diff --git a/EM/MotionCor2/README.md b/EM/MotionCor2/README.md new file mode 100644 index 0000000..56886f2 --- /dev/null +++ b/EM/MotionCor2/README.md @@ -0,0 +1,21 @@ +# MotionCor2 Installation + +1. Download MotionCor2 manually from https://emcore.ucsf.edu/ucsf-motioncor2 +2. Update files/variants +3. Run `./build ` +4. Move all executables to /opt/psi/EM/MotionCor2/$VERSION/bin +5. Move user manual to /opt/psi/EM/MotionCor2/$VERSION/ +6. Fix permissions: chmod 755 /opt/psi/EM/MotionCor2/$VERSION/bin + + +## Cuda versions + +| MotionCor2 | Cuda Versions | +|------------+---------------| +| 1.0.5 | 8.0 9.1 | +| 1.1.0 | 8.0 9.0 9.1 | +| 1.2.0 | 8.0 9.1 9.2 | +| 1.2.6 | 8.0 9.2 10.1 | +| 1.3.0 | 8.0 9.2 10.1 | + + diff --git a/EM/MotionCor2/build b/EM/MotionCor2/build new file mode 100755 index 0000000..cf2204e --- /dev/null +++ b/EM/MotionCor2/build @@ -0,0 +1,22 @@ +#!/usr/bin/env modbuild + +# Binary distribution with manual installation. See README.md + +pbuild::add_to_group 'EM' + +pbuild::prep() { + cp $BUILDBLOCK_DIR/files/LICENSE $PREFIX/ +} + +pbuild::configure() { + : +} + +pbuild::compile() { + : +} + +pbuild::install() { + : +} + diff --git a/EM/MotionCor2/files/LICENSE b/EM/MotionCor2/files/LICENSE new file mode 100644 index 0000000..27e353e --- /dev/null +++ b/EM/MotionCor2/files/LICENSE @@ -0,0 +1,95 @@ +UCSF MotionCor2 Non-Commercial Software License Agreement + +This license agreement ("License"), effective today, is made by and between you +("Licensee") and The Regents of the University of California, a California +corporation having its statewide administrative offices at 1111 Franklin Street, +Oakland, California 94607-5200 ("The Regents"), acting through its Office of +Technology Management, University of California San Francisco ("UCSF"), 3333 +California Street, Suite S-11, San Francisco, California 94143, and concerns +certain software known as "MotionCor2," a software for correction of electron +beam-induced sample motion in cryo-electron microscopy, for research purposes +and includes executable code, source code, and documentation ("Software"). The +Software was developed by the Keck Advanced Microscopy Laboratory and by Dr. +David Agard at UCSF while Dr. Agard was an employee of Howard Hughes Medical +Institute (“HHMI”). + +1. General. A non-exclusive, nontransferable, perpetual license is granted to +the Licensee to install and use the Software for academic, non-profit, or +government-sponsored research purposes. Use of the Software under this License +is restricted to non-commercial purposes. Commercial use of the Software +requires a separately executed written license agreement. + +2. Permitted Use and Restrictions. Licensee agrees that it will use the +Software, and any modifications, improvements, or derivatives to the Software +that the Licensee may create (collectively, "Improvements") solely for internal, +non-commercial purposes and shall not distribute or transfer the Software or +Improvements to any person or third parties without prior written permission +from The Regents. The term "non-commercial," as used in this License, means +academic or other scholarly research which (a) is not undertaken for profit, or +(b) is not intended to produce works, services, or data for commercial use, or +(c) is neither conducted, nor funded, by a person or an entity engaged in the +commercial use, application or exploitation of works similar to the Software. + +3. Ownership and Assignment of Copyright. The Licensee acknowledges that The +Regents hold copyright in the Software and associated documentation, and the +Software and associated documentation are the property of The Regents. The +Licensee agrees that any Improvements made by Licensee shall be subject to the +same terms and conditions as the Software. Licensee agrees not to assert a claim +of infringement in Licensee copyrights in Improvements in the event The Regents +prepares substantially similar modifications or derivative works. The Licensee +agrees to use his/her reasonable best efforts to protect the contents of the +Software and to prevent unauthorized disclosure by its agents, officers, +employees, and consultants. If the Licensee receives a request to furnish all or +any portion of the Software to a third party, Licensee will not fulfill such a +request but will refer the third party to the UCSF CryoEM Software web page so +that the third party's use of this Software will be subject to the terms and +conditions of this License. Notwithstanding the above, Licensee may disclose any +Improvements that do not involve disclosure of the Software. + +4. Copies. The Licensee may make a reasonable number of copies of the Software +for the purposes of backup, maintenance of the Software or the development of +derivative works based on the Software. These additional copies shall carry