#############################################################
#
# GUMPP: General Unified Microbiome Profiling Pipeline
#        http://gumpp.fe.uni-lj.si
#
# Quick start; details are given in config template
#              and in the users' manual
#
# http://gumpp.fe.uni-lj.si/config_template.txt
# http://gumpp.fe.uni-lj.si/gumpp_manual.pdf
#
#############################################################

# PREREQUISITES (need to be dealt with only once)

# 1. singularity container and squashfs file system
#    need to be installed on a computer to run GUMPP
#
#    installation through a repository of the actual
#    Linux distribution is necessary; other installation
#    methods (like Conda) generally do NOT work, since
#    Singularity is tightly coupled with the underlying
#    operating system


# 2. download GUMPP's image from
#    https://vision.fe.uni-lj.si/~bostjanm/raid/gumpp/gumpp_1p.sif
#    and save it into a directory of your choice


# SPECIFIC TO AN ACTUAL ANALYSIS

# 3. collect an arbitrary number of paired (R1 & R2)
#    fastq reads into a subdirectory of your choice
#    under your home directory (so that it is surely
#    accessible within the singularity container)

# 4. open your favorite plain text editor and prepare
#    a config file with a single line of text,
#    like the following one (remove trailing #):
#
#    in_dir = /home/your_login/directory_with_reads

# 5. save the file anywhere under your home directory,
#    say, /home/your_login/any_path/gumpp_config.txt

# 6. start GUMPP in a terminal by entering appropriately
#    adopted the following command.
#
#    singularity run /abs/path/gumpp_1p.sif /home/your_login/any_path/gumpp_config.txt

# 7. GUMPP will do an initial probing of your reads, and
#    deliver an on-screen report to aid you in further
#    setting of mandatory parameters for the actual analysis.

# 8. with your text editor augment the previous config
#    file with four parameters, according to GUMPP's
#    suggestions. Config file should look like this:
#
#    in_dir = /home/your_login/path_to_reads   (remains as before)
#    msp_screen_seq_start =      ...some suggested number
#    msp_screen_seq_end =        ...another suggested number
#    msp_screen_seq_min_length = ...yet anoter suggested number
#    msp_screen_seq_max_length = ...again another suggested number

# 9. Re-run GUMPP with the same command line as above.
#    This time the actual analysis will be completed.
#    If you know the above parameters in advance, then there
#    is no need for the probing run, and the above parameters
#    may be set in the config file for the first run.