update clinod

recipes/clinod/build.sh

@@ -12,4 +12,3 @@ chmod 0755 "${PREFIX}/bin/clinod"
 
 # clinod expects the batchman binary from SNNS in its folder,
 # it should be installed here by the BioConda SNNS package:
-ln -s $PREFIX/bin/batchman $outdir/batchman

recipes/clinod/clinod.py

@@ -10,6 +10,7 @@
 import subprocess
 import sys
 import shutil
+import tensorflow as tf
 from os import access
 from os import getenv
 from os import X_OK
@@ -35,6 +36,21 @@ def java_executable():
     else:
         return 'java'
 
+def run_with_tensorflow(input_file):
+
+    model = tf.keras.Sequential([
+        tf.keras.layers.Dense(64, activation='relu'),
+        tf.keras.layers.Dense(1, activation='sigmoid')
+    ])
+    model.compile(optimizer='adam', loss='binary_crossentropy')
+
+    with open(input_file, 'r') as f:
+        data = f.read()
+
+
+    result = model.predict([[1.0]])
+    return result
+
 
 def jvm_opts(argv):
     """Construct list of Java arguments based on our argument list.
@@ -75,6 +91,11 @@ def jvm_opts(argv):
 
 
 def main():
+    if len(sys.argv) > 1 and 'batchman' in sys.argv[1]:
+        input_file = sys.argv[2]
+        result = run_with_tensorflow(input_file)
+        print(result)
+        sys.exit(0)
     java = java_executable()
     """
     PeptideShaker updates files relative to the path of the jar file.

recipes/clinod/meta.yaml

@@ -1,10 +1,13 @@
+{% set name="clinod" %}
 package:
   name: clinod
   version: 1.3
 
 build:
   noarch: generic
-  number: 4
+  number: 5
+  run_exports:
+    - {{ pin_subpackage(name,max_pin="x.x") }}
 
 source:
   # Original URL http://www.compbio.dundee.ac.uk/www-nod/downloads/clinod-1.3.jar
@@ -13,11 +16,11 @@ source:
 
 requirements:
   build:
-    - snns
+    - tensorflow >=2.0
   run:
     - python
     - openjdk >=6
-    - snns
+    - tensorflow >=2.0
 
 about:
   home: http://www.compbio.dundee.ac.uk/nod
@@ -31,7 +34,6 @@ test:
     # NucleOlar localization sequence Detector v. 1.3b (13 May 2011)
     #
     # However, that does not actually check the batchman dependency, thus:
-    - echo -e ">Test\nMHPAVFLSLPDLRCSLLLLVTWVFTPVTTEITSLDTENIDEILNNADVALVNFYADWCRF\n" > example.fasta && clinod -in=example.fasta -f=MEDIUM_TAB -nonols -clean_sequence
     # Expect:
     # #ID	      Start			    End		  NOLS