SOFT : singlem
------
Site du soft: https://github.com/wwood/singlem
-------------

LICENSE:
--------

GPL3

See software documentation for more informations.

Location: /usr/local/bioinfo/src/singlem
---------

Load binaries and environment:
------------------------------

-> Version 0.13.0

module load system/singularity-3.5.3

WARNING:
========

This software is install through a Singularity container, not a Docker one.
The syntax of the command line is quite the same, but:
1) don't forget to load singularity module
2) transform the command "singlem SINGLEM_PARAMETERS" in your command line 
   by "singularity run BIND_OPTIONS CONTAINER_IMAGE_PATH SINGLEM_PARAMETERS"
where 
	- BIND_OPTIONS map local paths to paths inside the container: -B localA:insideA,localB:insideB,localC
	  if the inside path is not provided, it is considered to be equal to the local one
	  the Singularity -B option, is the equivalent of Docker -v option
	- CONTAINER_PATH : for version 0.13.0 "/usr/local/bioinfo/src/singlem/singlem_v0.13.0.simg"
	- SINGLEM_PARAMETERS : the singlem parameters you whould have put for a normal singlem call, but 
	  + with extended paths for all parameters which are files or folders
	  + with BIND_OPTIONS set for every path used above
	  
On the wenb site, the following command line is given as exemple:
singlem pipe --sequences my_sequences.fastq.gz --otu_table otu_table.csv --threads 24

with my_sequences.fastq.gz and otu_table.csv files present or generated in the current folder

The Docker equivalent command line provided on the web site too is hereunder:
docker run -v `pwd`:`pwd` wwood/singlem:v0.13.0 pipe --sequences `pwd`/my.fastq.gz --otu_table `pwd`/my.otu_table.csv --threads 14

The singularity command line will be:
singularity run -B $PWD /usr/local/bioinfo/src/singlem/singlem_v0.13.0.simg pipe --sequences $PWD/my.fastq.gz --otu_table $PWD/my.otu_table.csv --threads 14

In fact, the current working directory is allready mapped, thus the following command line is OK:
singularity run /usr/local/bioinfo/src/singlem/singlem_v0.13.0.simg pipe --sequences my.fastq.gz --otu_table my.otu_table.csv --threads 14

Be aware that output (stdout) of the singlem process through the container is strictly the same that the one obtained via the singlem binary,
but the error output (stderr), will contain some extra lines generated by singularity.

The call of singlem through the container behaves as a normal command:
- outputs can be redirected
- input/output cat be piped (here only output)

Example directory for use on cluster:
-------------------------------------

/usr/local/bioinfo/src/singlem/example_on_cluster/singlem.sh

If you use singlem on the Slurm cluster with threads option, don't forget to reserve CPUs too for your job ...


See software documentation and our FAQ (http://bioinfo.genotoul.fr/index.php/faq/) for more informations.