Add MotionCor2 build script
Installation is highly manual. This documents the MotionCor2 installation procedure and automates shared file installation. Adds 1.2.6 and 1.3.0 variants.
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EM/MotionCor2/README.md
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EM/MotionCor2/README.md
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# MotionCor2 Installation
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1. Download MotionCor2 manually from https://emcore.ucsf.edu/ucsf-motioncor2
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2. Update files/variants
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3. Run `./build <version>`
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4. Move all executables to /opt/psi/EM/MotionCor2/$VERSION/bin
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5. Move user manual to /opt/psi/EM/MotionCor2/$VERSION/
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6. Fix permissions: chmod 755 /opt/psi/EM/MotionCor2/$VERSION/bin
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## Cuda versions
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| MotionCor2 | Cuda Versions |
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|------------+---------------|
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| 1.0.5 | 8.0 9.1 |
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| 1.1.0 | 8.0 9.0 9.1 |
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| 1.2.0 | 8.0 9.1 9.2 |
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| 1.2.6 | 8.0 9.2 10.1 |
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| 1.3.0 | 8.0 9.2 10.1 |
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22
EM/MotionCor2/build
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EM/MotionCor2/build
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#!/usr/bin/env modbuild
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# Binary distribution with manual installation. See README.md
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pbuild::add_to_group 'EM'
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pbuild::prep() {
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cp $BUILDBLOCK_DIR/files/LICENSE $PREFIX/
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}
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pbuild::configure() {
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:
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}
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pbuild::compile() {
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:
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}
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pbuild::install() {
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:
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}
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95
EM/MotionCor2/files/LICENSE
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EM/MotionCor2/files/LICENSE
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UCSF MotionCor2 Non-Commercial Software License Agreement
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This license agreement ("License"), effective today, is made by and between you
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("Licensee") and The Regents of the University of California, a California
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corporation having its statewide administrative offices at 1111 Franklin Street,
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Oakland, California 94607-5200 ("The Regents"), acting through its Office of
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Technology Management, University of California San Francisco ("UCSF"), 3333
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California Street, Suite S-11, San Francisco, California 94143, and concerns
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certain software known as "MotionCor2," a software for correction of electron
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beam-induced sample motion in cryo-electron microscopy, for research purposes
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and includes executable code, source code, and documentation ("Software"). The
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Software was developed by the Keck Advanced Microscopy Laboratory and by Dr.
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David Agard at UCSF while Dr. Agard was an employee of Howard Hughes Medical
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Institute (“HHMI”).
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1. General. A non-exclusive, nontransferable, perpetual license is granted to
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the Licensee to install and use the Software for academic, non-profit, or
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government-sponsored research purposes. Use of the Software under this License
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is restricted to non-commercial purposes. Commercial use of the Software
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requires a separately executed written license agreement.
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2. Permitted Use and Restrictions. Licensee agrees that it will use the
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Software, and any modifications, improvements, or derivatives to the Software
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that the Licensee may create (collectively, "Improvements") solely for internal,
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non-commercial purposes and shall not distribute or transfer the Software or
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Improvements to any person or third parties without prior written permission
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from The Regents. The term "non-commercial," as used in this License, means
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academic or other scholarly research which (a) is not undertaken for profit, or
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(b) is not intended to produce works, services, or data for commercial use, or
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(c) is neither conducted, nor funded, by a person or an entity engaged in the
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commercial use, application or exploitation of works similar to the Software.
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3. Ownership and Assignment of Copyright. The Licensee acknowledges that The
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Regents hold copyright in the Software and associated documentation, and the
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Software and associated documentation are the property of The Regents. The
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Licensee agrees that any Improvements made by Licensee shall be subject to the
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same terms and conditions as the Software. Licensee agrees not to assert a claim
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of infringement in Licensee copyrights in Improvements in the event The Regents
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prepares substantially similar modifications or derivative works. The Licensee
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agrees to use his/her reasonable best efforts to protect the contents of the
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Software and to prevent unauthorized disclosure by its agents, officers,
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employees, and consultants. If the Licensee receives a request to furnish all or
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any portion of the Software to a third party, Licensee will not fulfill such a
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request but will refer the third party to the UCSF CryoEM Software web page so
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that the third party's use of this Software will be subject to the terms and
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conditions of this License. Notwithstanding the above, Licensee may disclose any
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Improvements that do not involve disclosure of the Software.
