readme update

README.md

@@ -6,23 +6,27 @@ OTU clustering with SWARM on RAPIDRUN data encapsulated in SNAKEMAKE
 # Prerequisites
 
 
-python3
+* python3
 
-pandas
-biopython
+* snakemake
 
+* singularity
 
-snakemake
-
-singularity
+python3 dependencies
 
+```
 pip3 install pandas
-
-
 pip3 install biopython
+```
 
+python3 dependencies to run `snakemake`:
 
-
+```
+pip3 install datrie
+pip3 install ConfigArgParse
+pip3 install appdirs
+pip3 install gitdb2
+```
 
 # Configuration / input files
 
@@ -38,4 +42,91 @@ You have to set 2 files:
 CORES=32
 CONFIGFILE="../01_infos/config_test.yaml"
 bash main.sh $CORES $CONFIGFILE
-```
\ No newline at end of file
+```
+
+
+# Run from scratch
+
+
+## clone repositories
+
+```
+git clone git@gitlab.mbb.univ-montp2.fr:edna/snakemake_rapidrun_swarm.git
+cd snakemake_rapidrun_swarm
+```
+
+## write demultiplexing table
+
+From
+- `01_infos/config_test.yaml` 
+	* `fichiers:` `rapidrun`
+	* `fichiers:` `dat`
+
+:warning: the colon "marker" into `fichiers:` `rapidrun` must be the same name as marker's keys of `fichiers:` `dat` into `01_infos/config_test.yaml` 
+
+This will generate a file `01_infos/all_demultiplex.csv` with each line arguments for command.
+
+```
+snakemake --configfile 01_infos/config_test.yaml -s readwrite_rapidrun_demultiplexing.py
+```
+
+
+## merge fastq
+
+From
+- `01_infos/config_test.yaml` 
+	* `fichiers:` `rapidrun`
+
+Deduce the `{run}` fastq paired-end to merge
+
+:warning: guadeloupe have been removed by hand into 02_assembly/Snakefile !!!
+
+
+```
+cd 02_assembly
+snakemake --configfile $CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20
+cd ..
+```
+
+## demultiplexing
+
+From
+- `01_infos/config_test.yaml` 
+	* `fichiers:` `rapidrun`
+
+will generate demultiplexed .fasta and .qual files for each `{projet}`/`{marker}`/`{sample}` into `03_demultiplexing`
+
+
+```
+cd 03_demultiplexing
+snakemake --configfile $CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20
+cd ..
+```
+
+## cat qualities
+
+From
+- `01_infos/config_test.yaml` 
+	* `fichiers:` `rapidrun`
+
+Simply concatenate and format .qual files by `{projet}`/`{marker}`
+
+```
+cd 04_cat_quality
+snakemake --configfile $CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20
+cd ..
+```
+
+## clustering
+
+```
+cd 05_clustering
+snakemake --configfile $CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20
+cd ..
+
+```
+
+
+
+
+