diff --git a/README.md b/README.md index 25487e8..65dfb77 100644 --- a/README.md +++ b/README.md @@ -8,21 +8,8 @@ CarveMe is a python-based tool for genome-scale metabolic model reconstruction. ### Documentation -For more details please check: http://carveme.readthedocs.io/ +For instructions on installation and usage please check: http://carveme.readthedocs.io/ -### Installation - -Can be easily installed using **pip**: -``` -pip install carveme -``` - -Additionally, you must install: - - diamond (conda install -c bioconda diamond) - - SCIP solver [optional] (conda install --c conda-forge pyscipopt) - - IBM CPLEX or Gurobi solver [recommended] (full version with academic license) - - ### Credits and License For citation purposes please refer to our paper: diff --git a/docs/installation.rst b/docs/installation.rst index 17f0324..a02b86c 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -10,21 +10,32 @@ CarveMe can be easily installed using the **pip** package manager: $ pip install carveme -Additionally, you must manually install these dependencies: +Additionally, you must manually install the diamond_ sequence aligner: -- diamond_ (conda install -c bioconda diamond) -- SCIP_ solver [optional] (conda install --c conda-forge pyscipopt) -- IBM CPLEX_ or Gurobi_ optimizer [recommended] (full version with academic license) +.. code-block:: console + + $ conda install -c bioconda diamond + + + +Solver +------ + +You also need an optimization solver. The recommended option is to install either IBM CPLEX_ or Gurobi_. +You need a full version with the respective academic license (demo version will not work). + +After installing CPLEX, **do not forget** to install the CPLEX python API. + +**Alternatively**, you can use the open source SCIP_ solver. This will be slower (expect at least 10 min per execution). + +.. code-block:: console + + $ conda install --c conda-forge pyscipopt .. _diamond: https://github.com/bbuchfink/diamond .. _SCIP: https://scipopt.org .. _CPLEX: https://www.ibm.com/analytics/cplex-optimizer .. _Gurobi: https://www.gurobi.com/downloads/gurobi-software - -Note that you will need to register with IBM to obtain an `academic license for CPLEX `_. - -**IMPORTANT:** After installing CPLEX, do not forget to install the CPLEX python API (see the CPLEX documentation_ for details). - .. _documentation: https://www.ibm.com/support/knowledgecenter/SSSA5P_12.7.1/ilog.odms.cplex.help/CPLEX/GettingStarted/topics/set_up/Python_setup.html Everything should be ready now! See the next section for instructions on how to start *carving*.