complete documentation for simulation

simulation/README.md

@@ -11,7 +11,7 @@ documentation, please refer to [CASISIM wiki](https://github.com/CAMI-challenge/
 
 CAMISIM contains a lot of dependencies and the list can be found [Here](https://github.com/CAMI-challenge/CAMISIM/wiki/User-manual#installation).
 
-However, we recommand the use of the docker image `cami/camisim:latest` or the singularity one (WIP).
+However, we recommand the use of the docker image `cami/camisim:latest` or the singularity one ([here](https://gitlab.pasteur.fr/metagenomics/singularity/tree/master/tools/camisim), only from docker for the moment).
 
 ## Run de novo metagenomes simulation
 
@@ -32,7 +32,21 @@ mkdir output
 docker run -it -v "/path/to/folder/example/:/input:rw" -v "/path/to/folder/output/:/output:rw" cami/camisim:latest metagenomesimulation.py /input/config.ini
 ```
 
-### With singularity
+### With singularity on TARS
+
+You can build the singularity image from the docker one. A recipe doing that is
+available [here](https://gitlab.pasteur.fr/metagenomics/singularity/tree/master/tools/camisim).
+
+You will probably need to mount also a tmp directory since the one by default from
+singularity seems to be too small for the tool.
+
+```bash
+module load singularity
+mkdir output tmp
+singularity run --bind /path/to/folder/example:/input,/path/to/folder/tmp:/tmp,/path/to/folder/output:/output /path/to/singularity.simg /input/config.ini
+```
+
+> **WARNING**: This process can require at least 12Gb of RAM
 
 ### Configuration file
 
@@ -42,6 +56,9 @@ You can here set the different parameters for your simulation. The customed file
 We will quickly go through the different part of this config file. You can find the
 complete description on the [Documentation](https://github.com/CAMI-challenge/CAMISIM/wiki/Configuration-File-Options).
 
+By default path can be kept by default. However, it is easier to use absolute path
+instead of relative one (by default) for singularity.
+
 #### Main
 
 ```ini
@@ -65,9 +82,9 @@ Since we do not need the data for a challenge, we can switch off the anonymous p
 
 ```ini
 [ReadSimulator]
-readsim=tools/art_illumina-2.3.6/art_illumina       # leave by default since we are in a container
-error_profiles=tools/art_illumina-2.3.6/profiles    # leave by default
-samtools=tools/samtools-1.3/samtools                # leave by default
+readsim=/usr/local/bin/tools/art_illumina-2.3.6/art_illumina       # leave by default since we are in a container
+error_profiles=/usr/local/bin/tools/art_illumina-2.3.6/profiles    # leave by default
+samtools=/usr/local/bin/tools/samtools-1.3/samtools                # leave by default
 profile=mbarc                                       # choose for ART: mi/hi/hi150/mbarc
 size=0.1                                            # size of a single sample in Gigabasepairs (Gbp)
 type=art                                            # simulation tool
@@ -84,7 +101,7 @@ that `mbarc` is recommended for bacterial communities.
 ```ini
 [CommunityDesign]
 #distribution_file_paths='out/abundance0.tsv', 'out/abundance1.tsv', 'out/abundance2.tsv', 'out/abundance3.tsv', 'out/abundance4.tsv', 'out/abundance5.tsv', 'out/abundance6.tsv', 'out/abundance7.tsv', 'out/abundance8.tsv', 'out/abundance9.tsv'
-ncbi_taxdump=tools/ncbi-taxonomy_20170222.tar.gz
+ncbi_taxdump=/usr/local/bin/tools/ncbi-taxonomy_20170222.tar.gz
 strain_simulation_template=scripts/StrainSimulationWrapper/sgEvolver/simulation_dir
 number_of_samples=10  # Number of samples to be created
 ```