Write cactus commit into src/ tree when installing through setup.py, …

…should work for hot-deployment and pip [ci skip]

.gitignore

@@ -15,4 +15,5 @@ dist
 *.a
 cactusSequences
 *~
-.cache
+.cache
+src/cactus/shared/version.py

setup.py

@@ -1,8 +1,17 @@
 from setuptools import setup, find_packages
 import os
+import subprocess
 
 os.system("pip install git+https://github.com/ComparativeGenomicsToolkit/sonLib@toil")
 
+versionFile = "src/cactus/shared/version.py"
+if os.path.exists(versionFile):
+    os.remove(versionFile)
+git_commit = subprocess.check_output("cd %s && git rev-parse HEAD" % os.path.dirname(__file__), shell=True).rstrip().strip()
+with open(versionFile, 'w') as versionFH:
+    versionFH.write("cactus_commit = '%s'" % git_commit)
+
+
 setup(
     name="progressiveCactus",
     version="1.0",

src/cactus/pipeline/ktserverControl.py

@@ -40,7 +40,7 @@
 from cactus.shared.experimentWrapper import DbElemWrapper
 from cactus.shared.experimentWrapper import ExperimentWrapper
 
-from cactus.shared.common import getCactusCommit
+from cactus.shared.version import cactus_commit
 
 ###############################################################################
 # run a server until killSwitchPath gets deleted
@@ -326,7 +326,7 @@ def pingKtServer(dbElem):
             dbElem.getDbHost(), getHostName()))
 
     cmd = ['docker', 'run', '--interactive', '--log-driver=none', '--net=host',
-                      'quay.io/adderan/ktremotemgr:%s' % getCactusCommit(), 'report',
+                      'quay.io/adderan/ktremotemgr:%s' % cactus_commit, 'report',
                       '-port', str(dbElem.getDbPort()),
                       '-host', dbElem.getDbHost()]
     logger.info("Ktremotemgr cmd = %s" % cmd)
@@ -479,7 +479,7 @@ def __getKtserverCommand(dbElem, exists = False, readOnly = False):
     serverOptions = __getKtServerOptions(dbElem)
     tuning = __getKtTuningOptions(dbElem, exists, readOnly)
     work_dir = os.path.dirname(os.path.abspath(logPath))
-    cmd = "docker run --interactive -v %s:/data --log-driver=none -p %d:%d --net=host quay.io/adderan/ktserver:%s -log %s -port %d %s" % (work_dir, port, port, getCactusCommit(), os.path.basename(logPath), port, serverOptions)
+    cmd = "docker run --interactive -v %s:/data --log-driver=none -p %d:%d --net=host quay.io/adderan/ktserver:%s -log %s -port %d %s" % (work_dir, port, port, cactus_commit, os.path.basename(logPath), port, serverOptions)
     if readOnly is True and dbElem.getDbSnapshot() == False:
         cmd += " -ord -onr"
     if dbElem.getDbHost() is not None:

src/cactus/shared/common.py

@@ -24,6 +24,8 @@
 from sonLib.bioio import nameValue
 from sonLib.bioio import popenCatch, popenPush
 
+from cactus.shared.version import cactus_commit
+
 _log = logging.getLogger(__name__)
 
 
@@ -743,10 +745,6 @@ def runGetChunks(sequenceFiles, chunksDir, chunkSize, overlapSize):
                                            overlapSize,
                                            chunksDir] + sequenceFiles).split("\n") if chunk != ""]
 
-def getCactusCommit():
-    commit = subprocess.check_output("cd %s && git rev-parse HEAD" % os.path.dirname(__file__), shell=True)
-    return commit.rstrip().strip()
-
 def cactus_call(tool,
                 work_dir=None,
                 parameters=None,
@@ -815,7 +813,7 @@ def adjustPath(path):
         base_docker_call.append('--rm')
 
 
-    tool = "%s/%s:%s" % (dockstore, tool, getCactusCommit())
+    tool = "%s/%s:%s" % (dockstore, tool, cactus_commit)
 
     parameters = [par for par in parameters if par != '']
     call = base_docker_call + [tool] + parameters