diff --git a/scripts/Makefile b/scripts/Makefile
deleted file mode 100644
index 4bdec5e..0000000
--- a/scripts/Makefile
+++ /dev/null
@@ -1,9 +0,0 @@
-all:
-
-
-run: install
-	python ../scpipe/r_pipeline.py
-
-install:
-	tar zcvf SCclust_0.1.7.tar.gz SCclust
-	Rscript -e 'install.packages("SCclust_0.1.7.tar.gz", repos = NULL, type="source")'
diff --git a/scripts/SCclust-1.0.0RC2.tar.gz b/scripts/SCclust-1.0.0RC2.tar.gz
deleted file mode 100644
index 7e1baf9..0000000
Binary files a/scripts/SCclust-1.0.0RC2.tar.gz and /dev/null differ
diff --git a/scripts/SCclust-1.0.0RC3.tar.gz b/scripts/SCclust-1.0.0RC3.tar.gz
deleted file mode 100644
index cb95309..0000000
Binary files a/scripts/SCclust-1.0.0RC3.tar.gz and /dev/null differ
diff --git a/scripts/conda-environment.yml b/scripts/conda-environment.yml
deleted file mode 100644
index d57fea9..0000000
--- a/scripts/conda-environment.yml
+++ /dev/null
@@ -1,221 +0,0 @@
-name: sgains3
-channels:
-- conda-forge
-- bioconda
-- r
-- defaults
-dependencies:
-- bcftools=1.5=3
-- bleach=1.4.2=py36_0
-- bowtie=1.2.1.1=py36pl5.22.0_0
-- htslib=1.5=0
-- perl-threaded=5.22.0=10
-- pysam=0.12.0.1=py36_htslib1.5_1
-- r-bh=1.60.0_2=r3.3.2_0
-- r-car=2.1_4=r3.3.2_0
-- r-catools=1.17.1=r3.3.2_1
-- r-data.table=1.10.4=r3.3.2_0
-- r-digest=0.6.12=r3.3.2_0
-- r-dplyr=0.5.0=r3.3.2_1
-- r-ggplot2=2.2.1=r3.3.2_0
-- r-htmlwidgets=0.5=r3.3.2_0
-- r-psych=1.5.8=r3.3.2_0
-- r-purrr=0.2.2=1
-- r-scales=0.4.1=r3.3.2_1
-- r-tibble=1.2=r3.3.2_1
-- r-yaml=2.1.13=r3.3.2_1
-- samtools=1.5=2
-- sra-tools=2.8.2=0
-- tbb=4.4_20150728=0
-- perl=5.22.0.1=0
-- biopython=1.69=np113py36_0
-- bzip2=1.0.6=h0376d23_1
-- ca-certificates=2017.08.26=h1d4fec5_0
-- cairo=1.14.8=0
-- certifi=2017.7.27.1=py36h8b7b77e_0
-- curl=7.54.1=0
-- decorator=4.1.2=py36hd076ac8_0
-- entrypoints=0.2.3=py36h1aec115_2
-- fontconfig=2.12.1=3
-- freetype=2.5.5=2
-- glib=2.50.2=1
-- gmp=6.1.2=hb3b607b_0
-- gsl=2.2.1=0
-- harfbuzz=0.9.39=2
-- html5lib=0.999999999=py36h2cfc398_0
-- icu=54.1=0
-- intel-openmp=2018.0.0=h15fc484_7
-- ipykernel=4.6.1=py36hbf841aa_0
-- ipython=6.1.0=py36hc72a948_1
-- ipython_genutils=0.2.0=py36hb52b0d5_0
-- jbig=2.1=hdba287a_0
-- jedi=0.10.2=py36h552def0_0
-- jinja2=2.9.6=py36h489bce4_1
-- jpeg=8d=2
-- jsonschema=2.6.0=py36h006f8b5_0
-- jupyter_client=5.1.0=py36h614e9ea_0
-- jupyter_core=4.3.0=py36h357a921_0
-- krb5=1.13.2=0
-- libedit=3.1=heed3624_0
-- libffi=3.2.1=h4deb6c0_3
-- libgcc=5.2.0=0
-- libgcc-ng=7.2.0=hcbc56d2_1
-- libgfortran-ng=7.2.0=h6fcbd8e_1
-- libiconv=1.14=0
-- libpng=1.6.30=1
-- libsodium=1.0.13=h31c71d8_2
-- libssh2=1.8.0=h8c220ad_2
-- libstdcxx-ng=7.2.0=h24385c6_1
-- libtiff=4.0.6=2
-- libxml2=2.9.4=0
