added in checks and tb-profiler installation

tbtamr/RunProfiler.py

@@ -3,7 +3,7 @@
 from collections import namedtuple
 from tbtamr.CustomLog import logger
 from tbtamr.TbTamr import Tbtamr
-
+from tbtamr.TbTamr_Utils import check
 
 class RunProfiler(Tbtamr):
     """
@@ -77,18 +77,9 @@ def _batch_collate(self, input_data):
         return cmd
 
     def _check_tbprofiler(self):
-        version_pat_3 = re.compile(r'\bv?(?P<major>[0-9]+)\.(?P<minor>[0-9]+)(?:\.(?P<release>[0-9]+)*)?(?:\.(?P<build>[0-9]+)*)?\b')
-        p = subprocess.run(f"tb-profiler version", capture_output=True, encoding = "utf-8", shell = True)
-        p = p.stdout
-        v = version_pat_3.search(p.strip())
-        if v:
-            v = v.group(0)
-            logger.info(f"TB Profiler version {v} detected.")    
-        else:
-            logger.critical(f"It seems something is not quite right with your TB profiler installation. Please check your installation and try again.")
-            raise SystemExit
-        return True
-
+
+        return check()
+
 
     def _run(self):
         """

tbtamr/TbTamr_Utils.py

@@ -0,0 +1,64 @@
+
+import pathlib, subprocess, re,json
+from collections import namedtuple
+from tbtamr.CustomLog import logger
+# from tbtamr.RunProfiler import RunProfiler
+
+# version_pat_3 = 
+
+def _run_cmd(cmd):
+    p = subprocess.run(f"{cmd}", capture_output=True, encoding = "utf-8", shell = True)
+    return p  
+
+def version_pattern():
+    return re.compile(r'\bv?(?P<major>[0-9]+)\.(?P<minor>[0-9]+)(?:\.(?P<release>[0-9]+)*)?(?:\.(?P<build>[0-9]+)*)?\b')
+
+def _run_check(_input, sft):
+    p = _run_cmd(cmd=_input)
+    _str = p.stdout
+    v = version_pattern().search(_str.strip())
+    if v:
+        v = v.group(0)
+        logger.info(f"{sft} version {v} detected.")              
+    elif sft == "snpEff" and p.returncode == 0:
+        logger.info(f"{' '.join(p.stdout.split())} detected.") 
+    elif sft == "tb-profiler":
+        logger.warning(f"It seems that {sft} is not installed correctly.")
+        res = input("Would you like to install it now? (y/n): ")
+        if res.lower() == 'y':
+            _install_tbprofiler()
+        elif res.lower() == 'n':
+            logger.critical(f"{sft} is required - please run 'tbtamr setup' now to proceed.")
+            raise SystemExit
+    else:
+        logger.critical(f"{sft} is not installed.")
+        raise SystemExit
+
+def check_deps():
+
+    with open(f"{pathlib.Path(__file__).parent / 'dep_config.json'}", "r") as j:
+
+        software = json.load(j)
+        logger.info(f"Checking that dependencies are installed and recording version.")
+
+        for sft in software:
+            _run_check(_input =software[sft], sft = sft)
+
+        return True
+
+def _install_tbprofiler():
+
+    pp = _run_cmd(cmd="pip3 install git+https://github.com/MDU-PHL/pathogen-profiler")
+    if pp.returncode == 0:
+        logger.info(f"pathogen-profiler from https://github.com/MDU-PHL/ installed.")
+        tbp = _run_cmd(cmd = "pip3 install git+https://github.com/MDU-PHL/TBProfiler")
+        if tbp.returncode == 0:
+            logger.info(f"TB-profiler https://github.com/MDU-PHL/ installed. You should now be good to go.")
+
+def check():
+
+    check_deps()
+    return True
+
+def install():
+    _install_tbprofiler()

tbtamr/dep_config.json

@@ -0,0 +1,12 @@
+{
+    "tb-profiler": "tb-profiler version 2>&1",
+    "samtools": "samtools --version 2>&1",
+    "bwa":"bwa 2>&1",
+    "snpEff":"snpEff -version 2>&1",
+    "samclip":"samclip --version 2>&1",
+    "freebayes":"freebayes --version 2>&1",
+    "bcftools":"bcftools --version 2>&1",
+    "bedtools":"bedtools --version 2>&1",
+    "delly":"delly --version 2>&1"
+}
+

tbtamr/tbtamr.py

@@ -3,14 +3,20 @@
 from tbtamr.AmrSetup import AmrSetup
 from tbtamr.RunProfiler import RunProfiler
 from tbtamr.Collate import Inferrence, Parse, Mdu
-
+from tbtamr.TbTamr_Utils import check,install
 from tbtamr.version import __version__
 
 """
 tbtamr is designed to implement TB-profiler and parse the results compatible for MDU use. It may also be used for other purposes where the format of output is compatible
 
 """
 
+def install_deps(args):
+    install()
+
+def check_deps(args):
+    check()
+
 def collate_results(args):
 
     to_collate = Parse(args)
@@ -186,10 +192,14 @@ def set_parsers():
         default= 80
     )
 
+    parser_setup_deps = subparsers.add_parser('setup', help='Install tbtamr dependencies.', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser_check_deps = subparsers.add_parser('check', help='Check tbtamr dependencies.', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
 
     parser_sub_run.set_defaults(func=run_pipeline)
     parser_sub_collate.set_defaults(func = collate_results)
     parser_sub_mdu.set_defaults(func = mdu)
+    parser_setup_deps.set_defaults(func = install_deps)
+    parser_check_deps.set_defaults(func = check_deps)
     args = parser.parse_args(args=None if sys.argv[1:]  else ['--help'])
     return args