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4. Copies. The Licensee may make a reasonable number of copies of the Software
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for the purposes of backup, maintenance of the Software or the development of
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derivative works based on the Software. These additional copies shall carry the
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copyright notice and shall be controlled by this License, and will be destroyed
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along with the original by the Licensee upon termination of the License.
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5. Acknowledgement. Licensee agrees that any publication of results obtained
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with the Software will acknowledge its use by an appropriate citation as
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specified in the documentation.
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6. Disclaimer of Warranties and Limitation of Liability. THE LICENSEE AGREES
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THAT ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. THE REGENTS MAKES NO REPRESENTATION OR WARRANTY THAT THE SOFTWARE
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WILL NOT INFRINGE ANY PATENT OR OTHER PROPRIETARY RIGHT. IN NO EVENT SHALL THE
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REGENTS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
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GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
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HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
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LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF
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THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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7. Termination. This License is effective until terminated by either party.
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Licensee's rights under this License will terminate automatically without notice
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from The Regents if Licensee fails to comply with any term(s) of this License.
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Licensee may terminate the License by giving written notice of termination to
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The Regents. Upon termination of this License, Licensee shall immediately
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discontinue all use of the Software and destroy the original and all copies,
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full or partial, of the Software, including any modifications or derivative
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works, and associated documentation.
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8. Governing Law and General Provisions. This License shall be governed by the
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laws of the State of California, excluding the application of its conflicts of
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law rules. This License shall not be governed by the United Nations Convention
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on Contracts for the International Sale of Goods, the application of which is
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expressly excluded. If any provisions of this License are held invalid or
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unenforceable for any reason, the remaining provisions shall remain in full
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force and effect. This License is binding upon any heirs and assigns of the
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Licensee. The License granted to Licensee hereunder may not be assigned or
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transferred to any other person or entity without the express consent of The
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Regents. This License constitutes the entire agreement between the parties with
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respect to the use of the Software licensed hereunder and supersedes all other
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previous or contemporaneous agreements or understandings between the parties,
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whether verbal or written, concerning the subject matter. Any translation of
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this License is done for local requirements and in the event of a dispute
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between the English and any non-English versions, the English version of this
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License shall govern.
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7
EM/MotionCor2/files/variants
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EM/MotionCor2/files/variants
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MotionCor2/1.0.2 stable
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MotionCor2/1.0.4 stable
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MotionCor2/1.0.5 stable
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MotionCor2/1.1.0 stable
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MotionCor2/1.2.0 stable
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MotionCor2/1.2.6 unstable
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MotionCor2/1.3.0 unstable
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28
EM/MotionCor2/modulefile
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EM/MotionCor2/modulefile
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#%Module1.0
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module-whatis "Anisotropic Correction of Beam-induced Motion for Improved Single-particle Electron Cryo-microscopy"
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module-url "http://msg.ucsf.edu/em/software/motioncor2.html"
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module-license "This software may only be downloaded and used for free by academic and/or non-profit users"
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module-maintainer "Spencer Bliven <spencer.bliven@psi.ch>"
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module-help "
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Correction of electron beam-induced sample motion is one of the major factors
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contributing to the recent resolution breakthroughs in cryo-electron
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microscopy. Based on observations that the electron beam induces doming of the
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thin vitreous ice layer, we developed an algorithm to correct anisotropic image
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motion at the single pixel level across the whole frame, suitable for both
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single particle and tomographic images. Iterative, patch-based motion detection
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is combined with spatial and temporal constraints and dose weighting. The
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multi-GPU accelerated program, MotionCor2, is sufficiently fast to keep up with
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automated data collection. The result is an exceptionally robust strategy that
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can work on a wide range of data sets, including those very close to focus or
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with very short integration times, obviating the need for particle polishing.
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Application significantly improves Thon ring quality and 3D reconstruction
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resolution.
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Cite publication: Shawn Q. Zheng, Eugene Palovcak, Jean-Paul Armache, Yifan
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Cheng and David A. Agard (2016) Anisotropic Correction of Beam-induced Motion
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for Improved Single-particle Electron Cryo-microscopy, Nature Methods,
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submitted. BioArxiv: http://biorxiv.org/content/early/2016/07/04/061960
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"
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