-- markupsafe=1.0=py36hd9260cd_1
-- mistune=0.7.4=py36hbab8784_0
-- mkl=2018.0.0=hb491cac_4
-- nbconvert=5.3.1=py36hb41ffb7_0
-- nbformat=4.4.0=py36h31c9010_0
-- ncurses=6.0=h06874d7_1
-- notebook=5.0.0=py36h0b20546_2
-- numpy=1.13.1=py36h5bc529a_2
-- openssl=1.0.2l=h9d1a558_3
-- pandas=0.20.3=py36h842e28d_2
-- pandoc=1.19.2.1=hea2e7c5_1
-- pandocfilters=1.4.2=py36ha6701b7_1
-- pango=1.40.3=1
-- pcre=8.39=1
-- pexpect=4.2.1=py36h3b9d41b_0
-- pickleshare=0.7.4=py36h63277f8_0
-- pip=9.0.1=py36h30f8307_2
-- pixman=0.34.0=ha72d70b_1
-- prompt_toolkit=1.0.15=py36h17d85b1_0
-- ptyprocess=0.5.2=py36h69acd42_0
-- pygments=2.2.0=py36h0d3125c_0
-- python=3.6.2=0
-- python-dateutil=2.6.1=py36h88d3b88_1
-- pytz=2017.2=py36hc2ccc2a_1
-- pyzmq=16.0.2=py36_0
-- readline=6.2=2
-- setuptools=36.5.0=py36he42e2e1_0
-- simplegeneric=0.8.1=py36h2cb9092_0
-- six=1.10.0=py36hcac75e4_1
-- sqlite=3.13.0=0
-- terminado=0.6=py36ha25a19f_0
-- testpath=0.3.1=py36h8cadb63_0
-- tk=8.5.18=0
-- tornado=4.5.2=py36h1283b2a_0
-- traitlets=4.3.2=py36h674d592_0
-- wcwidth=0.1.7=py36hdf4376a_0
-- webencodings=0.5.1=py36h800622e_1
-- wheel=0.29.0=py36he7f4e38_1
-- xz=5.2.3=h2bcbf08_1
-- zeromq=4.1.5=0
-- zlib=1.2.8=3
-- r-assertthat=0.1=r3.3.2_4
-- r-backports=1.0.4=r3.3.2_0
-- r-base=3.3.2=0
-- r-base64enc=0.1_3=r3.3.2_0
-- r-bitops=1.0_6=r3.3.2_2
-- r-boot=1.3_18=r3.3.2_0
-- r-broom=0.4.1=r3.3.2_0
-- r-caret=6.0_73=r3.3.2_0
-- r-class=7.3_14=r3.3.2_0
-- r-cluster=2.0.5=r3.3.2_0
-- r-codetools=0.2_15=r3.3.2_0
-- r-colorspace=1.3_1=r3.3.2_0
-- r-crayon=1.3.2=r3.3.2_0
-- r-curl=2.3=r3.3.2_0
-- r-dbi=0.5_1=r3.3.2_0
-- r-dichromat=2.0_0=r3.3.2_2
-- r-essentials=1.5.2=r3.3.2_0
-- r-evaluate=0.10=r3.3.2_0
-- r-forcats=0.1.1=r3.3.2_0
-- r-foreach=1.4.3=r3.3.2_0
-- r-foreign=0.8_67=r3.3.2_0
-- r-formatr=1.4=r3.3.2_0
-- r-gistr=0.3.6=r3.3.2_0
-- r-glmnet=2.0_5=r3.3.2_0
-- r-gtable=0.2.0=r3.3.2_0
-- r-haven=1.0.0=r3.3.2_0
-- r-hexbin=1.27.1=r3.3.2_0
-- r-highr=0.6=r3.3.2_0
-- r-hms=0.3=r3.3.2_0
-- r-htmltools=0.3.5=r3.3.2_0
-- r-httpuv=1.3.3=r3.3.2_0
-- r-httr=1.2.1=r3.3.2_0
-- r-irdisplay=0.4.4=r3.3.2_0
-- r-irkernel=0.7.1=r3.3.2_0
-- r-iterators=1.0.8=r3.3.2_0
-- r-jsonlite=1.1=r3.3.2_0
-- r-kernsmooth=2.23_15=r3.3.2_0
-- r-knitr=1.15.1=r3.3.2_0
-- r-labeling=0.3=r3.3.2_2
-- r-lattice=0.20_34=r3.3.2_0
-- r-lazyeval=0.2.0=r3.3.2_0
-- r-lme4=1.1_12=r3.3.2_0
-- r-lubridate=1.6.0=r3.3.2_0
-- r-magrittr=1.5=r3.3.2_2
-- r-maps=3.1.1=r3.3.2_0
-- r-markdown=0.7.7=r3.3.2_2
-- r-mass=7.3_45=r3.3.2_0
-- r-matrix=1.2_7.1=r3.3.2_0
-- r-matrixmodels=0.4_1=r3.3.2_0
-- r-mgcv=1.8_16=r3.3.2_0
-- r-mime=0.5=r3.3.2_0
-- r-minqa=1.2.4=r3.3.2_2
-- r-mnormt=1.5_5=r3.3.2_0
-- r-modelmetrics=1.1.0=r3.3.2_0
