@@ -70,7 +73,7 @@ where `[MetaCLADE2_DIR]` is MetaCLADE2 installation directory.
...
@@ -70,7 +73,7 @@ where `[MetaCLADE2_DIR]` is MetaCLADE2 installation directory.
-V, --version Print version
-V, --version Print version
SGE OPTIONS:
SGE OPTIONS:
--sge Run MetaCLADE jobs on a SGE HPC environment
--sge Run MetaCLADE2 jobs on a SGE HPC environment
--pe <name> Parallel environment to use (mandatory)
--pe <name> Parallel environment to use (mandatory)
--queue <name> Name of a specific queue where jobs are submitted
--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
--time-limit <hh:mm:ss> Time limit for submitted jobs formatted as hh:mm:ss
...
@@ -78,8 +81,13 @@ where `[MetaCLADE2_DIR]` is MetaCLADE2 installation directory.
...
@@ -78,8 +81,13 @@ where `[MetaCLADE2_DIR]` is MetaCLADE2 installation directory.
(e.g., use --time-limit 2:30:00 for setting a limit of 2h and 30m)
(e.g., use --time-limit 2:30:00 for setting a limit of 2h and 30m)
```
```
Scripts and computation results are stored in `[WORKING_DIR]/[DATASET_NAME]`. By default `[WORKING_DIR]` is the current directory (the one from which `metaclade2` command is run).
It is possible to change this path with the `-W|--work-dir` argument.
It is finally possible to delete intermediate files (after a successful execution) with
MetaCLADE2 optionnally accepts a configuration file that allows the user to set custom paths to the MetaCLADE model library.
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.
Lines starting with a semicolon are not taken into account and are considered as comments.
You **must** also provide absolute paths.
You **must** also provide absolute paths.
```
```
...
@@ -88,37 +96,9 @@ You **must** also provide absolute paths.
...
@@ -88,37 +96,9 @@ You **must** also provide absolute paths.
;hmms_path = /absolute/path/to/data/models/HMMs
;hmms_path = /absolute/path/to/data/models/HMMs
```
```
# MetaCLADE2 output architecture
# MetaCLADE jobs
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.
By default jobs are created in `[WORKING_DIR]/[DATASET_NAME]/jobs/`. By default `[WORKING_DIR]` is the current directory where the `metaclade2` command has been run.
Each line represents a domain annotation and has the following fields/columns:
Using the `--sge` parameter it is possible to automatically handle MetaCLADE2 pipeline in a SGE-based cluster (see [MetaCLADE2 usage](#metaclade2-usage) section).
Each (numbered) folder in this directory represents a step of the pipeline and contains several `*.sh` files (depending on the value provided with the `-j [NUMBER_OF_JOBS]` parameter):
```
[DATASET_NAME]_1.sh
[DATASET_NAME]_2.sh
...
[DATASET_NAME]_[NUMBER_OF_JOBS].sh
```
Jobs **must** be run in the following order:
```
[WORKING_DIR]/[DATASET_NAME]/jobs/1_search/
[WORKING_DIR]/[DATASET_NAME]/jobs/2_filter/
[WORKING_DIR]/[DATASET_NAME]/jobs/3_arch/
```
Each file in a given directory can be submitted independently to the HPC environment.
# MetaCLADE2 results
By default results are stored in the `[WORKING_DIR]/[DATASET_NAME]/results/` directory.
Each (numbered) folder in this directory contains the results after each step of the pipeline.
After running each step, the final annotation is saved in the file named
This will create at most two scrips (jobs) in each directory of the pipeline.
Alternatively, in a SGE-based cluster, the following command will run MetaCLADE2 submitting at most 2 jobs, each one using 4 CPUs, for each step of the pipeline:
Alternatively, if you are running MetaCLADE2 in a SGE cluster, the following script will run at most 2 jobs, each one using 2 CPUs, for each step of the pipeline:
