# =========================================================
#
# DEMO configuration file for
#
# GUMPP: General Unified Microbiome Profiling Pipeline 1p
#
# =========================================================
#
# GUMPP's web page:
# http://gumpp.fe.uni-lj.si
#
# GUMPP users' manual:
# http://gumpp.fe.uni-lj.si/gumpp_manual.pdf
#
# GUMPP Mothur-script writers' manual:
# http://gumpp.fe.uni-lj.si/script_manual.pdf





#####################################################
#
# Follow instructions below to run GUMPP demo
#
#####################################################

# 1. Make sure that Singularity 3.x is installed on your system.
#    To check its presence, open terminal window and
#    type:
#    singulartiy --version
#
#    In addition, Squash File System needs to be installed,
#    as well, which can be checked by entering command:
#    mksquashfs
#
#    These two pieces of software need to be installed
#    through a repository of the actual Linux distribution.
#    Other installation methods (like Conda) generally do
#    NOT work, since Singularity is tightly coupled with
#    the underlying operating system.


# 2. Create a new directory in the location under your
#    home directory, say, /home/john/gumpp_demo,
#    and download GUMPP singularity image into it:
#    https://vision.fe.uni-lj.si/~bostjanm/raid/gumpp/gumpp_1p.sif

# 3. Download input reads dataset MiSeq SOP from the Mothur's
#    website https://mothur.org/wiki/miseq_sop
#
#    The file in question is accessible by the link:
#    https://mothur.org/MiSeqDevelopmentData/StabilityNoMetaG.tar
#
#    Save the above file in the same directory as the
#    GUMPP's singularity image.
#    Extract its contents (for example by opening a
#    terminal window and executing:
#    cd /home/john/gumpp_demo
#    tar -xvf StabilityNoMetaG.tar
#    (replace /home/john/gumpp_demo with the actual directory).

# 4. Save this config file in the same directory.
#    Set the below parameter in_dir to the path
#    of the directory in question.

in_dir = /home/john/gumpp_demo

# 5. Optionally, select type of analysis by uncommenting
#    the appropriate line by deleting its leading hash "#".
#    Several analyses may be enabled simultaneously.
#
#analysis_asv=yes
#analysis_otu=yes
#analysis_gen=yes

# 6. start GUMPP in a terminal by entering the following
#    appropriately adopted command.
#
#    singularity run /home/john/gumpp_demo/gumpp_1p.sif /home/john/gumpp_demo/gump_demo_config.txt

# 7. The GUMPP workflow should start running, and eventually
#    deliver the results in a subdirectory of the above
#    specified directory. The progress of the analysis can
#    be monitored on the screen.





#####################################################
#
# The parameters below are specific to the MiSeq SOP
# dataset. If you modifying them in an inappropriate
# way, the workflow will be unable to complete the
# expected analysis.
#
#####################################################

# If you want to run the probing phase, where GUMPP
# gives suggestions for the values below,
# comment-out one or both parameters
# msp_screen_seq_start or msp_screen_seq_end,
# before running (or rerunning) GUMPP.

msp_screen_seq_start = 13862
msp_screen_seq_end = 23444

msp_sub_sample_size = 3000

msp_screen_seq_min_length = 245
msp_screen_seq_max_length = 255