-- r-modelr=0.1.0=r3.3.2_0
-- r-munsell=0.4.3=r3.3.2_0
-- r-nlme=3.1_128=r3.3.2_0
-- r-nloptr=1.0.4=r3.3.2_2
-- r-nnet=7.3_12=r3.3.2_0
-- r-openssl=0.9.5=r3.3.2_0
-- r-pbdzmq=0.2_4=r3.3.2_0
-- r-pbkrtest=0.4_6=r3.3.2_0
-- r-plyr=1.8.4=r3.3.2_0
-- r-pryr=0.1.2=r3.3.2_0
-- r-quantmod=0.4_7=r3.3.2_0
-- r-quantreg=5.29=r3.3.2_0
-- r-r6=2.2.0=r3.3.2_0
-- r-randomforest=4.6_12=r3.3.2_0
-- r-rbokeh=0.5.0=r3.3.2_0
-- r-rcolorbrewer=1.1_2=r3.3.2_3
-- r-rcpp=0.12.8=r3.3.2_0
-- r-rcppeigen=0.3.2.9.0=r3.3.2_0
-- r-readr=1.0.0=r3.3.2_0
-- r-readxl=0.1.1=r3.3.2_0
-- r-recommended=3.3.2=r3.3.2_0
-- r-repr=0.10=r3.3.2_0
-- r-reshape2=1.4.2=r3.3.2_0
-- r-rmarkdown=1.3=r3.3.2_0
-- r-rpart=4.1_10=r3.3.2_0
-- r-rprojroot=1.1=r3.3.2_0
-- r-rvest=0.3.2=r3.3.2_0
-- r-selectr=0.3_0=r3.3.2_0
-- r-shiny=0.14.2=r3.3.2_0
-- r-sourcetools=0.1.5=r3.3.2_0
-- r-sparsem=1.74=r3.3.2_0
-- r-spatial=7.3_11=r3.3.2_0
-- r-stringi=1.1.2=r3.3.2_0
-- r-stringr=1.1.0=r3.3.2_0
-- r-survival=2.40_1=r3.3.2_0
-- r-tidyr=0.6.0=r3.3.2_0
-- r-tidyverse=1.0.0=r3.3.2_0
-- r-ttr=0.23_1=r3.3.2_0
-- r-uuid=0.1_2=r3.3.2_0
-- r-xml2=1.0.0=r3.3.2_0
-- r-xtable=1.8_2=r3.3.2_0
-- r-xts=0.9_7=r3.3.2_2
-- r-zoo=1.7_13=r3.3.2_0
-- pip:
-  - ipython-genutils==0.2.0
-  - jupyter-client==5.1.0
-  - jupyter-core==4.3.0
-  - prompt-toolkit==1.0.15
-  - py==1.4.34
-  - pytest==3.2.2
-  - pytest-asyncio==0.8.0
-  - python-box==3.1.1
-  - pyyaml==3.12
-  - setproctitle==1.1.10
-  - termcolor==1.1.0
-
diff --git a/scripts/setup.R b/scripts/setup.R
deleted file mode 100644
index 0ae5efa..0000000
--- a/scripts/setup.R
+++ /dev/null
@@ -1,9 +0,0 @@
-library(devtools)
-
-
-source("https://bioconductor.org/biocLite.R")
-biocLite("DNAcopy")
-
-install.packages("futile.logger")
-
-install.packages("SCclust-1.0.0RC3.tar.gz", repos = NULL, type="source")
\ No newline at end of file
diff --git a/setup.py b/setup.py
index 9958027..4ac0149 100644
--- 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
index 66947b8..4a1bda3 100644
--- 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):
@@ -65,7 +69,7 @@ def run(self):
         rscript = os.path.abspath(
             os.path.join(
                 basedir,
-                '../../'
+                '../'
                 'scripts/pipeline.R'
             ))
         print(colored("executing Rscript with: {}".format(rscript), "yellow"))
@@ -73,7 +77,7 @@ def run(self):
         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 b/sgains/scripts/pipeline.R
similarity index 75%
rename from scripts/pipeline.R
rename to sgains/scripts/pipeline.R
index cfb71a2..e4e6cdc 100644
--- a/scripts/pipeline.R
+++ b/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,