reproducbility_tutorial_20

1  cd /scratch
2  git clone https://github.com/MACampbell17/reproducbility_tutorial_20.git
3  ls
4  wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
5  bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda
6  ln -s /opt/conda/pkgs/*/bin/* /bin
7  ln -s /opt/conda/pkgs/*/lib/* /usr/lib
8  /opt/conda/bin/conda install -c conda-forge -y jupyterlab=1.2.3
9  /opt/conda/bin/conda install -c conda-forge -y nodejs=10.13.0

10 /opt/conda/bin/pip install bash_kernel 11 /opt/conda/bin/pip install ipykernel 12 /opt/conda/bin/python3 -m bash_kernel.install 13 conda search 14 conda search edgeR 15 /opt/conda/bin/jupyter lab --no-browser --allow-root --ip=0.0.0.0 --NotebookApp.token='' --NotebookApp.password='' --notebook-dir='/scratch/reproducibility-tutorial/' 16 /opt/conda/bin/conda search -c bioconda snakemake 17 /opt/conda/bin/conda install -c bioconda -c conda-forge -y snakemake=5.8.1 18 ln -s /opt/conda/bin/* /bin 19 ln -s /opt/conda/lib/* /usr/lib 20 snakemake --version 21 sudo apt-get update 22 sudo apt-get install -y apt-transport-https ca-certificates curl gnupg-agent software-properties-common 23 curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add - 24 sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu
25 $(lsb_release -cs)
26 stable" 27 sudo apt-get update 28 sudo apt-get install -y docker-ce docker-ce-cli containerd.io 29 docker run hello-world 30 history 31 nano 32 exit 33 cd /scratch 34 df -h 35 ls 36 cd /scratch 37 git clone https://github.com/MACampbell17/reproducbility_tutorial_20.git 38 ls 39 wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh 40 wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh 41 ln -s /opt/conda/pkgs//bin/ /bin 42 ln -s /opt/conda/pkgs//lib/ /usr/lib 43 /opt/conda/bin/conda install -c conda-forge -y jupyterlab=1.2.3 44 /opt/conda/bin/conda install -c conda-forge -y nodejs=10.13.0 45 /opt/conda/bin/conda search -c bioconda snakemake 46 ln -s /opt/conda/pkgs//bin/ /bin 47 ln -s /opt/conda/pkgs//lib/ /usr/lib 48 /opt/conda/bin/conda search -c bioconda snakemake 49 cd scratch 50 sudo apt-get update 51 sudo apt-get install -y apt-transport-https ca-certificates curl gnupg-agent software-properties-common 52 curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add - 53 sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu
54 $(lsb_release -cs)
55 stable" 56 sudo apt-get update 57 sudo apt-get install -y docker-ce docker-ce-cli containerd.io 58 docker run hello-world 59 history 60 /opt/conda/bin/conda install -c conda-forge -y jupyterlab=1.2.3 61 bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda 62 ln -s /opt/conda/pkgs//bin/ /bin 63 ln -s /opt/conda/pkgs//lib/ /usr/lib 64 /opt/conda/bin/conda install -c conda-forge -y jupyterlab=1.2.3 65 /opt/conda/bin/conda install -c conda-forge -y nodejs=10.13.0 66 /opt/conda/bin/pip install bash_kernel 67 /opt/conda/bin/pip install ipykernel 68 /opt/conda/bin/python3 -m bash_kernel.install 69 /opt/conda/bin/jupyter lab --no-browser --allow-root --ip=0.0.0.0 --NotebookApp.token='' --NotebookApp.password='' --notebook-dir='/scratch/reproducibility-tutorial/' 70 history 71 cd /scratch 72 git clone https://github.com/MACampbell17/reproducbility_tutorial_20.git 73 wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh 74 bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda 75 ln -s /opt/conda/pkgs//bin/ /bin 76 ln -s /opt/conda/pkgs//lib/ /usr/lib 77 sudo apt-get update 78 sudo apt-get install -y apt-transport-https ca-certificates curl gnupg-agent software-properties-common 79 curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add - 80 sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu
81 $(lsb_release -cs)
