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        "author": "Grigory Sharov",
        "author_email": "sharov.grigory@gmail.com",
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        "description": "=============\nSpider plugin\n=============\n\nThis plugin provide wrappers around several programs of `SPIDER <https://spider.wadsworth.org/spider_doc/spider/docs/spider.html>`_ software suite.\n\n.. figure:: http://scipion-test.cnb.csic.es:9980/badges/spider_devel.svg\n   :align: left\n   :alt: build status\n\nInstallation\n------------\n\nYou will need to use `2.0 <https://github.com/I2PC/scipion/releases/tag/V2.0.0>`_ version of Scipion to be able to run these protocols. To install the plugin, you have two options:\n\na) Stable version\n\n.. code-block::\n\n    scipion installp -p scipion-em-spider\n\nb) Developer's version\n\n    * download repository\n\n    .. code-block::\n\n        git clone https://github.com/scipion-em/scipion-em-spider.git\n\n    * install\n\n    .. code-block::\n\n        scipion installp -p path_to_scipion-em-spider --devel\n\nSPIDER binaries will be installed automatically with the plugin, but you can also link an existing installation. \nDefault installation path assumed is ``software/em/spider-25.02``, if you want to change it, set *SPIDER_HOME* in ``scipion.conf`` file to the folder where the SPIDER is installed. Additional information about using SPIDER with MPI can be found on a separate `page <https://github.com/scipion-em/scipion-em-spider/wiki/How-to-Install-MPI>`_. Unfortunately, at the moment we do not support MPI in our SPIDER wrappers, since it requires a lot of effort to refactor almost all protocols. :(\nDepending on you CPU type you might want to change the default binary from ``spider_linux_mp_intel64`` to a different one by explicitly setting *SPIDER* variable. Similarly you can modify *SPIDER_MPI* variable (default ``spider_linux_mpi_opt64``).\n\nTo check the installation, simply run one of the following Scipion tests:\n\n.. code-block::\n\n    scipion test spider.tests.test_protocols_spider_reconstruct.TestSpiderReconstruct\n    scipion test spider.tests.test_protocols_spider_align.TestSpiderAlign\n    scipion test spider.tests.test_workflow_spiderMDA.TestSpiderWorkflow\n    scipion test spider.tests.test_workflow_spiderMDA.TestSpiderConvert\n    scipion test spider.tests.test_protocols_spider_projmatch.TestSpiderRefinement\n\n\nA complete list of tests can also be seen by executing ``scipion test --show --grep spider``\n\nSupported versions\n------------------\n\n25.02\n\nIn 2018 the plugin was updated to support the latest (at that moment) SPIDER version - 25.02. This required a lot of code refactoring and the support of old SPIDER version 21.03 had to be discontinued. The full changelog since Scipion-1.x is available `here <https://github.com/scipion-em/scipion-em-spider/issues/1>`_.\n\nProtocols\n---------\n\n* `Align AP SR <https://github.com/scipion-em/scipion-em-spider/wiki/SpiderProtAlignAPSR>`_\n* `Align pairwise <https://github.com/scipion-em/scipion-em-spider/wiki/SpiderProtAlignPairwise>`_\n* `CA PCA <https://github.com/scipion-em/scipion-em-spider/wiki/SpiderProtCAPCA>`_\n* `Classification protocols: Diday, K-means, Ward <https://github.com/scipion-em/scipion-em-spider/wiki/SpiderProtClassify>`_\n* Custom 2D mask\n* Filter particles\n* Reconstruct Fourier\n* Refinement\n\nReferences\n----------\n\n1. \\J. Frank et al. (1996). SPIDER and WEB: Processing and visualization of images in 3D electron microscopy and related fields. JSB. 116: 190-199.",
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