better comments in config

database/README.md

@@ -11,11 +11,11 @@ The important files:
 
 To produce your database:
 
-1. `git clone https://github.com/Bobay-Ochman/ConSpeciFix.git`
+1. Download the latest stable release from [our github](https://github.com/Bobay-Ochman/ConSpeciFix/releases).
 2. update the `genomes_proks.txt` with the newest list from [NCBI](https://www.ncbi.nlm.nih.gov/genome/browse#!/prokaryotes/)
 3. Edit path variables in `ConSpeciFix/database/config`
 4. `cd ConSpeciFix/database`
-5. `python species.py`
+5. Run `python species.py` to produce the list of all possible species to build into the database.
 6. Remove any unwanted species from `species.txt`
 7. `python runner.py`
 
@@ -83,4 +83,8 @@ The following scripts allow the Exclusion Criterion to run in order to identify
 - `kmeans.py` creates the Rscript that identfies two modes in the distribution with a kmeans test and produces graphs of the distribution file, as well as `vector.txt` and `key.txt`.
 - `split_kmeans.py` analyses the results of kmeans.py and produces `kmeans.txt`
 - `kmeansGraph.py` generates Rscript that graphs the result of `kmeans.txt` and identifies outliers, outputing `kmeans.pdf` and `for_removal.txt`
-- `criterion.py` writes the final results into `criterion.txt`
+- `criterion.py` writes the final results into `criterion.txt`
+
+### Additional Scripts
+
+Some additional scripts for mass database editing are included in `database/auxScripts`. These scripts are not a part of the pipeline, but can be used to aid in analysis, progress reporting, aggregating results, or cleaning up the data produced. Code in this section is provided as-is, and is not intended to be stable or complete.

database/config.py

@@ -35,8 +35,8 @@
 # RAXML where the binaries themselves are optomized for multithreading
 MAX_THREADS = multiprocessing.cpu_count()
 
-#Used to ignore species that would take computationally very long times
-MAX_SPECIES_SIZE = 1000000000
+# Used to ignore species that would take computationally very long times
+MAX_SPECIES_SIZE = 500
 
 
 ############### Things users will not need to change ###############

personalCompare/README.md

@@ -10,9 +10,9 @@ The important files:
 
 To run your folder comparison:
 
-1. `git clone https://github.com/Bobay-Ochman/ConSpeciFix.git`
-2. Edit path variables in `ConSpeciFix/personalCompare/config`
-3. `cd ConSpeciFix/personalCompare`
+1. Download the latest stable release from [our github](https://github.com/Bobay-Ochman/ConSpeciFix/releases).
+2. Edit path variables in `ConSpeciFix-#.#.#/personalCompare/config`
+3. `cd ConSpeciFix-#.#.#/personalCompare`
 4. `python runner.py`
 
 ## The Hard Way

personalCompare/config.py

@@ -8,13 +8,11 @@
 ############### VARIABLES USERS WILL NEED TO CHANGE ###############
 
 
-#Path to output should be followed by a tailing slash
-#This is where the full database will be built,
-# and if all the species are being processed,
-# this can be upwards of 500GB
-PATH_TO_FOLDER = '/stor/home/be4833/testSpec/genes'
+# This is where your folder of strains should be located
+# Path should be followed by a tailing slash
+PATH_TO_FOLDER = '/user/documents/myCoolProject/myGenomes/'
 
-#your local instalations for the following programs,
+# Your local instalations for the following programs,
 # or simply the name of the program if it can be accessed from the command line
 # for example
 # RAXML_PATH = '/Users/Admin/programs/standard-RAxML-master/raxmlHPC-SSE3'
@@ -26,9 +24,9 @@
 
 # command line character to pipe output to a file.
 # On most shells, use ' &> '.
-PIPE_CHAR = ' > '
+PIPE_CHAR = ' &> '
 # if the & is interpreted as launching a new subprocess instead of the pipe,
-# a simple ' > ' will work instead.
+# a simple ' > ' will work as well, though STD.ERR will still be printed.
 
 
 ############### VARIABLES USERS MIGHT NEED TO CHANGE ###############