82 stable" 83 sudo apt-get update 84 sudo apt-get install -y docker-ce docker-ce-cli containerd.io 85 docker run hello-world 86 cd /scratch/reproducibility-tutorial/ 87 history >>README.md 88 ls 89 cd /scratch/reproducibility-tutorial_20/ 90 cd /reproducibility-tutorial_20/ 91 cd reproducibility-tutorial_20/ 92 cd /scratch/reproducibility_tutorial_20/ 93 cd reproducibility_tutorial_20/ 94 ls 95 cd reproducbility_tutorial_20/ 96 history >>README.md 97 nano README.md 98 cd 99 cd 100 cd scratch 101 cd /scratch 102 git clone 103 git clone https://github.com/MACampbell17/reproducbility_tutorial_20.git 104 ls 105 cd reprod* 106 ls 107 cd /scratch/ 108 ls 109 chown -R mac17 /scratch/reproducbility_tutorial_20/ 110 mkdir /scratch/test-workflow 111 cd /scratch/test-workflow 112 iget -P /iplant/home/shared/cyverse_training/datasets/PRJNA79729/fastq_files/SRR064156.fastq.gz . 113 iget -P /iplant/home/shared/cyverse_training/datasets/PRJNA79729/fastq_files/SRR064156.fastq.gz 114 iget -P /iplant/home/shared/cyverse_training/datasets/PRJNA79729/fastq_files/SRR064156.fastq.gz 115 cd 116 /scratch/ 117 cd /scratch/ 118 mkdir -p /scratch/reproducibility-tutorial/experiment/sra_files/metadata 119 mv SraRunTable.txt /scratch/reproducibility-tutorial/experiment/sra_files/metadata 120 cd /scratch 121 git clone https://github.com/MACampbell17/reproducbility_tutorial_20.git 122 nano 123 ls 124 nano repro* 125 ls repro* 126 nano READ* 127 cd /scratch 128 git clone https://github.com/MACampbell17/reproducbility_tutorial_20.git 129 cd/scratch 130 ls 131 cd /scratch 132 git clone https://github.com/MACampbell17/reproducbility_tutorial_20.git 133 sudo apt-get update 134 sudo apt-get install -y apt-transport-https ca-certificates curl gnupg-agent software-properties-common 135 curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add - 136 sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu
137 $(lsb_release -cs)
138 stable" 139 sudo apt-get update 140 sudo apt-get install -y docker-ce docker-ce-cli containerd.io 141 docker run hello-world 142 cd /scratch/reproducbility_reproducbility_tutorial_20/ 143 cd /scratch/reproducbility_tutorial_20/ 144 history >>README.md 145 nano README.md 146 chown -R YOURCYVERSEUSERNAME /scratch/reproducbility_tutorial_20/ 147 chown -R mac17 /scratch/reproducbility_tutorial_20/ 148 scp ~/Downloads/SraRunTable.txt mac17@128.196.142.6:/scratch/ 149 scp ~/Downloads/SraRunTable.txt mac17@128.196.142.6:reproducbility_tutorial_20/ 150 ls 151 scp ~/Downloads/SraRunTable.txt mac17@128.196.142.6:reproducbility_tutorial_20/ 152 ls 153 cd /scratch 154 git clone https://github.com/MACampbell17/reproducibility_tutorial.git 155 sudo apt-get update 156 sudo apt-get install -y apt-transport-https ca-certificates curl gnupg-agent software-properties-common 157 curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add - 158 sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu
159 $(lsb_release -cs)
160 stable" 161 sudo apt-get update 162 sudo apt-get install -y docker-ce docker-ce-cli containerd.io 163 docker run hello-world 164 cd /scratch/reproducibility-tutorial/ 165 cd /scratch/reproducibility-tutorial/ 166 cd /scratch/reproducibility_tutorial/ 167 history >>README.md 168 nano README.md 169 chown -R mac17 /scratch/reproducibility_tutorial/ 170 cd 171 ls 172 cd /scratch 173 ls 174 chown -R mac17 /scratch/reproducibility_tutorial/ 175 cd reproducibility_tutorial 176 ls 177 cd 178 cd /scratch 179 ls 180 cd /scratch 181 git clone https://github.com/MACampbell17/reproducibility_tutorial.git 182 sudo apt-get update 183 sudo apt-get install -y apt-transport-https ca-certificates curl gnupg-agent software-properties-common 184 curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add - 185 sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu
$(lsb_release -cs)
stable" 186 sudo apt-get update 187 sudo apt-get install -y docker-ce docker-ce-cli containerd.io 188 docker run hello-world 189 cd /scratch/reproducibility_tutorial/ 190 history >>README.md