the +copyright notice and shall be controlled by this License, and will be destroyed +along with the original by the Licensee upon termination of the License. + +5. Acknowledgement. Licensee agrees that any publication of results obtained +with the Software will acknowledge its use by an appropriate citation as +specified in the documentation. + +6. Disclaimer of Warranties and Limitation of Liability. THE LICENSEE AGREES +THAT ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. THE REGENTS MAKES NO REPRESENTATION OR WARRANTY THAT THE SOFTWARE +WILL NOT INFRINGE ANY PATENT OR OTHER PROPRIETARY RIGHT. IN NO EVENT SHALL THE +REGENTS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE +GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) +HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT +LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF +THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +7. Termination. This License is effective until terminated by either party. +Licensee's rights under this License will terminate automatically without notice +from The Regents if Licensee fails to comply with any term(s) of this License. +Licensee may terminate the License by giving written notice of termination to +The Regents. Upon termination of this License, Licensee shall immediately +discontinue all use of the Software and destroy the original and all copies, +full or partial, of the Software, including any modifications or derivative +works, and associated documentation. + +8. Governing Law and General Provisions. This License shall be governed by the +laws of the State of California, excluding the application of its conflicts of +law rules. This License shall not be governed by the United Nations Convention +on Contracts for the International Sale of Goods, the application of which is +expressly excluded. If any provisions of this License are held invalid or +unenforceable for any reason, the remaining provisions shall remain in full +force and effect. This License is binding upon any heirs and assigns of the +Licensee. The License granted to Licensee hereunder may not be assigned or +transferred to any other person or entity without the express consent of The +Regents. This License constitutes the entire agreement between the parties with +respect to the use of the Software licensed hereunder and supersedes all other +previous or contemporaneous agreements or understandings between the parties, +whether verbal or written, concerning the subject matter. Any translation of +this License is done for local requirements and in the event of a dispute +between the English and any non-English versions, the English version of this +License shall govern. diff --git a/EM/MotionCor2/files/variants b/EM/MotionCor2/files/variants new file mode 100644 index 0000000..2218f9d --- /dev/null +++ b/EM/MotionCor2/files/variants @@ -0,0 +1,7 @@ +MotionCor2/1.0.2 stable +MotionCor2/1.0.4 stable +MotionCor2/1.0.5 stable +MotionCor2/1.1.0 stable +MotionCor2/1.2.0 stable +MotionCor2/1.2.6 unstable +MotionCor2/1.3.0 unstable diff --git a/EM/MotionCor2/modulefile b/EM/MotionCor2/modulefile new file mode 100644 index 0000000..1860f35 --- /dev/null +++ b/EM/MotionCor2/modulefile @@ -0,0 +1,28 @@ +#%Module1.0 + +module-whatis "Anisotropic Correction of Beam-induced Motion for Improved Single-particle Electron Cryo-microscopy" +module-url "http://msg.ucsf.edu/em/software/motioncor2.html" +module-license "This software may only be downloaded and used for free by academic and/or non-profit users" +module-maintainer "Spencer Bliven " + +module-help " +Correction of electron beam-induced sample motion is one of the major factors +contributing to the recent resolution breakthroughs in cryo-electron +microscopy. Based on observations that the electron beam induces doming of the +thin vitreous ice layer, we developed an algorithm to correct anisotropic image +motion at the single pixel level across the whole frame, suitable for both +single particle and tomographic images. Iterative, patch-based motion detection +is combined with spatial and temporal constraints and dose weighting. The +multi-GPU accelerated program, MotionCor2, is sufficiently fast to keep up with +automated data collection. The result is an exceptionally robust strategy that +can work on a wide range of data sets, including those very close to focus or +with very short integration times, obviating the need for particle polishing. +Application significantly improves Thon ring quality and 3D reconstruction +resolution. + +Cite publication: Shawn Q. Zheng, Eugene Palovcak, Jean-Paul Armache, Yifan +Cheng and David A. Agard (2016) Anisotropic Correction of Beam-induced Motion +for Improved Single-particle Electron Cryo-microscopy, Nature Methods, +submitted. BioArxiv: http://biorxiv.org/content/early/2016/07/04/061960 +" +