Don't remove DIA-NN from FragPipe installation.

recipes/fragpipe/build.sh

@@ -4,9 +4,6 @@
 TARGET="$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM"
 mkdir -p "$TARGET"
 
-# DIA-NN license is currently incompatible with bioconda
-rm -rf fragpipe_source/tools/diann{,_so}
-rm -rf fragpipe_source/tools/diann{,_so}
 cp -rp fragpipe_source/* "$TARGET"
 
 # Copy wrapper script, which checks license keys, into bin.

recipes/fragpipe/fragpipe

@@ -34,15 +34,6 @@ while [[ $# -gt 0 ]]; do
     shift
 done
 
-if [[ ! -z "$workflow_file" ]]; then
-    # Because the DIA-NN license is incompatible with bioconda, we remove the feature.
-    grep 'diann.run-dia-nn=true' "$workflow_file" >/dev/null
-    if [[ $? -eq 0 ]]; then
-        echo "Error: DIA-NN is disabled in the FragPipe bioconda package."
-        exit 1
-    fi
-fi
-
 if [[ -z $msfragger_key || -z $ionquant_key ]]; then
     echo "$license_agreement_text"
     exit 1

recipes/fragpipe/licenses/diann_LICENSE.txt

@@ -0,0 +1,46 @@
+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.
+
+1. General. 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.
+
+2. Permitted License Uses and Restrictions. This License allows you to install and use the DIA-NN software.
+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.
+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. 
+
+3. 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.
+
+4. 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.
+
+5. All third-party software included in this DIA-NN software distribution retains its original license (see below).
+For the inclusion in this DIA-NN software distribution, the source code of MSToolkit and MiniDNN was modified.
+
+MiniDNN
+ - folder within this distribution: /MiniDNN
+ - URL: https://github.com/yixuan/MiniDNN
+ - License information: /MiniDNN/LICENSE.txt
+
+MSToolkit
+ - folder within this distribution: /mstoolkit
+ - URL: https://github.com/mhoopmann/mstoolkit
+ - License information: /mstoolkit/LICENSE.txt
+
+Eigen
+ - folder within this distribution: /eigen
+ - URL: http://eigen.tuxfamily.org/
+ - License information: eigen/COPYING.README

recipes/fragpipe/meta.yaml

@@ -12,7 +12,7 @@ package:
   version: {{ version }}
 
 build:
-  number: 3
+  number: 4
   noarch: generic
   run_exports:
     - {{ pin_subpackage('fragpipe', max_pin="x.x") }}