Added more descriptive missing dependency errors

plugins/contact_network/ngg.py

@@ -20,7 +20,12 @@ def ngg(exe, params, out_fn, config, verbose=True):
         error("Invalid NiemaGraphGen exe: %s" % exe)
     if verbose:
         print_log("Command: %s" % ' '.join(command))
-    f = open(out_fn['contact_network'], 'w'); call(command, stdout=f); f.close()
+    f = open(out_fn['contact_network'], 'w')
+    try:
+        call(command, stdout=f)
+    except FileNotFoundError as e:
+        error("Unable to run NiemaGraphGen. Make sure all ngg_* executables are in your PATH (e.g. /usr/local/bin)")
+    f.close()
     if verbose:
         print_log("Contact Network written to: %s" % out_fn['contact_network'])
 def ngg_barabasi_albert(params, out_fn, config, verbose=True):

plugins/sequence_evolution/seqgen.py

@@ -40,7 +40,12 @@ def seqgen(mode, params, out_fn, config, verbose=True):
     command += [seqgen_tree_fn]
     if verbose:
         print_log("Command: %s" % ' '.join(command))
-    out_f = open(out_fn['sequences'], 'w'); log_f = open(seqgen_log_fn, 'w'); call(command, stdout=out_f, stderr=log_f); log_f.close(); out_f.close()
+    out_f = open(out_fn['sequences'], 'w'); log_f = open(seqgen_log_fn, 'w')
+    try:
+        call(command, stdout=out_f, stderr=log_f)
+    except FileNotFoundError as e:
+        error("Unable to run seq-gen. Make sure seq-gen executable is in your PATH (e.g. /usr/local/bin)")
+    log_f.close(); out_f.close()
     if stat(out_fn['sequences']).st_size < 2:
         error("Seq-Gen crashed. See log file: %s" % seqgen_log_fn)
     if verbose:

plugins/transmission_network/gemf.py

@@ -79,7 +79,10 @@ def gemf_favites(model, params, out_fn, config, verbose=True):
     ]
     if verbose:
         print_log("Command: %s" % ' '.join(command))
-    call(command)
+    try:
+        call(command)
+    except FileNotFoundError as e:
+        error("Unable to run GEMF_FAVITES. Make sure GEMF_FAVITES.py and GEMF executables are in your PATH (e.g. /usr/local/bin)")
     move('%s/transmission_network.txt' % gemf_out, out_fn['transmission_network'])
     if verbose:
         print_log("Transmission Network written to: %s" % out_fn['transmission_network'])

plugins/viral_phylogeny_trans/coatran.py

@@ -17,7 +17,12 @@ def coatran(exe, params, out_fn, config, verbose=True):
         error("Invalid CoaTran exe: %s" % exe)
     if verbose:
         print_log("Command: %s" % ' '.join(command))
-    f = open(out_fn['viral_phylogeny_all_chains_time'], 'w'); call(command, stdout=f); f.close()
+    f = open(out_fn['viral_phylogeny_all_chains_time'], 'w')
+    try:
+        call(command, stdout=f)
+    except FileNotFoundError as e:
+        error("Unable to run CoaTran. Make sure all coatran_* executables are in your PATH (e.g. /usr/local/bin)")
+    f.close()
     if stat(out_fn['viral_phylogeny_all_chains_time']).st_size < 2:
         error("CoaTran crashed")
     if verbose: