diff --git a/README.md b/README.md
index 51eb71c..95058c9 100644
--- a/README.md
+++ b/README.md
@@ -68,8 +68,8 @@ Probe filtering workflow:
   * [x] Add GTF file reading & saving as parquet/csv step
   * [x] Add EnsembleID support in entrez query
   * [x] Verify bowtie parameters run on endo and exo targets
-  * [ ] Allow selection of isoform in entrez query
-  * [ ] Select intron/exon based on blast from sequence
+  * [x] Select intron/exon based on blast from sequence - doesn't make sense given all different isoforms and variations
+  * [x] Allow selection of isoform in entrez query - not available / different transcript id's yield same sequence
 
 * **Interface**
   * [x] Clean up output files
diff --git a/efishent/__init__.py b/efishent/__init__.py
new file mode 100644
index 0000000..7a9c708
--- /dev/null
+++ b/efishent/__init__.py
@@ -0,0 +1,21 @@
+"""eFISHent"""
+
+__version__ = "0.0.1"
+
+import logging
+
+# Silence luigi-interface
+logging.getLogger("luigi-interface").setLevel(level=logging.CRITICAL)
+
+from . import alignment
+from . import basic_filtering
+from . import cleanup
+from . import cli
+from . import config
+from . import constants
+from . import generate_probes
+from . import kmers
+from . import optimization
+from . import prepare_sequence
+from . import secondary_structure
+from . import util
diff --git a/src/__main__.py b/efishent/__main__.py
similarity index 79%
rename from src/__main__.py
rename to efishent/__main__.py
index 28c968a..31fc276 100644
--- a/src/__main__.py
+++ b/efishent/__main__.py
@@ -1,6 +1,6 @@
 """Entrypoint module for the application."""
 
-from cli import main
+from .cli import main
 
 if __name__ == "__main__":
     main()
diff --git a/src/alignment.py b/efishent/alignment.py
similarity index 97%
rename from src/alignment.py
rename to efishent/alignment.py
index 9e0418a..e4f9d30 100644
--- a/src/alignment.py
+++ b/efishent/alignment.py
@@ -16,14 +16,14 @@
 import numpy as np
 import pandas as pd
 
-from config import GeneralConfig
-from config import ProbeConfig
-from config import SequenceConfig
-from basic_filtering import BasicFiltering
-from prepare_sequence import BuildBlastDatabase
-from prepare_sequence import PrepareSequence
-import constants
-import util
+from .config import GeneralConfig
+from .config import ProbeConfig
+from .config import SequenceConfig
+from .basic_filtering import BasicFiltering
+from .prepare_sequence import BuildBlastDatabase
+from .prepare_sequence import PrepareSequence
+from . import constants
+from . import util
 
 
 class BuildBowtieIndex(luigi.Task):
@@ -112,6 +112,17 @@ def output(self):
             )
         return tasks
 
+    @staticmethod
+    def read_count_table() -> pd.DataFrame:
+        """Read and verify a RNAseq FPRKM count table."""
+        df_counts = pd.read_csv(ProbeConfig().encode_count_table, sep="\t")
+        counts = df_counts[df_counts["gene_id"].str.contains("ENSG")].copy()
+        counts["clean_id"] = counts["gene_id"].apply(lambda x: x.split(".")[0])
+        return counts[constants.COUNTS_COLUMNS]
+
+    def read_gtf_file(self):
+        return pd.read_parquet(self.input()["gtf"].path)[constants.GTF_COLUMNS]
+
     def align_probes(self, fname_fasta: str, fname_sam: str) -> None:
         """Align probes to the reference genome."""
         # Convert fasta to fastq - bowtie doesn't return read names if not in fastq...
@@ -162,17 +173,6 @@ def filter_unique_probes(self, fname_sam: str) -> pd.DataFrame:
         )
         return df
 
