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#
# MetaBakery: Customized BioBakery wmgx workflow
#             http://metabakery.fe.uni-lj.si
#
# Quick start guide; details are given in the users' manual
#                    and in the config template:
#
# http://metabakery.fe.uni-lj.si/metabakery_manual.pdf
# http://metabakery.fe.uni-lj.si/config_template.txt
#
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PREREQUISITES (need to be dealt with only once)

1. Singularity container and squashfs file system
   need to be installed on a computer to run MetaBakery

   Installation through a repository of the actual
   Linux distribution is recommended; other installation
   methods (like Conda) generally do NOT work, since
   Singularity is tightly coupled with the underlying
   operating system. Recently, Ubuntu Linux does not
   provide Singularity through its own repository,
   but installation is still possible (please , see
   the MetaBakery users' manual).


2. Download MetaBakery's edition of your choice:
    edition 4, size 72 GB: https://vision.fe.uni-lj.si/~bostjanm/raid/mbakery/mbakery_2b_edit4.sif
    edition 3, size 67 GB: https://vision.fe.uni-lj.si/~bostjanm/raid/mbakery/mbakery_2b_edit3.sif
    edition 2, size 30 GB: https://vision.fe.uni-lj.si/~bostjanm/raid/mbakery/mbakery_2b_edit2.sif

   ------------------------------------------------------------------------
   NOTE: if large files make downloading difficult, please take a look at:
         http://metabakery.fe.uni-lj.si/download_smaller_pieces.txt
   ------------------------------------------------------------------------


SPECIFIC TO AN ACTUAL ANALYSIS

3. Collect an arbitrary number of paired (R1 & R2)
   and/or unpaired (R1) fastq reads into a subdirectory
   of your choice under your home directory.

   PLEASE NOTE: input files must be stored under your home directory
                in order to be accessible by MetaBakery.
                Other possibilities exist, but they depend on the
                actual configuration of the Singularity system.

   Instead of your own input files, the following files
   are also suitable for the task:

   https://vision.fe.uni-lj.si/~bostjanm/raid/mbakery/mbakery_test_A_R1.fq.gz
   https://vision.fe.uni-lj.si/~bostjanm/raid/mbakery/mbakery_test_A_R2.fq.gz

   https://vision.fe.uni-lj.si/~bostjanm/raid/mbakery/mbakery_test_B_R1.fq.gz
   https://vision.fe.uni-lj.si/~bostjanm/raid/mbakery/mbakery_test_B_R2.fq.gz

   https://vision.fe.uni-lj.si/~bostjanm/raid/mbakery/mbakery_test_C_R1.fq.gz
   https://vision.fe.uni-lj.si/~bostjanm/raid/mbakery/mbakery_test_C_R2.fq.gz

   https://vision.fe.uni-lj.si/~bostjanm/raid/mbakery/mbakery_test_D_R1.fq.gz
   https://vision.fe.uni-lj.si/~bostjanm/raid/mbakery/mbakery_test_D_R2.fq.gz

   https://vision.fe.uni-lj.si/~bostjanm/raid/mbakery/mbakery_test_E_R1.fq.gz
   https://vision.fe.uni-lj.si/~bostjanm/raid/mbakery/mbakery_test_E_R2.fq.gz

   https://vision.fe.uni-lj.si/~bostjanm/raid/mbakery/mbakery_test_F_R1.fq.gz
   https://vision.fe.uni-lj.si/~bostjanm/raid/mbakery/mbakery_test_F_R2.fq.gz

   https://vision.fe.uni-lj.si/~bostjanm/raid/mbakery/mbakery_test_G_R1.fq.gz
   https://vision.fe.uni-lj.si/~bostjanm/raid/mbakery/mbakery_test_G_R2.fq.gz

   https://vision.fe.uni-lj.si/~bostjanm/raid/mbakery/mbakery_test_H_R1.fq.gz
   https://vision.fe.uni-lj.si/~bostjanm/raid/mbakery/mbakery_test_H_R2.fq.gz

   Procesing of these inputs takes a while (see below).
   It is possible to get the first impression about
   MetaBakery by analyzing only a subset of the above
   inputs. In fact, any single fastq pair suffices.
   However, with reduced input set some processing steps
   (Strainphlan, MelonnPan and Mothur calculators)
   may not deliver results. Nonetheless, the overall
   working of MetaBakery can still be demonstrated.

   NOTE: with this dataset the following warning may
         result (depending on MetaBakery edition)
         due to an insufficient viral content
         of the set. This is not na error.

         Failed Mothur summary.single for k__Viruses ...


4. Start MetaBakery in a terminal by entering
   the following appropriately adopted command.

   singularity run /abs/path/mbakery_2b_[edition].sif /home/your_login/path_to/directory_with_fastq


5. MetaBakery should start processing and eventually deliver
   results in a subdirectory of a directory with input fastq files.

   Execution time for the entire above fastq dataset is about
   three to four hours on a computer with 64 CPUs and prolong
   on a less powerful hardware (but execution times do not drop
   linearly with the number of processors, since some steps
   are poorly parallelized).

   Execution time may be shortened by reducing
   the input set as hinted above in section 3.

   Also, it is much more pleasant to see your own fastq
   inputs in action instead of the demo ones. Please note
   that a rich enough inputs are needed to obtain results
   from Strainphlan, MelonnPan and Mothur calculators.