - 0.12% (4.36 MB)
[#033] sha256:68f117d90d3144ce2b6c6d27db475c9545b96f0c085ddcdcacf61c882b5b16cc - 0.03% (1.13 MB)
[#034] sha256:e371fbce446c30a3065cc1759ce4c2a1233a3fff91c05492a101208c64edddc1 - 0.0% (3.82 KB)
[#035] sha256:fc326ef9949c8f996513e90c2cbc4737e94f2f8c4ca69987e4144285676e739b - 0.47% (17.2 MB)
[#036] sha256:9df875059dab7c7cfe8b71450b60e0f54d4ae7daf37a628854d00092093eef3a - 0.02% (625 KB)
[#037] sha256:fb5bbbe1fdfa54dced66289295fbcbf4d57a10508c0f9f2cb4f8fc7a56112bc7 - 8.23% (303 MB)
[#038] sha256:e632e8bf1d6f0226f35eeb90801d71c4e25cbb8bef82227d211004c997b64062 - 3.29% (121 MB)
[#039] sha256:99e2dc42457032560d9a2dbe3ee74f1c355bcd842c2cc2067cbf0683863e53c2 - 18.2% (671 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/
2023-09-15 15:18:12 UTC/bin/bash -o pipefail -c #(nop) USER root
2024-05-10 08:33:12 UTC/bin/bash -o pipefail -c #(nop) COPY dir:3b8c665533be0ef74cb09f276358fd5f32cfcc5f3578b86e581e7f2b242404b1 in /opt/
2024-05-10 08:33:15 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/MakeHub
2024-05-10 08:34:30 UTC/bin/bash -o pipefail -c apt-get update --yes && apt-get install -y libboost-iostreams-dev zlib1g-dev libboost-all-dev libboost-all-dev libbamtools-dev
2024-05-10 08:34:32 UTC/bin/bash -o pipefail -c #(nop) ENV AUGUSTUS_CONFIG_PATH=/opt/Augustus/config/
2024-05-10 08:35:47 UTC/bin/bash -o pipefail -c apt update && apt install -yq augustus augustus-data augustus-doc cm-super dvipng ffmpeg time && apt clean all && fix-permissions "${AUGUSTUS_CONFIG_PATH}"
2024-05-10 08:36:12 UTC/bin/bash -o pipefail -c apt update && apt install -yq libyaml-perl libhash-merge-perl libparallel-forkmanager-perl libscalar-util-numeric-perl libclass-data-inheritable-perl libexception-class-perl libtest-pod-perl libfile-which-perl libmce-perl libthread-queue-perl libmath-utils-perl libscalar-list-utils-perl && apt clean all
2024-05-10 08:36:12 UTC/bin/bash -o pipefail -c #(nop) USER 1000
2024-05-10 08:42:26 UTC/bin/bash -o pipefail -c mamba install --quiet -c bioconda -c anaconda --yes biopython && mamba clean --all -f -y && fix-permissions "${CONDA_DIR}" && fix-permissions "/home/${NB_USER}"
2024-05-10 08:42:30 UTC/bin/bash -o pipefail -c #(nop) USER root
2024-05-10 08:42:33 UTC/bin/bash -o pipefail -c apt-get remove -y augustus augustus-data augustus-doc
2024-05-10 08:42:33 UTC/bin/bash -o pipefail -c #(nop) ENV AUGUSTUS_BIN_PATH=/opt/Augustus/bin/
2024-05-10 08:42:33 UTC/bin/bash -o pipefail -c #(nop) ENV AUGUSTUS_SCRIPTS_PATH=/opt/Augustus/scripts/
2024-05-10 08:42:33 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/MakeHub:/opt/Augustus/scripts/:/opt/Augustus/bin/
2024-05-10 08:42:41 UTC/bin/bash -o pipefail -c cd /opt && git clone https://github.com/Gaius-Augustus/TSEBRA
2024-05-10 08:42:42 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:/opt/cdbfasta:/opt/MakeHub:/opt/Augustus/scripts/:/opt/Augustus/bin/:/opt/TSEBRA/bin
2024-05-10 08:43:13 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
2024-05-10 08:43:13 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/MakeHub:/opt/Augustus/scripts/:/opt/Augustus/bin/:/opt/TSEBRA/bin:/opt/MakeHub
2024-05-10 08:43:17 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
2024-05-10 10:41:48 UTC/bin/bash -o pipefail -c apt update && apt install -yq genometools libgenometools0 libgenometools0-dev && apt clean all
2024-05-10 10:41:53 UTC/bin/bash -o pipefail -c apt update && apt install -yq bamtools && apt clean all
2024-05-10 10:41:53 UTC/bin/bash -o pipefail -c #(nop) USER 1000
2024-05-10 10:42:20 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/${NB_USER}"
2024-05-10 10:42:51 UTC/bin/bash -o pipefail -c mamba install --quiet -c anaconda --yes pandas && mamba clean --all -f -y && fix-permissions "${CONDA_DIR}" && fix-permissions "/home/${NB_USER}"
2024-05-10 10:42:51 UTC/bin/bash -o pipefail -c #(nop) WORKDIR /home/jovyan
2024-05-10 10:42:51 UTC/bin/bash -o pipefail -c #(nop) USER root
2024-05-10 10:42:53 UTC/bin/bash -o pipefail -c cd /opt && wget https://github.com/huangnengCSU/compleasm/releases/download/v0.2.5/compleasm-0.2.5_x64-linux.tar.bz2 && tar -xvjf compleasm-0.2.5_x64-linux.tar.bz2 && rm compleasm-0.2.5_x64-linux.tar.bz2
2024-05-10 10:43:10 UTC/bin/bash -o pipefail -c cd /opt && git clone https://github.com/Gaius-Augustus/BRAKER.git && cd BRAKER && cd example && wget http://bioinf.uni-greifswald.de/augustus/datasets/RNAseq.bam
2024-05-10 10:43:11 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/MakeHub:/opt/Augustus/scripts/:/opt/Augustus/bin/:/opt/TSEBRA/bin:/opt/MakeHub:/opt/BRAKER/scripts
2024-05-10 10:43:22 UTC/bin/bash -o pipefail -c cd /opt && git clone https://github.com/KatharinaHoff/GeneMark-ETP.git && cd GeneMark-ETP && git checkout longread_experimental_dev && cd .. && mv GeneMark-ETP ETP && chmod a+x /opt/ETP/bin/*py /opt/ETP/bin/*pl /opt/ETP/tools/*
2024-05-10 10:43:58 UTC/bin/bash -o pipefail -c cd /opt && git clone https://github.com/gatech-genemark/EukSpecies-BRAKER2.git
2024-05-10 10:44:00 UTC/bin/bash -o pipefail -c #(nop) ENV GENEMARK_PATH=/opt/ETP/bin
2024-05-10 10:44:00 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/MakeHub:/opt/Augustus/scripts/:/opt/Augustus/bin/:/opt/TSEBRA/bin:/opt/MakeHub:/opt/BRAKER/scripts:/opt/ETP/bin:/opt/ETP/tools:/opt/ETP/bin/gmes/ProtHint/bin:/opt/ETP/bin/gmes:/opt/compleasm_kit:/opt/EukSpecies-BRAKER2/bin
2024-05-10 10:44:00 UTC/bin/bash -o pipefail -c #(nop) USER 1000
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