-    @staticmethod
-    def read_count_table() -> pd.DataFrame:
-        """Read and verify a RNAseq FPRKM count table."""
-        df_counts = pd.read_csv(ProbeConfig().encode_count_table, sep="\t")
-        counts = df_counts[df_counts["gene_id"].str.contains("ENSG")].copy()
-        counts["clean_id"] = counts["gene_id"].apply(lambda x: x.split(".")[0])
-        return counts[constants.COUNTS_COLUMNS]
-
-    def read_gtf_file(self):
-        return pd.read_parquet(self.input()["gtf"].path)[constants.GTF_COLUMNS]
-
     def filter_gene_of_interest(self, df: pd.DataFrame) -> pd.DataFrame:
         """Filter FPKM table to exclude the gene of interest."""
         # Filter using provided EnsembleID directly
diff --git a/src/basic_filtering.py b/efishent/basic_filtering.py
similarity index 94%
rename from src/basic_filtering.py
rename to efishent/basic_filtering.py
index a165fc5..d9d9bbd 100644
--- a/src/basic_filtering.py
+++ b/efishent/basic_filtering.py
@@ -10,10 +10,10 @@
 import Bio.SeqUtils.MeltingTemp
 import luigi
 
-from config import GeneralConfig
-from config import ProbeConfig
-from generate_probes import GenerateAllProbes
-import util
+from .config import GeneralConfig
+from .config import ProbeConfig
+from .generate_probes import GenerateAllProbes
+from . import util
 
 
 def get_melting_temp(sequence: str) -> float:
diff --git a/src/cleanup.py b/efishent/cleanup.py
similarity index 88%
rename from src/cleanup.py
rename to efishent/cleanup.py
index 16ea48b..62d2db6 100644
--- a/src/cleanup.py
+++ b/efishent/cleanup.py
@@ -15,17 +15,17 @@
 import pandas as pd
 import Bio.SeqIO
 
-from alignment import AlignProbeCandidates
-from basic_filtering import get_gc_content
-from basic_filtering import get_melting_temp
-from config import ProbeConfig
-from config import RunConfig
-from config import SequenceConfig
-from kmers import BuildJellyfishIndex
-from kmers import get_max_kmer_count
-from optimization import OptimizeProbeCoverage
-from secondary_structure import get_free_energy
-import util
+from .alignment import AlignProbeCandidates
+from .basic_filtering import get_gc_content
+from .basic_filtering import get_melting_temp
+from .config import ProbeConfig
+from .config import RunConfig
+from .config import SequenceConfig
+from .kmers import BuildJellyfishIndex
+from .kmers import get_max_kmer_count
+from .optimization import OptimizeProbeCoverage
+from .secondary_structure import get_free_energy
+from . import util
 
 
 class CleanUpOutput(luigi.Task):
diff --git a/src/cli.py b/efishent/cli.py
similarity index 91%
rename from src/cli.py
rename to efishent/cli.py
index 52087a0..4110fed 100644
--- a/src/cli.py
+++ b/efishent/cli.py
@@ -2,18 +2,19 @@
 import configparser
 import logging
 import os
+import sys
 import tempfile
 
 import luigi
 
-from alignment import BuildBowtieIndex
-from cleanup import CleanUpOutput
-from config import GeneralConfig
-from config import ProbeConfig
-from config import RunConfig
-from config import SequenceConfig
-from kmers import BuildJellyfishIndex
-from util import UniCode
+from .alignment import BuildBowtieIndex
+from .cleanup import CleanUpOutput
+from .config import GeneralConfig
+from .config import ProbeConfig
+from .config import RunConfig
+from .config import SequenceConfig
+from .kmers import BuildJellyfishIndex
+from .util import UniCode
 
 CONFIG_CLASSES = [GeneralConfig, RunConfig, SequenceConfig, ProbeConfig]
 
@@ -110,6 +111,12 @@ def _parse_args() -> argparse.Namespace:
     )
     _add_groups(parser)
     _add_utilities(parser)
+    try:
+        if len(sys.argv) == 1:
+            parser.print_help()
+            parser.exit(0)
+    except Exception as e:
+        print(e)
     return parser.parse_args()
 
