ITASSER script improvements

SBRG · Jun 24, 2017 · 9f7c142 · 9f7c142
1 parent 3548b31
commit 9f7c142
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Showing 3 changed files with 9 additions and 4 deletions.
diff --git a/setup.py b/setup.py
@@ -5,12 +5,12 @@
 
 setup(
         name='ssbio',
-        version='0.9.8',
+        version='0.9.8.1',
         author='Nathan Mih',
         author_email='nmih@ucsd.edu',
         license='MIT',
         url='http://github.com/SBRG/ssbio',
-        download_url = 'https://github.com/SBRG/ssbio/archive/v0.9.8.tar.gz',
+        download_url = 'https://github.com/SBRG/ssbio/archive/v0.9.8.1.tar.gz',
         description='Tools to enable structural systems biology',
         packages=find_packages(),
         package_dir={'ssbio': 'ssbio'},

diff --git a/ssbio/core/protein.py b/ssbio/core/protein.py
@@ -641,6 +641,7 @@ def prep_itasser_modeling(self, itasser_installation, itlib_folder, runtype, cre
         repseq = self.representative_sequence
 
         itasser_kwargs = {'light': True,
+                          'java_home': None,
                           'binding_site_pred': False,
                           'ec_pred': False,
                           'go_pred': False,
@@ -653,6 +654,7 @@ def prep_itasser_modeling(self, itasser_installation, itlib_folder, runtype, cre
         ITASSERPrep(ident=self.id, seq_str=repseq.seq_str, root_dir=self.homology_models_dir,
                     itasser_path=itasser_installation, itlib_path=itlib_folder,
                     runtype=runtype, print_exec=print_exec, execute_dir=execute_from_dir,
+                    java_home=itasser_kwargs['java_home'],
                     light=itasser_kwargs['light'],
                     binding_site_pred=itasser_kwargs['binding_site_pred'],
                     ec_pred=itasser_kwargs['ec_pred'],

diff --git a/ssbio/protein/structure/homology/itasser/itasserprep.py b/ssbio/protein/structure/homology/itasser/itasserprep.py
@@ -14,7 +14,7 @@ class ITASSERPrep():
     """
 
     def __init__(self, ident, seq_str, root_dir, itasser_path, itlib_path,
-                 execute_dir=None, light=True, runtype='local', print_exec=False, java_home='${JAVA_HOME}',
+                 execute_dir=None, light=True, runtype='local', print_exec=False, java_home=None,
                  binding_site_pred=False, ec_pred=False, go_pred=False, additional_options=None,
                  job_scheduler_header=None):
         """Create the I-TASSER folder and also an executable script to run I-TASSER
@@ -81,7 +81,10 @@ def __init__(self, ident, seq_str, root_dir, itasser_path, itlib_path,
             additional_options += '-GO true '
         self.additional_options = additional_options
 
-        self.java_home = java_home
+        if not java_home:
+            self.java_home = '${JAVA_HOME}'
+        else:
+            self.java_home = java_home
         self.job_scheduler_header = job_scheduler_header
 
         if runtype == 'local' or runtype == 'torque':