From 5431faa6af0bf16c1bf68f6e5abcf5a4f324ab03 Mon Sep 17 00:00:00 2001
From: David Emms <david_emms@hotmail.com>
Date: Wed, 7 Sep 2016 09:55:50 +0100
Subject: [PATCH] Exit gracefully if orthologue dependencies not met
---
orthofinder/scripts/get_orthologues.py | 9 ++++++---
1 file changed, 6 insertions(+), 3 deletions(-)
diff --git a/orthofinder/scripts/get_orthologues.py b/orthofinder/scripts/get_orthologues.py
index 82e32d7..3cf29a7 100755
--- a/orthofinder/scripts/get_orthologues.py
+++ b/orthofinder/scripts/get_orthologues.py
@@ -476,7 +476,7 @@ def CanRunDependencies(workingDir):
if os.path.exists(outFN): os.remove(outFN)
if not util.CanRunCommand("fastme -i %s -o %s" % (testFN, outFN), qAllowStderr=False):
print("ERROR: Cannot run fastme")
- print("Please check FastME is installed and that the executables are in the system path\n")
+ print("Please check FastME is installed and that the executables are in the system path.\n")
return False
os.remove(testFN)
os.remove(outFN)
@@ -485,7 +485,7 @@ def CanRunDependencies(workingDir):
# DLCPar
if not util.CanRunCommand("dlcpar_search --version", qAllowStderr=False):
print("ERROR: Cannot run dlcpar_search")
- print("Please check DLCpar is installed and that the executables are in the system path\n")
+ print("Please check DLCpar is installed and that the executables are in the system path.\n")
return False
return True
@@ -535,7 +535,10 @@ def GetOrthologues(orthofinderWorkingDir, orthofinderResultsDir, clustersFilenam
print("\n1. Checking required programs are installed")
print( "-------------------------------------------")
- if not CanRunDependencies(orthofinderWorkingDir): util.Fail()
+ if not CanRunDependencies(orthofinderWorkingDir):
+ print("Orthogroups have been inferred but the dependencies for inferring gene trees and\northologues have not been met. Please review previous messages for more information.")
+ sys.exit()
+
print("\n2. Reading sequence similarity scores")
print( "-------------------------------------")
--
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