 
@@ -143,6 +150,7 @@ def set_logging_level(verbose: bool, debug: bool) -> logging.Logger:
         custom_level = logging.WARNING
 
     logging.getLogger("luigi").setLevel(luigi_level)
+    logging.getLogger("luigi-interface").setLevel(luigi_level)
     luigi.interface.core.log_level = luigi_level
 
     logger = logging.getLogger("custom-logger")
diff --git a/src/config.py b/efishent/config.py
similarity index 63%
rename from src/config.py
rename to efishent/config.py
index 1ae1cc3..3c02c5e 100644
--- a/src/config.py
+++ b/efishent/config.py
@@ -10,7 +10,6 @@
     - number of threads
     - method of optimization
     - optimization time limit
-    - verbosity
 
 Probe specific options:
     - (sequence file) or (gene name & organism)
@@ -30,19 +29,19 @@
 
 class GeneralConfig(luigi.Config):
     reference_genome = luigi.Parameter(
-        description="Path to reference genome fasta file.",
+        description="Path to reference genome fasta/fa file.",
         significant=True,
-        default=None,
+        default="",
     )
     reference_annotation = luigi.Parameter(
-        description="Path to reference genome annotation file.", default=None
+        description="Path to reference genome annotation (gene transfer format / gtf) file.",
+        default="",
     )
-    threads = luigi.IntParameter(description="Number of threads to use.", default=42)
-    verbosity = luigi.IntParameter(description="Verbosity level.", default=1)
+    threads = luigi.IntParameter(description="Number of threads to launch.", default=42)
     output_dir = luigi.Parameter(
         description="Path to output directory. "
         "If not specified, will use the current directory.",
-        default=None,
+        default="",
     )
 
 
@@ -54,7 +53,11 @@ class RunConfig(luigi.Config):
         description="Save intermediate files?", default=False
     )
     optimization_method = luigi.Parameter(
-        description="Optimization method to use [options: optimal, greedy].",
+        description="Optimization method to use. "
+        "Greedy will procedurally select the next longest probe. "
+        "Optimal will optimize probes for maximum gene coverage - "
+        "slow if many overlaps are present (typically with non-stringent parameter settings). "
+        "[options: optimal, greedy].",
         default="greedy",
     )
     optimization_time_limit = luigi.IntParameter(
@@ -66,22 +69,21 @@ class RunConfig(luigi.Config):
 
 class SequenceConfig(luigi.Config):
     sequence_file = luigi.Parameter(
-        description="Path to the gene's sequence file.", default=""
+        description="Path to the gene's sequence file. "
+        "Use this if the sequence can't be easily downloaded or if only certain regions should be targeted.",
+        default="",
     )
     ensemble_id = luigi.Parameter(
         description="Ensembl ID of the gene of interest."
         "Can be used instead of gene and organism name to download the gene of interest."
-        "Used to filter out the gene of interest from FPKM based filtering.",
+        "Used to filter out the gene of interest from FPKM based filtering - "
+        "will do an automated blast-based filtering if not passed.",
         default="",
     )
     gene_name = luigi.Parameter(description="Gene name.", default="")
     organism_name = luigi.Parameter(
         description="Latin name of the organism.", default=""
     )
-    is_intronic = luigi.BoolParameter(
-        description="Is the probe intronic?", default=False
-    )
-    is_exonic = luigi.BoolParameter(description="Is the probe exonic?", default=True)
     is_plus_strand = luigi.BoolParameter(
         description="Is the probe targeting the plus strand?", default=True
     )
@@ -91,19 +93,30 @@ class SequenceConfig(luigi.Config):
 
