diff --git a/README.md b/README.md index 4fd91fc..44b709a 100644 --- a/README.md +++ b/README.md @@ -18,23 +18,19 @@ We use MKL implementation from Shogun's modular interface for Python. The Python ```MATLAB git clone https://github.molgen.mpg.de/snikumbh/comik cd comik -chmod +x mkl.py -export PATH=".:$PATH" +sh install.sh ``` ## Usage: -Example function call from inside Matlab: -For simulated dataset 1 provided in the folder `sample_data` +See the example config file `config-comik.txt`, for an example function call from inside Matlab: +For simulated dataset 1 provided in the folder `sample_data/simulated_dataset1` ```Matlab comik_wrapper('config-comik.txt'); ``` -See the example config file `config-comik.txt`. _CoMIK_ requires two FASTA files as input -- the first FASTA file containing sequences in the positive class; the second FASTA file containing the sequences in the negative class. Other params are explained below. -Further details: - -Values for the following parameters are required +Values for the following parameters are required to be set: - positive FASTA filename [type: str] - negative FASTA filename [type: str] @@ -43,7 +39,7 @@ Values for the following parameters are required - Indices of the test sequences [type: int, given as a Matlab vector] - output-folder-name [type: str] -The rest have default values, which are good starting points. +The rest have default values, which can be good starting points. Param name | type | default value | Additional comments -----------|-------|---------------|--------------------- diff --git a/export_paths.sh b/export_paths.sh deleted file mode 100644 index fdec56c..0000000 --- a/export_paths.sh +++ /dev/null @@ -1,3 +0,0 @@ -export PYTHONPATH="/home/snikumbh/working_folder/python/Python-2.7.13:/home/snikumbh/working_folder/codes/shogun-home/shogun-install/lib/python2.7/dist-packages:/home/snikumbh/.local/lib/python2.7/site-packages" -export PATH="/home/snikumbh/working_folder/python/Python-2.7.13:/home/snikumbh/.local/lib/python2.7/site-packages:/home/snikumbh/.local/bin:$PATH" -export LD_LIBRARY_PATH="{$LD_LIBRARY_PATH}:/home/snikumbh/working_folder/codes/shogun-home/shogun-install/lib:/home/snikumbh/working_folder/codes/shogun-home/shogun-install/lib/for_new_servers" diff --git a/install.sh b/install.sh new file mode 100644 index 0000000..6622bbb --- /dev/null +++ b/install.sh @@ -0,0 +1,5 @@ +#Install CoMIK + +chmod +x mkl.py +export PATH=".:$PATH" +