Diann 2.0.2 available.

Author: ypriverol

diann-2.0.2/Dockerfile

@@ -0,0 +1,53 @@
+FROM ubuntu:22.04
+
+# Some metadata
+LABEL base_image="ubuntu:22.04"
+LABEL version="2"
+LABEL software="diann"
+LABEL software.version="2.0"
+LABEL about.summary="DIA-NN - a universal software for data-independent acquisition (DIA) proteomics data processing."
+LABEL about.home="https://github.com/vdemichev/DiaNN"
+LABEL about.documentation="https://github.com/vdemichev/DiaNN"
+LABEL about.license_file="https://github.com/vdemichev/DiaNN/LICENSE.txt"
+LABEL about.tags="Proteomics"
+LABEL maintainer="Yasset Perez-Riverol <ypriverol@gmail.com>"
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Update package lists and ensure package versions are up to date, Install necessary packages
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    unzip \
+    libgomp1 \
+    locales && \
+    rm -rf /var/lib/apt/lists/*
+
+# Configure locale to avoid runtime errors
+RUN locale-gen en_US.UTF-8 && \
+    update-locale LANG=en_US.UTF-8
+
+# Set environment variables for locale
+ENV LANG=en_US.UTF-8
+ENV LANGUAGE=en_US:en
+ENV LC_ALL=en_US.UTF-8
+
+# Download and install DIA-NN
+RUN wget --no-check-certificate https://github.com/vdemichev/DiaNN/releases/download/2.0/DIA-NN-2.0.2-Academia-Linux.zip -O /tmp/DIA-NN-2.0.2-Academia-Linux.zip && \
+    unzip /tmp/DIA-NN-2.0.2-Academia-Linux.zip -d /usr/ && \
+    rm /tmp/DIA-NN-2.0.2-Academia-Linux.zip
+
+# Remove unnecessary packages
+RUN apt-get remove -y wget unzip && apt-get autoremove -y && apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Set appropriate permissions for the DIA-NN folder
+RUN chmod +x /usr/diann-2.0.2/diann-linux
+
+# Create a symbolic link and add to PATH
+RUN ln -s /usr/diann-2.0.2/diann-linux /usr/diann-2.0.2/diann
+ENV PATH="$PATH:/usr/diann-2.0.2"
+
+WORKDIR /data/
+
+# NOTE: It is entirely the user's responsibility to ensure compliance with DIA-NN license terms.
+# Please review the licensing terms for DIA-NN before using or distributing this Docker image.

diann-2.0.2/LICENSE.txt

@@ -0,0 +1,63 @@
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, 
+INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. 
+IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS 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.
+
+Herein the terms 'DIA-NN' or 'DIA-NN software' are used to refer to specifically the
+version of the DIA-NN software which packs this license file in its distribution package.
+
+1. Special DIA-NN software usage scenarios.
+Collaborative use refers to any usage of the DIA-NN software solely for the purpose of
+carrying out a joint collaborative project between yourself or your institution and the Demichev 
+laboratory at the Charité – Universitätsmedizin Berlin. The nature of the project and the intended 
+use of the DIA-NN software in this case must be agreed with the Demichev laboratory in advance.
+
+2. The DIA-NN software is licensed to you for use only under the terms of this License, 
+and all rights not expressly granted to you are reserved. The rights granted herein are limited to Vadim Demichev’s intellectual
+property rights in the DIA-NN software and do not include any other patents or intellectual property rights.
+
+3. Permitted use. Provided the usage restrictions imposed by this License are satisfied,
+this License allows you to install and use the DIA-NN software solely for the purpose of
+academic research or education. Commercial or for-profit use of the DIA-NN software is not permitted. You may make one copy of the DIA-NN software in machine-readable form for backup purposes only, 
+provided that the backup copy must include all copyright or other proprietary notices contained on the original.
+Usage of DIA-NN in the cloud or on any computer setups that are not in your immediate possession is only permitted under Collaborative use. Except as and only to the extent expressly 
+permitted in this License or by applicable law, you may not copy, decompile, reverse engineer, disassemble, 
+attempt to derive the source code of, modify, or create derivative works of the DIA-NN software or any part thereof. 
+
+4. The following is explicitly not permitted: (i) use of DIA-NN primarily intended or directed towards commercial advantage or monetary compensation, (ii) use of DIA-NN by a commercial or for-profit organisation or on behalf of such organisation.
+
+5. Transfer. You may not rent, lease, lend or sublicense the DIA-NN software. You may, however, make a one-time permanent transfer 
+of all of your license rights to the DIA-NN software to another party, provided that: (a) the transfer must include all of the DIA-NN software, 
+including all its component parts, original media, printed materials and this License; (b) you do not retain any copies of the DIA-NN software, 
+full or partial, including copies stored on a computer or other storage device; and (c) the party receiving the DIA-NN software reads 
+and agrees to accept the terms and conditions of this License.
+
+6. Attribution. If you share, distribute or publish any materials that were produced using the DIA-NN software ("Derived Materials"), you must indicate 
+within these Derived Materials that they were produced using the DIA-NN software. You may satisfy this condition in any reasonable manner 
+based on the medium, means, and context in which you share the Derived Materials. For example, the required attribution can be expressed by including
+one of the statements "Processed using DIA-NN", "Generated using DIA-NN" or "Produced using DIA-NN" in the Derived Materials.
+
+7. All third-party software included in this DIA-NN software distribution retains its original license.
+For the inclusion in this DIA-NN software distribution, the source code of MSToolkit and MiniDNN was modified.
+If not packaged within this distribution, please find the source code of the third-party software at https://github.com/vdemichev/DiaNN
+or at the respective website of the third-party software.
+
+8. Experimental functionality.
+Any of the DIA-NN commands/options that are not referenced at https://github.com/vdemichev/DiaNN/blob/master/README.md 
+are considered Experimental functionality. The following DIA-NN commands/options are also considered Experimental functionality:
+--extract
+--mgf
+Experimental functionality is in the process of being actively developed and is thus shared 'on collaborative basis' 
+before it is published in a peer-reviewed publication. It is not tested as thoroughly as the rest of DIA-NN and 
+needs to be used with caution, with expertise in the internal workings of DIA-NN potentially required for correct use. 
+Any peer-reviewed publication or academic preprint derived from any usage of Experimental functionality that occurs 
+before a peer-reviewed manuscript describing the respective Experimental functionality is published must therefore 
+be published in collaboration and co-authorship with the Demichev laboratory. Using Experimental functionality is not
+permitted if you do not agree to the above. A peer-reviewed manuscript is considered to describe a particular 
+Experimental functionality if (i) it is referenced at https://github.com/vdemichev/DiaNN/blob/master/README.md 
+as describing this functionality and (ii) the date when it was made available online by the publisher falls after 
+the date on which the specific version of the DIA-NN software to which this license refers to was built.
+