 
 class ProbeConfig(luigi.Config):
-    min_length = luigi.IntParameter(description="Minimum probe length.", default=21)
-    max_length = luigi.IntParameter(description="Maximum probe length.", default=25)
+    min_length = luigi.IntParameter(
+        description="Minimum probe length in nucleotides.", default=21
+    )
+    max_length = luigi.IntParameter(
+        description="Maximum probe length in nucleotides.", default=25
+    )
     spacing = luigi.IntParameter(
         description="Minimum distance in nucleotides between probes.", default=2
     )
     min_tm = luigi.FloatParameter(
-        description="Minimum melting temperature.", default=40.0
+        description="Minimum melting temperature in degrees C. "
+        "Formamide and Na concentration will affect melting temperature!",
+        default=40.0,
     )
     max_tm = luigi.FloatParameter(
-        description="Maximum melting temperature.", default=60.0
+        description="Maximum melting temperature in degrees C (see minimum).",
+        default=60.0,
+    )
+    min_gc = luigi.FloatParameter(
+        description="Minimum GC content in percentage.", default=20.0
+    )
+    max_gc = luigi.FloatParameter(
+        description="Maximum GC content in percentage.", default=80.0
     )
-    min_gc = luigi.FloatParameter(description="Minimum GC content.", default=20.0)
-    max_gc = luigi.FloatParameter(description="Maximum GC content.", default=80.0)
     formamide_concentration = luigi.FloatParameter(
         description="Formamide concentration as a percentage of the total buffer.",
         default=0.0,
@@ -111,14 +124,16 @@ class ProbeConfig(luigi.Config):
     na_concentration = luigi.FloatParameter(
         description="Na concentration in mM.", default=390.0
     )
-    kmer_length = luigi.IntParameter(
-        description="Length of k-mer used to filter probe sequences.", default=15
-    )
     max_off_targets = luigi.IntParameter(
-        description="Maximum number of off-targets.", default=0
+        description="Maximum number of off-targets binding anywhere BUT "
+        "the gene of interest in the genome.",
+        default=0,
     )
     encode_count_table = luigi.Parameter(
-        description="Path to the ENCODE RNAseq count table.", default=None
+        description="Path to the ENCODE RNAseq count table. "
+        "Must contain the columns 'gene_id' and 'FPKM'. "
+        "'gene_id' must use ensembl ID's!",
+        default="",
     )
     max_off_target_fpkm = luigi.FloatParameter(
         description=(
@@ -128,9 +143,14 @@ class ProbeConfig(luigi.Config):
         ),
         default=10.0,
     )
+    kmer_length = luigi.IntParameter(
+        description="Length of k-mer used to filter probe sequences.", default=15
+    )
     max_kmers = luigi.IntParameter(
         description="Highest count of sub-k-mers found in reference genome.", default=5
     )
     max_deltaG = luigi.FloatParameter(
-        description="Maximum deltaG in kcal/mol.", default=-10.0
+        description="Maximum predicted deltaG in kcal/mol. "
+        "Note: deltaGs range from 0 (no secondary structures) to increasingly negative values!",
+        default=-10.0,
     )
diff --git a/src/constants.py b/efishent/constants.py
similarity index 100%
rename from src/constants.py
rename to efishent/constants.py
diff --git a/src/generate_probes.py b/efishent/generate_probes.py
similarity index 92%
rename from src/generate_probes.py
rename to efishent/generate_probes.py
index f13334a..32176a7 100644
--- a/src/generate_probes.py
+++ b/efishent/generate_probes.py
@@ -12,9 +12,9 @@
 import Bio.SeqUtils.MeltingTemp
 import luigi
 
-from config import ProbeConfig
-from prepare_sequence import PrepareSequence
-import util
+from .config import ProbeConfig
+from .prepare_sequence import PrepareSequence
+from . import util
 
 
 class GenerateAllProbes(luigi.Task):
@@ -48,4 +48,3 @@ def run(self):
 
         util.log_and_check_candidates(self.logger, "GenerateAllProbes", len(candidates))
         Bio.SeqIO.write(candidates, self.output().path, "fasta")
-
diff --git a/src/kmers.py b/efishent/kmers.py
similarity index 96%
rename from src/kmers.py
rename to efishent/kmers.py
index 675bdab..f5b3763 100644
--- a/src/kmers.py
+++ b/efishent/kmers.py
@@ -12,10 +12,10 @@
 import Bio.SeqRecord
 import luigi
 
