repackage sgains

KrasnitzLab · Nov 6, 2018 · 55aac5d · 55aac5d
1 parent c6c53df
commit 55aac5d
Show file tree

Hide file tree

Showing 8 changed files with 31 additions and 258 deletions.
diff --git a/scripts/Makefile b/scripts/Makefile
diff --git a/scripts/SCclust-1.0.0RC2.tar.gz b/scripts/SCclust-1.0.0RC2.tar.gz
diff --git a/scripts/SCclust-1.0.0RC3.tar.gz b/scripts/SCclust-1.0.0RC3.tar.gz
diff --git a/scripts/conda-environment.yml b/scripts/conda-environment.yml
diff --git a/scripts/setup.R b/scripts/setup.R
diff --git a/setup.py b/setup.py
@@ -13,14 +13,22 @@
     long_description=long_description,
     long_description_content_type="text/markdown",
     url="https://github.com/KrasnitzLab/sgains",
-    packages=setuptools.find_packages(
-        # 'sgains',
-        exclude=[
-            'docs', 'tests', 
-            'commands.tests',
-            'pipeline.tests',
-        ]
-    ),
+    # packages=setuptools.find_packages(
+    #     # 'sgains',
+    #     exclude=[
+    #         'docs', 'tests', 
+    #         'commands.tests',
+    #         'pipeline.tests',
+    #     ]
+    # ),
+    packages=['sgains', 'sgains.commands', 'sgains.pipelines'],
+    package_dir={
+        'sgains': 'sgains',
+    },
+    package_data={
+        'sgains': ['scripts/*.R'],
+    },
+    include_package_data=True,
     entry_points={
         'console_scripts': [
             'sgains-tools=sgains.cli:main',

diff --git a/sgains/pipelines/r_pipeline.py b/sgains/pipelines/r_pipeline.py
@@ -3,11 +3,15 @@
 
 @author: lubo
 '''
-import subprocess
-from sgains.config import Config, NonEmptyWorkDirectory
 import os
-from termcolor import colored
+import sys
+
 import shutil
+import subprocess
+
+from termcolor import colored
+
+from sgains.config import Config, NonEmptyWorkDirectory
 
 
 class Rpipeline(object):
@@ -65,15 +69,15 @@ def run(self):
         rscript = os.path.abspath(
             os.path.join(
                 basedir,
-                '../../'
+                '../'
                 'scripts/pipeline.R'
             ))
         print(colored("executing Rscript with: {}".format(rscript), "yellow"))
 
         if not self.config.dry_run:
             with open(os.devnull, 'w') as shutup:
 
-                assert os.path.exists(rscript)
+                assert os.path.exists(rscript), rscript
                 subprocess.check_call(
                     [
                         'Rscript', rscript,
@@ -86,8 +90,8 @@ def run(self):
                         str(sharemin)
                     ],
                     shell=False,
-                    # stdout=sys.stdout, stderr=sys.stdout,
-                    stdout=shutup, stderr=shutup,
+                    stdout=sys.stdout, stderr=sys.stdout,
+                    # stdout=shutup, stderr=shutup,
                 )
 
 

diff --git a/scripts/pipeline.R → sgains/scripts/pipeline.R b/scripts/pipeline.R → sgains/scripts/pipeline.R
@@ -1,10 +1,10 @@
 library("SCclust")
-library("futile.logger")
+# library("futile.logger")
 
 options(echo=TRUE)
 
-flog.threshold(DEBUG)
-flog.info("running sgains scclust pipeline script")
+# flog.threshold(DEBUG)
+# flog.info("running sgains scclust pipeline script")
 
 args <- commandArgs(trailingOnly = TRUE)
 
@@ -23,7 +23,7 @@ nsim <- as.integer(args[7])
 sharemin <- as.double(args[8])
 
 
-flog.debug("varbin_dir:", varbin_dir)
+# flog.debug("varbin_dir:", varbin_dir)
 
 sgains_pipeline(
     scgv_dir, case_name,