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downloads:sphire_beta_20170602 [2017/07/03 10:03] fmerino [Installing Unblur & Summovie] |
downloads:sphire_beta_20170602 [2018/06/20 13:12] |
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- | ====== SPHIRE beta 2017/06/02 ====== | ||
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- | ===== Download ===== | ||
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- | For this release, we officially support only the installer for CentOS6, which we tested carefully. Nevertheless, | ||
- | SPHIRE does not support Windows. | ||
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- | /* | ||
- | *[[http:// | ||
- | * [[https:// | ||
- | */ | ||
- | |||
- | * [[https:// | ||
- | * [[https:// | ||
- | * [[https:// | ||
- | * [[https:// | ||
- | * [[http:// | ||
- | |||
- | \\ | ||
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- | ===== Tutorial issues ===== | ||
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- | **Note 2017/ | ||
- | Because so many commands are changed, we were not able to provide an up-to-date tutorial and precalculated results for this version yet. | ||
- | However, we provide a short tutorial that was used in our workshop. | ||
- | As soon as it is available, we will let you know via our mailing list! | ||
- | |||
- | Until then, please use our old SPHIRE demo dataset which you can download from [[: | ||
- | There are small changes in the GUI settings and outputs. | ||
- | Nevertheless, | ||
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- | ===== Installation preparation ===== | ||
- | |||
- | In order to avoid conflicts with existing installations, | ||
- | |||
- | Especially, the output of | ||
- | < | ||
- | echo $PATH | ||
- | </ | ||
- | should not contain paths to any existing OpenMPI, EMAN2, EMAN, and SPARX installations and | ||
- | < | ||
- | which ompi_info | ||
- | </ | ||
- | should output | ||
- | < | ||
- | ompi_info not found. | ||
- | </ | ||
- | |||
- | In case that one is still present, contact your system administrator and ask him/her to remove those PATH variables from the system wide environment settings. | ||
- | \\ | ||
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- | ===== Installation instructions ===== | ||
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- | The following installation describes the installation of binary packages. (You can find additional information about the installation at the [[http:// | ||
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- | Download the installer, run it by typing | ||
- | < | ||
- | cd < | ||
- | bash sphire_beta_20170602.sh | ||
- | </ | ||
- | and follow the instruction of the installer. | ||
- | |||
- | This creates the directory you specified during installation (default ${HOME}/ | ||
- | |||
- | Now restart your terminal (Logout & Login) and make sure that the path to the <path to EMAN2 directory>/ | ||
- | < | ||
- | echo $PATH | ||
- | <path to EMAN2 directory>/ | ||
- | </ | ||
- | |||
- | The shipped version of OpenMPI and system wide OpenMPI installations will not work most of the time. | ||
- | That is why we recommend to follow the reinstallation process below. | ||
- | (If you wish to install your own OpenMPI, you can find information at the [[http:// | ||
- | |||
- | 1. Change to the installation directory you specified during installation | ||
- | < | ||
- | 2. Remove the OpenMPI provided: | ||
- | < | ||
- | 3. Rebuild OpenMPI: | ||
- | < | ||
- | 4. Rebuild Pydusa: | ||
- | < | ||
- | **Note 2017/ | ||
- | 5. Install Pydusa: | ||
- | < | ||
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- | Now restart your terminal (Logout & Login). | ||
- | \\ | ||
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- | ===== Test the installation ===== | ||
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- | If the following commands do not throw any errors, the installation is successful. | ||
- | < | ||
- | sparx | ||
- | In [1]: import mpi | ||
- | In [2]: Util.version() | ||
- | Compile time of util_sparx.cpp | ||
- | Modification time: 05/ | ||
- | In [3]: quit | ||
- | </ | ||
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- | Congratulations you installed SPHIRE! | ||
- | \\ | ||
- | |||
- | ===== Installations issues ===== | ||
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- | **During rebuild step 4, an error might occur.** | ||
- | Can't build / | ||
- | Downloaded bytes did not match Content-Length | ||
- | url: http:// | ||
- | target_path: | ||
- | Content-Length: | ||
- | downloaded bytes: 208916 | ||
- | | ||
- | If you encounter this error, please do the following: | ||
- | rm conda-bld/ | ||
- | bash utils/ | ||
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- | ===== Release notes ===== | ||
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- | - **ISAC2** โ Rapid and stable 2D Clustering | ||
- | We optimized the popular ISAC algorithm for 2D Clustering (Yang et al., Structure, 2012). | ||
- | ISAC yields now validated 2D class averages **> 10-15x faster** than before. | ||
- | In addition, the new Beautifier tool allows further refinement and sharpening of the ISAC 2D class averages in order to reveal high-resolution features in 2D. | ||
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- | - **MERIDIEN** โ Rapid ML 3D Refinement | ||
- | We introduced the polar coordinates methodology (Penczek et al., 1992) and optimized the parallelization of the program to speed up the structure refinement, reduce the memory requirements and enable calculation on single nodes. | ||
- | MERIDIEN is now **> 10-15x faster** than the previous version. | ||
- | Cryo-EM structure determination with SPHIRE is now possible within a few days on small clusters and desktop machines. | ||
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- | - **RSORT3D** โ Reproducible 3D sorting | ||
- | We re-implemented and improved the 3D sorting procedure and methodology. The updated RSORT3D is **3-4x faster** and capable to run on desktop machines. | ||
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- | - **Icosahedral, | ||
- | Refinement of particles with icosahedral, | ||
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- | - **Easy installation** | ||
- | The release of **SPHIRE Beta Patch 1** is synchronized with the release of EMAN 2.2. The new Anaconda Installer allows a fast and smooth co-installation of both programs. At the moment we //only support CentOS6//, but we work hard on developing a //MacOS Installer// for the upcoming stable release. | ||
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- | (Follow us on Twitter: https:// | ||
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- | ===== Installing Unblur & Summovie ===== | ||
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- | Please follow the installation instructions on the developer' | ||
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- | ===== Known Issues ===== | ||
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- | A list of the known issues can be found here: [[: | ||