Instructions are uploaded.

README.md

@@ -1,5 +1,36 @@
 # Installation
 
+These installation instructions are streamlined for Linux. The tool SHI7EN is installable on OSX/Windows with a few minor tweaks to this tutorial. This package requires anaconda, which is a system agnostic package and virtual environment manager. Follow the installation instructions for your system at <http://conda.pydata.org/miniconda.html>.
+
+Once anaconda is installed, create a new virtual environment with python3.
+
+```
+conda create -n shi7en python=3
+```
+
+Now activate the environment.
+
 ```
-pip install git+https://github.com/bhillmann/NINJA-shi7.git --upgrade --no-cache-dir
+# OSX, Linux
+source activate shi7en
 ```
+
+With the shogun environment activated, install the developmental SHI7EN toolchain.
+
+```
+# Put condas and pip setuptools in sync
+pip install -I --upgrade setuptools
+
+# If you want to use flash
+conda install -c bioconda flash
+
+# If you want to use trimmomatic
+conda install -c bioconda trimmomatic
+
+# Install shi7en
+pip install git+https://github.com/knights-lab/shi7en --upgrade --no-cache-dir
+```
+
+With the flags provided to pip, copying and pasting any of these commands will redo the installation if a failure happened.
+
+The final step of the procedure is to add the binary shi7en_trimmer to your path. That binary is available on the release page.

ninja_shi7/shi7en.py → shi7en/shi7en.py

@@ -14,7 +14,7 @@
 
 def make_arg_parser():
     parser = argparse.ArgumentParser(description='This is the commandline interface for NINJA-SHI7',
-                                     usage='python ninja_shi7.py -i <input> -o <output> -t_trim <threads>...')
+                                     usage='python shi7eb.py -i <input> -o <output> -t_trim <threads>...')
     parser.add_argument('--adaptor', help='Set the type of the adaptor (default: None)', choices=[None, 'Nextera', 'TruSeq3', 'TruSeq2'], default=None)
     parser.add_argument('-SE', help='Run in Single End mode (default: Disabled)', dest='single_end', action='store_true')
     # TODO: Download the adaptors from Trimmomatic
@@ -162,8 +162,8 @@ def trimmer(input_fastqs, output_path, trim_length, trim_qual, threads=1, shell=
     output_filenames = []
     for path_input_fastq in input_fastqs:
         path_output_fastq = os.path.join(output_path, format_basename(path_input_fastq) + '.fastq')
-        ninja_shi7_cmd = ['ninja_shi7_trimmer', path_input_fastq, path_output_fastq, trim_length, trim_qual, 'FLOOR', 5, 'ASS_QUALITY', 30]
-        logging.info(run_command(ninja_shi7_cmd, shell=shell))
+        shi7en_cmd = ['shi7en_trimmer', path_input_fastq, path_output_fastq, trim_length, trim_qual, 'FLOOR', 5, 'ASS_QUALITY', 30]
+        logging.info(run_command(shi7en_cmd, shell=shell))
         output_filenames.append(path_output_fastq)
     return output_filenames