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ssh <username>@stampede2.tacc.utexas.edu |
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Now that we have backed up your profiles so you won't lose any previous settings, you can copy our predefined GVA2022.bashrc file from the /corral-repl/utexas/BioITeam/scriptsgva_course/ folder to your $HOME folder as .bashrc and the predefined GVA2022.profile as .profile from the same location before using the chmod command to change the permissions to read and write for the user only.
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logout # or exit |
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ssh <username>@stampede2.tacc.utexas.edu |
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cdh ln -s $SCRATCH scratch ln -s $WORK work ln -s $BI BioITeam |
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Stampede2 is a computer cluster connected to three file servers (each with unique characteristics), and other computer infrastructure. For the purpose of this class, and your own work, you only need to understand the basics of the 3 file servers to know how to use them effectively. The 3 servers are named, "HOME", "WORK2WORK", and "SCRATCH", and we will work with them all over the next 5 days
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This is not necessary if you followed the wget commands above. Again In a new browser or tab you would navigate to https://docs.conda.io/en/latest/miniconda.html but instead of right clicking on the "Miniconda3 Linux 64-bit" in the linux installers section and choosing copy link address you would simply left click and allow the file to download directly to your browser's Downloads folder. Using information from the SCP tutorial you would then transfer the local 'Miniconda3-latest-Linux-x86_64.sh' file to the stampede2 remote location '$WORK2$WORK/src'. Note that you are downloading a file that will work on TACC, but not on your own computer. Don't get confused thinking you need windows or mac versions.
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The following packages will be downloaded: package | build ---------------------------|----------------- dbus-1.13.18 | hb2f20db_0 504 KB fastqc-0.11.9 | hdfd78af_1 9.7 MB bioconda font-ttf-dejavu-sans-mono-2.37| h6964260hd3eb1b0_0 335 KB ------------------------------------------------------------ glib-2.69.1 | h4ff587b_1 1.7 MB libxml2-2.9.14 | Total:h74e7548_0 718 KB 10 openjdk-11.0.13 MB The following NEW packages will be INSTALLED: | fastqc h87a67e3_0 bioconda/noarch::fastqc-0.11.9-hdfd78af_1341.0 MB font--ttf-dejavu-s~ pkgs/main/noarch::font-ttf-dejavu-sans-mono-2.37-h6964260_0 openjdk--------------------------------------------------------- Total: 354.0 MB The following NEW packages will be INSTALLED: _libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main _openmp_mutex pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu dbus pkgs/main/linux-64::dbus-1.13.18-hb2f20db_0 expat pkgs/main/linux-64::expat-2.4.4-h295c915_0 fastqc bioconda/noarch::fastqc-0.11.9-hdfd78af_1 font-ttf-dejavu-s~ pkgs/main/noarch::font-ttf-dejavu-sans-mono-2.37-hd3eb1b0_0 fontconfig pkgs/main/linux-64::fontconfig-2.13.1-h6c09931_0 freetype pkgs/main/linux-64::freetype-2.11.0-h70c0345_0 glib pkgs/main/linux-64::glib-2.69.1-h4ff587b_1 icu pkgs/main/linux-64::icu-58.2-he6710b0_3 libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2 libgcc-ng pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1 libgomp pkgs/main/linux-64::libgomp-11.2.0-h1234567_1 libpng pkgs/main/linux-64::libpng-1.6.37-hbc83047_0 libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1 libuuid pkgs/main/linux-64::libuuid-1.0.3-h7f8727e_2 libxcb pkgs/main/linux-64::libxcb-1.15-h7f8727e_0 libxml2 pkgs/main/linux-64::libxml2-2.9.14-h74e7548_0 openjdk pkgs/main/linux-64::openjdk-11.0.13-h87a67e3_0 pcre pkgs/main/linux-64::pcre-8.45-h295c915_0 perl pkgs/main/linux-64::perl-5.26.2-h14c3975_0 xz pkgs/main/linux-64::xz-5.2.5-h7f8727e_1 zlib pkgs/main/linux-64::openjdkzlib-81.02.15212-h7b6447c_3h7f8727e_2 Proceed ([y]/n)? y Downloading and Extracting Packages fastqc-0.11.9 | 9.7 MB | ####################################################################################################################################################################################### | 100% font-ttf-dejavu-sans | 335 KB | ####################################################################################################################################################################################### | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done |
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In previous years, the pip installation program was used to install a few programs. While those programs will be installed through conda this year, the link here is provided to give a detailed walk through of how to use pip on TACC resources. This is particularly helpful for making use of the '--user' flag during the installation process as you do not have the expected permissions to install things in the default directories.
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