-from config import GeneralConfig
-from config import ProbeConfig
-from alignment import AlignProbeCandidates
-import util
+from .config import GeneralConfig
+from .config import ProbeConfig
+from .alignment import AlignProbeCandidates
+from . import util
 
 
 def get_max_kmer_count(sequence: Bio.SeqRecord, jellyfish_path: str) -> int:
diff --git a/src/luigi.cfg b/efishent/luigi.cfg
similarity index 98%
rename from src/luigi.cfg
rename to efishent/luigi.cfg
index 790c938..b817e48 100644
--- a/src/luigi.cfg
+++ b/efishent/luigi.cfg
@@ -2,7 +2,6 @@
 reference_genome: ../dm6/dm6.fa
 reference_annotation:
 threads: 42
-verbosity: 1
 output_dir:
 
 [RunConfig]
diff --git a/src/optimization.py b/efishent/optimization.py
similarity index 97%
rename from src/optimization.py
rename to efishent/optimization.py
index 42a4590..f96e6c3 100644
--- a/src/optimization.py
+++ b/efishent/optimization.py
@@ -15,10 +15,10 @@
 import pandas as pd
 import pyomo.environ as pe
 
-from config import GeneralConfig, ProbeConfig
-from config import RunConfig
-from secondary_structure import SecondaryStructureFiltering
-import util
+from .config import GeneralConfig, ProbeConfig
+from .config import RunConfig
+from .secondary_structure import SecondaryStructureFiltering
+from . import util
 
 
 class OptimizeProbeCoverage(luigi.Task):
diff --git a/src/prepare_sequence.py b/efishent/prepare_sequence.py
similarity index 85%
rename from src/prepare_sequence.py
rename to efishent/prepare_sequence.py
index 72e6fe1..c0955dd 100644
--- a/src/prepare_sequence.py
+++ b/efishent/prepare_sequence.py
@@ -10,9 +10,9 @@
 import Bio.SeqIO
 import luigi
 
-from config import GeneralConfig
-from config import SequenceConfig
-import util
+from .config import GeneralConfig
+from .config import SequenceConfig
+from . import util
 
 
 class DownloadEntrezGeneSequence(luigi.Task):
@@ -66,6 +66,8 @@ def run(self):
 
 
 class BuildBlastDatabase(luigi.Task):
+    """Build local nucleotide blast database."""
+
     def output(self):
         return [
             luigi.LocalTarget(f"{util.get_genome_name()}.{extension}")
@@ -94,26 +96,14 @@ class PrepareSequence(luigi.Task):
 
     def requires(self):
         tasks = {}
-        if SequenceConfig().sequence_file == "None":
+        if not SequenceConfig().sequence_file:
             tasks["entrez"] = DownloadEntrezGeneSequence()
-        if SequenceConfig().is_exonic or SequenceConfig().is_intronic:
-            tasks["blast"] = BuildBlastDatabase()
         return tasks
 
     def output(self):
         fname = f"{util.get_gene_name()}_sequence.fasta"
         return luigi.LocalTarget(os.path.join(util.get_output_dir(), fname))
 
-    def select_gene_region(
-        self, sequence: Bio.SeqRecord.SeqRecord
-    ) -> Bio.SeqRecord.SeqRecord:
-        """Select exon/intronic regions."""
-        # TODO select exon/intron/both
-        # Create blast database
-        # Blast sequence against database
-        # Parse blast output
-        # Select regions based on genome annotation
-
     def run(self):
         input_file = (
             self.input()["entrez"].path
@@ -138,6 +128,4 @@ def run(self):
             sequence = sequence.reverse_complement(id=True, description=True)
             self.logger.debug("Converted sequence to reverse complement.")
 
