Merge pull request #13 from broadinstitute/dp-bump-core

bump viral-core

Dockerfile

@@ -1,4 +1,4 @@
-FROM quay.io/broadinstitute/viral-core:2.1.1
+FROM quay.io/broadinstitute/viral-core:2.1.3
 
 LABEL maintainer "[email protected]"
 

assemble/gap2seq.py

@@ -21,8 +21,7 @@
 import util.file
 import util.misc
 
-TOOL_NAME = 'gap2seq'
-TOOL_VERSION = '3.1.1a2'
+TOOL_NAME = 'Gap2Seq'
 
 log = logging.getLogger(__name__)
 
@@ -31,11 +30,11 @@ class Gap2SeqTool(tools.Tool):
 
     def __init__(self, install_methods=None):
         if install_methods is None:
-            install_methods = [tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION, executable='Gap2Seq')]
-        tools.Tool.__init__(self, install_methods=install_methods)
+            install_methods = [tools.PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]
+        super(Gap2SeqTool, self).__init__(install_methods=install_methods)
 
     def version(self):
-        return TOOL_VERSION
+        return None
 
     def execute(self, args):    # pylint: disable=W0221
         tool_cmd = [self.install_and_get_path()] + list(args)

assemble/mafft.py

@@ -12,10 +12,10 @@
 import util.misc
 import os
 import os.path
+import shutil
 import subprocess
 
 TOOL_NAME = "mafft"
-TOOL_VERSION = '7.464'
 
 _log = logging.getLogger(__name__)
 
@@ -24,12 +24,16 @@ class MafftTool(tools.Tool):
 
     def __init__(self, install_methods=None):
         if install_methods is None:
-            install_methods = []
-            install_methods.append(tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION))
-        tools.Tool.__init__(self, install_methods=install_methods)
+            install_methods = [tools.PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]
+        super(MafftTool, self).__init__(install_methods=install_methods)
 
     def version(self):
-        return TOOL_VERSION
+        if self.tool_version is None:
+            self._get_tool_version()
+        return self.tool_version
+
+    def _get_tool_version(self):
+        self.tool_version = subprocess.check_output([self.install_and_get_path(), '--version']).decode('UTF-8').strip().split()[0]
 
     def __seqIdsAreAllUnique(self, filePath, inputFormat="fasta"):
         seqIds = []

assemble/mummer.py

@@ -10,11 +10,11 @@
 import os
 import os.path
 import random
+import shutil
 import subprocess
 import Bio.SeqIO
 
-TOOL_NAME = "mummer4"
-tool_version = '4.0.0beta2'
+TOOL_NAME = "mummer"
 
 log = logging.getLogger(__name__)
 
@@ -23,13 +23,16 @@ class MummerTool(tools.Tool):
 
     def __init__(self, install_methods=None):
         if install_methods is None:
-            install_methods = [
-                tools.CondaPackage(TOOL_NAME, executable="mummer", version=tool_version)
-                ]
-        tools.Tool.__init__(self, install_methods=install_methods)
+            install_methods = [tools.PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]
+        super(MummerTool, self).__init__(install_methods=install_methods)
 
     def version(self):
-        return tool_version
+        if self.tool_version is None:
+            self._get_tool_version()
+        return self.tool_version
+
+    def _get_tool_version(self):
+        self.tool_version = subprocess.check_output([self.install_and_get_path(), '-version']).decode('UTF-8').strip()
 
     def executable_path(self):
         exec_path = tools.Tool.executable_path(self)

assemble/muscle.py

@@ -10,12 +10,11 @@
 
 import os
 import os.path
+import shutil
 import subprocess
 import logging
 
 TOOL_NAME = "muscle"
-TOOL_VERSION = '3.8.1551'
-CONDA_TOOL_VERSION = '3.8.1551'
 
 _log = logging.getLogger(__name__)
 
@@ -24,12 +23,16 @@ class MuscleTool(tools.Tool):
 
     def __init__(self, install_methods=None):
         if install_methods is None:
-            install_methods = []
-            install_methods.append(tools.CondaPackage(TOOL_NAME, version=CONDA_TOOL_VERSION))
-        tools.Tool.__init__(self, install_methods=install_methods)
+            install_methods = [tools.PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]
+        super(MuscleTool, self).__init__(install_methods=install_methods)
 
     def version(self):
-        return TOOL_VERSION
+        if self.tool_version is None:
+            self._get_tool_version()
+        return self.tool_version
+
+    def _get_tool_version(self):
+        self.tool_version = subprocess.check_output([self.install_and_get_path(), '-version']).decode('UTF-8').strip().split()[1]
 
     # pylint: disable=W0221
     def execute(

assemble/spades.py

@@ -19,8 +19,7 @@
 import util.file
 import util.misc
 
-TOOL_NAME = 'spades'
-TOOL_VERSION = '3.12.0'
+TOOL_NAME = 'spades.py'
 
 log = logging.getLogger(__name__)
 
@@ -29,12 +28,16 @@ class SpadesTool(tools.Tool):
 
     def __init__(self, install_methods=None):
         if install_methods is None:
-            install_methods = [tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION, executable='spades.py',
-                                                  verifycmd='spades.py --version')]
-        tools.Tool.__init__(self, install_methods=install_methods)
+            install_methods = [tools.PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]
+        super(SpadesTool, self).__init__(install_methods=install_methods)
 
     def version(self):
-        return TOOL_VERSION
+        if self.tool_version is None:
+            self._get_tool_version()
+        return self.tool_version
+
+    def _get_tool_version(self):
+        self.tool_version = subprocess.check_output([self.install_and_get_path(), '--version']).decode('UTF-8').strip().split()[1]
 
     def execute(self, args):    # pylint: disable=W0221
         tool_cmd = [self.install_and_get_path()] + list(map(str, args))

assemble/trinity.py

@@ -19,9 +19,7 @@
 import tools
 import util.misc
 
-TOOL_NAME = "trinity"
-TOOL_VERSION = "2011-11-26"
-CONDA_TOOL_VERSION = "date.2011_11_26" # conda versions cannot have hyphens...
+TOOL_NAME = "Trinity"
 
 log = logging.getLogger(__name__)
 
@@ -51,12 +49,11 @@ class TrinityTool(tools.Tool):
 
     def __init__(self, install_methods=None):
         if install_methods is None:
-            install_methods = []
-            install_methods.append(tools.CondaPackage(TOOL_NAME, executable="Trinity", version=CONDA_TOOL_VERSION))
-        tools.Tool.__init__(self, install_methods=install_methods)
+            install_methods = [tools.PrexistingUnixCommand(shutil.which(TOOL_NAME), require_executability=True)]
+        super(TrinityTool, self).__init__(install_methods=install_methods)
 
     def version(self):
-        return TOOL_VERSION
+        return None
 
     def execute(self,
                 inFastq1,