From 1d6be3bc05b2acdf42486b43864d8b18d8b25541 Mon Sep 17 00:00:00 2001
From: pirovc <4673375+pirovc@users.noreply.github.com>
Date: Fri, 28 Apr 2023 15:54:56 +0200
Subject: [PATCH] v1.5.1 fix path script build-custom (#246)

* v1.5.1 fix path script build-custom

* gu v0.6.1
---
 CMakeLists.txt      |  2 +-
 libs/genome_updater |  2 +-
 setup.py            |  2 +-
 src/ganon/config.py | 22 ++++++++++------------
 4 files changed, 13 insertions(+), 15 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 078ae5fa..a41ee0ff 100755
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -3,7 +3,7 @@
 # =============================================================================
 
 cmake_minimum_required( VERSION 3.10 FATAL_ERROR )
-project( ganon VERSION 1.5.0 LANGUAGES CXX )
+project( ganon VERSION 1.5.1 LANGUAGES CXX )
 
 # -----------------------------------------------------------------------------
 # build setup
diff --git a/libs/genome_updater b/libs/genome_updater
index a512fae6..077e4aee 160000
--- a/libs/genome_updater
+++ b/libs/genome_updater
@@ -1 +1 @@
-Subproject commit a512fae629fb0732d1b9e9c4837968dcbcd23f3d
+Subproject commit 077e4aee4dc9e2019477e4a8bbd41227d52f92db
diff --git a/setup.py b/setup.py
index d28b1b4e..483d8570 100755
--- a/setup.py
+++ b/setup.py
@@ -13,7 +13,7 @@ def read(filename):
 
 setup(
     name="ganon",
-    version="1.5.0",
+    version="1.5.1",
     url="https://www.github.com/pirovc/ganon",
     license='MIT',
     author="Vitor C. Piro",
diff --git a/src/ganon/config.py b/src/ganon/config.py
index 440b6c1b..4a59a16e 100644
--- a/src/ganon/config.py
+++ b/src/ganon/config.py
@@ -8,7 +8,7 @@
 
 class Config:
 
-    version = "1.5.0"
+    version = "1.5.1"
     path_exec = {"build": "", "classify": "", "get_seq_info": "", "genome_updater": ""}
     empty = False
 
@@ -463,15 +463,8 @@ def validate(self):
     def set_paths(self):
         missing_path = False
         self.ganon_path = self.ganon_path + "/" if self.ganon_path else ""
-        if self.which in ["build", "update"]:
-            ganon_get_seq_info_paths = [self.ganon_path, self.ganon_path+"scripts/", self.ganon_path+"../scripts/"] if self.ganon_path else [None, "scripts/"]
-            for p in ganon_get_seq_info_paths:
-                self.path_exec["get_seq_info"] = shutil.which("ganon-get-seq-info.sh", path=p)
-                if self.path_exec["get_seq_info"] is not None: break
-            if self.path_exec["get_seq_info"] is None:
-                print_log("ganon-get-seq-info.sh script was not found. Please inform a specific path with --ganon-path")
-                missing_path = True
 
+        if self.which in ["build", "update", "build-custom"]:
             ganon_genome_updater_paths = [self.ganon_path, self.ganon_path+"libs/genome_updater/", self.ganon_path+"../libs/genome_updater/"] if self.ganon_path else [None, "libs/genome_updater/"]
             for p in ganon_genome_updater_paths:
                 self.path_exec["genome_updater"] = shutil.which("genome_updater.sh", path=p)
@@ -480,8 +473,14 @@ def set_paths(self):
                 print_log("genome_updater.sh was not found. Please inform a specific path with --ganon-path")
                 missing_path = True
 
+            ganon_get_seq_info_paths = [self.ganon_path, self.ganon_path+"scripts/", self.ganon_path+"../scripts/"] if self.ganon_path else [None, "scripts/"]
+            for p in ganon_get_seq_info_paths:
+                self.path_exec["get_seq_info"] = shutil.which("ganon-get-seq-info.sh", path=p)
+                if self.path_exec["get_seq_info"] is not None: break
+            if self.path_exec["get_seq_info"] is None:
+                print_log("ganon-get-seq-info.sh script was not found. Please inform a specific path with --ganon-path")
+                missing_path = True
 
-        if self.which in ["build-custom"]:
             # if path is given, look for binaries only there
             ganon_build_paths = [self.ganon_path, self.ganon_path+"build/"] if self.ganon_path else [None, "build/"]
             for p in ganon_build_paths:
@@ -491,7 +490,7 @@ def set_paths(self):
                 print_log("ganon-build binary was not found. Please inform a specific path with --ganon-path")
                 missing_path = True
 
-            if self.hibf:
+            if hasattr(self, 'hibf') and self.hibf:
                 self.raptor_path = self.raptor_path + "/" if self.raptor_path else ""
                 raptor_paths = [self.raptor_path, self.raptor_path+"build/bin/"] if self.raptor_path else [None, "build/"]
                 for p in raptor_paths:
@@ -501,7 +500,6 @@ def set_paths(self):
                     print_log("raptor binary was not found. Please inform a specific path with --raptor-path")
                     missing_path = True
 
-        
         if self.which in ["classify"]:
             ganon_classify_paths = [self.ganon_path, self.ganon_path+"build/"] if self.ganon_path else [None, "build/"]
             for p in ganon_classify_paths: