Parsing prediction tool output

.circleci/config.yml

@@ -6,7 +6,7 @@ orbs:
 jobs:
   build-and-test:
     docker:
-      - image: circleci/python:3.7.5
+      - image: circleci/python:3.8.5
 
     working_directory: ~/phd_eastbio
 
@@ -23,7 +23,7 @@ jobs:
           command: |
             python3 -m venv venv
             . venv/bin/activate
-            pip install -r requirements.txt
+            pip3 install -r requirements.txt
 
       - save_cache:
           paths:
@@ -34,7 +34,7 @@ jobs:
           name: install package
           command: |
             . venv/bin/activate
-            pip install -e .
+            pip3 install -e .
 
       - run:
           name: run tests

README.md

@@ -44,28 +44,24 @@ Development plans are stored within the [Wiki](https://github.com/HobnobMancer/p
 
 ## Installation
 
-1. Navigate the directory you wish to store pyrewton in, then clone this repository.
-`git clone https://github.com/HobnobMancer/pyrewton.git`
+The easiest method is to use pip to install `pyrewton` and all requirements.
 
-1. Create a virtual environment with dependencies, then activate the environment.   
+1. Create a virtual environment with dependencies, then activate the environment - _where venv_name is an chosen name for the virtual environment_
 `conda create -n <venv_name> python=3.8 diamond hmmer prodigal -c conda-forge -c bioconda`   
 `conda activate <venv_name>`
 
-2. Install all requirements from requirements.txt file. The requirements.txt file is stored in the root of this repository.  
-`pip3 install -r <path to requirements.txt file>`   
+2. Clone the repository
+`git clone https://github.com/HobnobMancer/pyrewton.git`
 
-3. Install pyrewton.
+3. Install pyrewton
 `pip3 install -e <path to directory containing setup.py file>`   
 Do not forget to use the **-e** option when install using pip3, otherwise each time pyrewton is invoked a ModuleNotFound error will be raised. Pass the path to the **directory** containign the setup.py file not the path to the setup.py file; if you are currently in the root directory of the repoistory where the file is located, simply use '.' to indicate the current working directory.
 
-4. Install third party tools.   
-Pyrewton invokves 3 third party tools: dbCAN, CUPP and eCAMI.
-
-To install dbCAN follow the instructions within their [GitHub repository](https://github.com/linnabrown/run_dbcan), **BUT ignore** steps 1 and 2 of their installtion guide, becuase the necessary virtual environment was already created in the second step of this installation and it meets all requirements of dbCAN. Install dbCAN within **'pyrewton/cazymes/prediction/tools/dbcan'** directory within the repository, otherwise pyrewton will not be able to find the tool.  
-
-To install eCAMI follow the instructions within their [GitHub respository](https://github.com/yinlabniu/eCAMI). eCAMI must be installed within the directory pyrewton/cazymes/prediction/tools/ecami. Following the method from the eCAMI repository will write eCAMI to 'pyrewton/cazymes/prediction/tools/ecami/**eCAMI**', to avoid this perform the installation within 'pyrewton/cazymes/prediction/tools' and rename 'eCAMI' to 'ecami', thus install eCAMI in **'pyrewton/cazymes/prediction/tools/ecami'**.   
+4. Install the third party CAZyme prediction tools
+The easiest way to do this, and ensure they are installed into the correct directories is to use:  
+`python3 <path to pyrewton setup.py> cpt -p .`
 
-To install CUPP download the CUPP files from the [DTU Bioengineering server](https://www.bioengineering.dtu.dk/english/ResearchNy/Research-Sections/Section-for-Protein-Chemistry-and-Enzyme-Technology/Enzyme-Technology/CUPP), and store the files in **'pyrewton/cazymes/prediction/tools/cupp'**. It is not necessary to download all the files becuase the .tar and .tar.gz directories each contain all the files, therefore, download either the .tar _or_ .tar.gz directories and unpackage them or download all the files located within 'CUPP_v1.0.14'.
+For alternative methods of installation see the full documentation at [Read the Docs](https://phd-project-scripts.readthedocs.io/en/latest/).
 
 <p>&nbsp;</p>
 

installation.sh

@@ -0,0 +1,37 @@
+#!/bin/bash
+
+# :args $1: absolute path to pyrewton prediction/tools dir
+
+# Installing the CAZyme prediciton tools dbCAN, eCAMI and CUPP
+# Requirements for these tools are installed via requirements.txt
+
+cd $1
+
+# install dbCAN
+test -d dbcan || mkdir dbcan
+cd dbcan
+
+test -d db || mkdir db
+cd db \
+    && wget http://bcb.unl.edu/dbCAN2/download/CAZyDB.07312019.fa.nr && diamond makedb --in CAZyDB.07312019.fa.nr -d CAZy \
+    && wget http://bcb.unl.edu/dbCAN2/download/Databases/dbCAN-HMMdb-V8.txt && mv dbCAN-HMMdb-V8.txt dbCAN.txt && hmmpress dbCAN.txt \
+    && wget http://bcb.unl.edu/dbCAN2/download/Databases/tcdb.fa && diamond makedb --in tcdb.fa -d tcdb \
+    && wget http://bcb.unl.edu/dbCAN2/download/Databases/tf-1.hmm && hmmpress tf-1.hmm \
+    && wget http://bcb.unl.edu/dbCAN2/download/Databases/tf-2.hmm && hmmpress tf-2.hmm \
+    && wget http://bcb.unl.edu/dbCAN2/download/Databases/stp.hmm && hmmpress stp.hmm \
+    && cd ../ && wget http://bcb.unl.edu/dbCAN2/download/Samples/EscheriaColiK12MG1655.fna \
+    && wget http://bcb.unl.edu/dbCAN2/download/Samples/EscheriaColiK12MG1655.faa \
+    && wget http://bcb.unl.edu/dbCAN2/download/Samples/EscheriaColiK12MG1655.gff
+# To check the installtion of dbCAN has worked, navigate to the dbCAN directory and run:
+# run_dbcan.py EscheriaColiK12MG1655.fna prok --out_dir output_EscheriaColiK12MG1655
+
+# download eCAMI
+cd $1
+git clone https://github.com/zhanglabNKU/eCAMI.git ecami
+
+# download CUPP
+curl -o CUPP_v1.0.14.tar.gz "https://files.dtu.dk/fss/public/link/public/stream/read/CUPP_v1.0.14.tar.gz?linkToken=hLin6ni4p-SWuKfp&itemName=CUPP_program"
+tar -xzf CUPP_v1.0.14.tar.gz
+mv CUPP_v1.0.14 cupp
+# delete old file
+rm CUPP_v1.0.14.tar.gz