added more install information

Author: bgoli

README.md

@@ -5,9 +5,9 @@ CBMPy Metadraft: a flexible and extensible, GUI-based genome-scale model reconst
 
 ### System dependencies
 
-MetaDraft requires working versions of Python, Perl, Java and NCBI Blast2. Once you have downloaded MetaDraft and it's Python dependencies, please run the *system test* script to that can be found in the MetaDraft directory:
+MetaDraft requires working versions of Python, Perl, Java and NCBI Blast2. Once you have downloaded MetaDraft and it's Python dependencies, please run the *system test* script to that can be found in the MetaDraft directory `python systemtest.py`.
 
-`python system-test.py`
+Typically the default Java runtime (JRE) installed on your system is all that is require, for Windows this can be obtained from [https://www.java.com/]. On Linux please use your favourite package manager, for example, when using Ubuntu/Debian based oeprating systems, try `sudo apt-get install default-jre`. 
 
 MetaDraft has been successfully tested using Windows 10, Ubuntu Linux 16.04/18.04, Python 2.7, Python 3.6, PyQt4 and PyQt5. MetaDraft is developed on Windows Anaconda Python 2.7 with PyQt5.
 
@@ -19,17 +19,22 @@ Clone the cbmpy-metadraft git repository:
 
 `git clone https://github.com/SystemsBioinformatics/cbmpy-metadraft.git`
 
-MetaDraft ships with a single model template, to install the current template set, based on the BiGG2 repository, activate the template submodule:
+MetaDraft ships with a single model template, to install the current template set, based on the BiGG2 repository, change into the MetaDraft directory and activate the template submodule:
 
+`cd cbmpy-metadraft`
 `git submodule update --init --remote -- modeldb/2018-1/`
 
-You have now downloaded the latest version of MetaDraft, next please install the required Python dependencies. How you do this will depend on whether you want to use Conda or PIP.
+You have now downloaded the latest version of MetaDraft, next please run the system test script `python systemtest.py` to check your installation and then proceed to install the required Python dependencies. How you do this will depend on whether you use Conda or PIP.
 
 ## Creating a custom Anaconda Python environment
 
-The following commands will create custom virtual environments with all the Python dependencies needed to run MetaDraft. Of course it is also possible to install the individual packages using "conda" or "pip" see the *requirements.txt* file for details of the required packages (see "pip" instructions below).
+The following commands will create custom virtual environments with all the Python dependencies needed to run MetaDraft. It is also possible to install the individual packages using "conda" or "pip" see the *requirements.txt* file for details of the required packages (see "pip" instructions below).
 
-### For a Python 2 (recommended)
+Adding the the core packages (minimal) to an existing CONDA environment:
+
+`conda install -c bgoli -c sbmlteam sip pyqt python-libsbml xlrd xlwt cbmpy biopython`
+
+### New Python 2 CONDA environment (recommended)
 
 Ubuntu (Linux-64)
 
@@ -43,7 +48,7 @@ Windows 10 (Win-64)
 conda activate metadraft2
 ./runwin.bat`
 
-### For Python 3
+### New Python 3 CONDA environment
 
 Windows 10 (Win-64)
 
@@ -59,9 +64,9 @@ Using PyPI it is only possible to use Python 3. You can either install the packa
 
 `pip install -r requirements.txt`
 
-or individually install the core packages:
+or individually install the core packages (minimal):
 
-`pip install ipython sip PyQt5 python-libsbml xlrd xlwt cbmpy biopython`
+`pip install sip PyQt5 python-libsbml xlrd xlwt cbmpy biopython`
 
 Brett G. Olivier (b.g.olivier@vu.nl)
 

libpython/biotools.py

@@ -867,7 +867,7 @@ def createSeqplusModelMetaIdx(fmod, oid, oclass, metadraft_lib_model):
      - *class* the model category e.g. 'vu'
      - *metadraft_lib_model* the target MetaDraft lib_model directory
 
-     'edb', 'vu', "d:\@virdrives\google\work\python\metadraft\lib_model"
+     'edb', 'vu', "<path>"
 
     """
 
@@ -920,7 +920,6 @@ def createCDSdb(list_of_files):
         output[gbkf] = []
         GBFile = open(gbkf, 'r')
         GBcds = Bio.SeqIO.InsdcIO.GenBankCdsFeatureIterator(GBFile)
-        cntr = 0
         for cds in GBcds:
             if cds.seq != None:
                 data = {'pid' : cds.id,

libpython/qtmetadraft.py

@@ -1907,15 +1907,6 @@ def deleteGeneFromTree(D, delid):
             G.setNotes('These {} reactions were included from the {} model using MetaDraft (https://github.com/SystemsBioinformatics/metadraft) ver. {}'.format(len(new_groups[o]['grpd']), o, metadraft_version))
             G.addMember([self._DAT_MODELS[o].getReaction(r_) for r_ in new_groups[o]['grpd']])
 
-        IDIOT = False
-        #for r_ in self.model.getReactionIds():
-            #if self.model.getGPRforReaction(r_) is None:
-                #print('-->', r_)
-                #IDIOT = True
-        if IDIOT:
-            self.model.serializeToDisk('debug_model.dat')
-            print('SERELEEZIFIED MODEL ...')
-
         return self.model
 
     @pyqtSlot()
@@ -3700,7 +3691,7 @@ def buildHtmlStringsGene(self, gene, genesrc):
                     assoc = assoc.replace(gene, '<strong>{}</strong>'.format(gene))
 
                 except AttributeError as why:
-                    o_.serializeToDisk(o_.getId())
+                    #o_.serializeToDisk(o_.getId())
                     print('ERROR: {} - {}'.format(gene, o_.getId()))
                     print(why)
                     assoc = '<span style="color: red;"><strong>{}</strong></span> '.format('UNKNOWN')