-        # sequence = self.select_gene_region(sequence)
-
         Bio.SeqIO.write(sequence, self.output().path, format="fasta")
diff --git a/src/secondary_structure.py b/efishent/secondary_structure.py
similarity index 94%
rename from src/secondary_structure.py
rename to efishent/secondary_structure.py
index 54e8718..61fbe9b 100644
--- a/src/secondary_structure.py
+++ b/efishent/secondary_structure.py
@@ -13,10 +13,10 @@
 import Bio.SeqRecord
 import luigi
 
-from config import GeneralConfig
-from config import ProbeConfig
-from kmers import KMerFiltering
-import util
+from .config import GeneralConfig
+from .config import ProbeConfig
+from .kmers import KMerFiltering
+from . import util
 
 
 def get_free_energy(sequence: Bio.SeqRecord) -> float:
diff --git a/src/util.py b/efishent/util.py
similarity index 98%
rename from src/util.py
rename to efishent/util.py
index 16f1200..43d3281 100644
--- a/src/util.py
+++ b/efishent/util.py
@@ -1,4 +1,3 @@
-import copy
 import hashlib
 import logging
 import os
@@ -8,8 +7,8 @@
 import luigi
 import pandas as pd
 
-from config import GeneralConfig
-from config import SequenceConfig
+from .config import GeneralConfig
+from .config import SequenceConfig
 
 
 FASTA_EXT = (".fasta", ".fna", ".ffn", ".faa", ".frn", ".fa")
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..0673b42
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,61 @@
+"""Setup file for pypi package called efishent."""
+
+# TODO write makefile for basic deployment using
+# python setup.py sdist
+# twine upload dist/latest-version.tar.gz
+
+import textwrap
+from setuptools import find_packages
+from setuptools import setup
+
+setup(
+    # Description
+    name="efishent",
+    version="0.0.1",
+    license="MIT",
+    description="RNA FISH oligos/probes design tool.",
+    long_description_content_type="text/plain",
+    long_description=textwrap.dedent("""TDB."""),
+    # Installation
+    python_requires=">3.9",
+    packages=find_packages(),
+    include_package_data=True,
+    zip_safe=False,
+    install_requires=[
+        "matplotlib",
+        "numpy",
+        "pandas",
+        "luigi",
+        "gtfparse",
+        "biopython",
+        "tqdm",
+        "pyomo",
+    ],
+    entry_points={"console_scripts": ["efishent = efishent.cli:main"]},
+    # Metadata
+    author="Bastian Eichenberger",
+    author_email="bastian@eichenbergers.ch",
+    url="https://github.com/bbquercus/efishent/",
+    project_urls={
+        "Documentation": "https://github.com/BBQuercus/efishent/wiki",
+        "Changelog": "https://github.com/BBQuercus/efishent/releases",
+        "Issue Tracker": "https://github.com/bbquercus/efishent/issues",
+    },
+    keywords=["biomedical", "bioinformatics", "RNA probe design"],
+    classifiers=[
+        # complete classifier list: http://pypi.python.org/pypi?%3Aaction=list_classifiers
+        "Development Status :: 3 - Alpha",
+        "Environment :: Console",
+        "Intended Audience :: Developers",
+        "Intended Audience :: Science/Research",
+        "License :: OSI Approved :: MIT License",
+        "Operating System :: MacOS",
+        "Operating System :: Microsoft :: Windows",
+        "Operating System :: POSIX",
+        "Operating System :: Unix",
+        "Programming Language :: Python :: 3 :: Only",
+        "Programming Language :: Python",
+        "Topic :: Scientific/Engineering :: Bio-Informatics",
+        "Topic :: Utilities",
+    ],
+)
diff --git a/src/__init__.py b/src/__init__.py
deleted file mode 100644
index e69de29..0000000