updated readme and config files

README.md

@@ -18,7 +18,7 @@ We introduce MetaCLADE2, and improved profile-based domain annotation pipeline b
 # Software requirements
 
 + [HMMer-3](http://hmmer.org)
-+ [DAMA](http://www.lcqb.upmc.fr/DAMA)
++ [DAMA](http://www.lcqb.upmc.fr/DAMA) (needed only if the `-a`/`--arch` option is used)
 + [GNU parallel](https://www.gnu.org/software/parallel) (optional but strongly recommended)
 
 
@@ -34,6 +34,34 @@ export PATH=[MetaCLADE2_DIR]:${PATH}
 ```
 where `[MetaCLADE2_DIR]` is MetaCLADE2 installation directory.
 
+### MetaCLADE model library
+
+MetaCLADE2 is no more compatible with the Pfam27-based library built for MetaCLADE v1.
+An improved version of the model library (currently based on Pfam32) can be downloaded here: [metaclade\_pfam32.tar.gz](http://gitlab.lcqb.upmc.fr/vicedomini/metaclade2)
+
+The gzipped tar archive has to be extracted with the command `tar -xf metaclade_pfam32.tar.gz`.
+By default the `CCMs` and `HMMs` directories are expected to be found in the `data/models/` path relative to the main MetaCLADE directory.
+It is however possible to put MetaCLADE's model library in a custom location, and set the absolute paths of both the `CCMs` and `HMMs` directories
+with a user configuration file (see the section below).
+
+The `CCMsRed` correpond to a reduced version of the full `CCMs` library. It should provide faster run times, however with decreased annotation perfomances.
+To use such a library in place of the `CCMs` library, a user configuration file should be provided (see the section below).
+The `ccms_path` parameter has to be set with the absolute path of the `CCMsRed` directory.
+
+### User configuration file (optional)
+MetaCLADE2 optionnally accepts a configuration file that allows the user to set custom paths to the MetaCLADE2 model library, to HMMER-3, and Phyton3.
+The file could be provided with the option `--user-cfg`.
+Lines starting with a semicolon are not taken into account and are considered as comments. You **must** also provide absolute paths.
+```
+[metaclade]
+;ccms_path    = /absolute/path/to/models/CCMs
+;hmms_path    = /absolute/path/to/models/HMMs
+
+[programs]
+;hmmer_path  = "/absolute/path/to/hmmer-3/directory/"
+;python_path = "/absolute/path/to/python3/directory/"
+;dama_path   = "/aboslute/path/to/DAMA/directory/"
+```
 
 # MetaCLADE2 usage
 
@@ -89,20 +117,6 @@ It is finally possible to delete intermediate files (after a successful executio
 In case MetaCLADE2 does not terminate successfully, such files have to be manually deleted.
 
 
-#### Optional MetaCLADE2 configuration file
-MetaCLADE2 optionnally accepts a configuration file that allows the user to set custom paths to the MetaCLADE2 model library, to HMMER-3, and Phyton3.
-The file could be provided with the option `--user-cfg`.
-Lines starting with a semicolon are not taken into account and are considered as comments. You **must** also provide absolute paths.
-```
-[metaclade]
-;ccms_path    = /absolute/path/to/models/CCMs
-;hmms_path    = /absolute/path/to/models/HMMs
-
-[programs]
-;hmmer_path  = "/absolute/path/to/hmmer-3/bin"
-;python_path = "/absolute/path/to/python3/bin"
-```
-
 # MetaCLADE2 output architecture
 The domain architecture for the sequences provided in input is saved as a TSV file to `[WORKING_DIR]/[DATASET_NAME]/[DATASET_NAME].arch.tsv` (or to the path specified with the `-o|--output` argument.
 Each line represents a domain annotation and has the following fields/columns:

config/mclade.default.cfg

@@ -30,7 +30,7 @@ dama_arch    = %(scripts_path)s/dama_arch.py
 hmmsearch_exec = hmmsearch
 ;python_path    =
 python_exec    = python3
-dama_path      = /home/blachon/Documents/Tools/DAMA/Release/src
+;dama_path      = 
 dama_exec      = DAMA
 
 [run]

config/mclade.user.cfg

@@ -3,5 +3,6 @@
 ;hmms_path    = /absolute/path/to/models/HMMs
 
 [programs]
-;hmmer_path  = "/absolute/path/to/hmmer-3/bin"
-;python_path = "/absolute/path/to/python3/bin"
+;hmmer_path  = "/absolute/path/to/hmmer-3/dir"
+;python_path = "/absolute/path/to/python3/dir"
+;dama_path   = "/absolute/path/to/DAMA/dir"