updated config files, readme, and version number

README.md

@@ -55,6 +55,7 @@ where `[MetaCLADE2_DIR]` is MetaCLADE2 installation directory.
     -D, --domain-file <path>  File that contains the Pfam accession numbers
                               of the domains to be considered (one per line)
     -W, --work-dir <path>     Working directory (default:current directory)
+    -U, --user-cfg <path>     User config file for overriding default MetaCLADE2 configuration
     --remove-temp             Remove temporary intermediate files, keeping only results and logs
 
   DAMA OPTIONS:
@@ -67,13 +68,14 @@ where `[MetaCLADE2_DIR]` is MetaCLADE2 installation directory.
                                   (default:50)
 
   OTHER OPTIONS:
-    -j, --jobs <num>     Number of jobs to be created (default:16)
-    -t, --threads <num>  Number of threads for each job (default:1)
+    -t, --threads <num>  Number of threads (default:4)
     -h, --help           Print this help message
     -V, --version        Print version
 
   SGE OPTIONS:
-    --sge                    Run MetaCLADE2 jobs on a SGE HPC environment
+    --sge                    Run MetaCLADE jobs on a SGE HPC environment
+    -j, --jobs <num>         Number of jobs to be created/submitted (default:1)
+                             Use -t|--threads to define the number of threads for each job
     --pe <name>              Parallel environment to use (mandatory)
     --queue <name>           Name of a specific queue where jobs are submitted
     --time-limit <hh:mm:ss>  Time limit for submitted jobs formatted as hh:mm:ss
@@ -87,14 +89,18 @@ 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 (available soon)
-MetaCLADE2 optionnally accepts a configuration file that allows the user to set custom paths to the MetaCLADE2 model library.
-Lines starting with a semicolon are not taken into account and are considered as comments. 
-You **must** also provide absolute paths.
+#### 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/data/models/CCMs
-;hmms_path    = /absolute/path/to/data/models/HMMs
+;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

config/mclade.default.cfg

@@ -4,7 +4,7 @@
 mclade_root =
 
 [metaclade]
-models_path      = /home/blachon/Documents/Tools/MetaCLADE_models/models
+models_path      = %(mclade_root)s/data/models
 ccms_path        = %(models_path)s/CCMs
 ccms_ext         = .hmm.gz
 hmms_path        = %(models_path)s/HMMs

config/mclade.user.cfg

 [metaclade]
-;models_path  = /absolute/path/to/models
 ;ccms_path    = /absolute/path/to/models/CCMs
 ;hmms_path    = /absolute/path/to/models/HMMs
-;domain_list  = /absolute/path/to/pfam32.domains
 
 [programs]
 ;hmmer_path  = "/absolute/path/to/hmmer-3/bin"

metaclade2-common

@@ -16,8 +16,8 @@
 
 # Common functions and definitions
 PV_NAME="MetaCLADE"
-PV_VERSION='2.0'
-PV_DATE='20200509'
+PV_VERSION='2.1'
+PV_DATE='20201108'
 
 function abspath() { echo "$(cd "$(dirname "$1")"; pwd -P)/$(basename "$1")"; }