Merge branch 'motioncor2' into 'master'

Add MotionCor2 build script

See merge request Pmodules/buildblocks!80

EM/MotionCor2/README.md

+# MotionCor2 Installation
+
+1. Download MotionCor2 manually from https://emcore.ucsf.edu/ucsf-motioncor2
+2. Update files/variants
+3. Run `./build <version>`
+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  |
+
+

EM/MotionCor2/build

+#!/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() {
+    :
+}
+

EM/MotionCor2/files/LICENSE

+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.

EM/MotionCor2/files/variants

+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	

EM/MotionCor2/modulefile

+#%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 <spencer.bliven@psi.ch>"
+
+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
+"
+