running rake

[splaisan]

Dear
Working on a RHEL7 24cores
I installed all and the ext/app's do work
I edited opts.yaml (including creating .ooc
'rake' does not trigger anything!
what did I miss?
Thanks for help

drwxr-xr-x. 2 splaisan bits 4.0K Jun 12 11:09 data
drwxr-xr-x. 5 splaisan bits 65 Jun 12 10:46 ext
drwxr-xr-x. 8 splaisan bits 4.0K Jun 12 10:30 .git
-rw-r--r--. 1 splaisan bits 1.5K Jun 12 10:30 opts_example.yaml
-rw-r--r--. 1 splaisan bits 1.6K Jun 12 11:10 opts.yaml
-rw-r--r--. 1 splaisan bits 7.9K Jun 12 10:30 Rakefile
-rw-r--r--. 1 splaisan bits 6.0K Jun 12 10:30 README.md
drwxr-xr-x. 2 splaisan bits 4.0K Jun 12 10:30 scripts

splaisan@NUC-SRV-01:/opt/biotools/flo$ ll data/
total 2.3G
drwxr-xr-x. 2 splaisan bits 4.0K Jun 12 11:09 .
drwxr-xr-x. 6 splaisan bits 4.0K Jun 12 11:14 ..
-rw-r--r--. 1 splaisan bits 1.9M Jun 12 11:09 11.ooc
-rw-r--r--. 1 splaisan bits 1.1G Jun 12 11:05 CA0.2_contigs.fasta
-rw-r--r--. 1 splaisan bits 77M Jun 12 11:02 CA0.2_gene_models_noseq.gff3
-rw-r--r--. 1 splaisan bits 1.2G Jun 12 11:05 hybrid_CA0.2.fasta

splaisan@NUC-SRV-01:/opt/biotools/flo$ cat opts.yaml

# Location of binaries expected by flo.
#
# These will be added to PATH before the pipeline is run. The paths below
# are created by `scripts/install.sh`.Comment out or edit the paths based
# on how you installed UCSC-Kent toolkit, GNU Parallel and genometools.
:add_to_path:
  - 'ext/kent/bin'
  - 'ext/parallel-20150722/src'
  - 'ext/genometools-1.5.6/bin'

# Location of source and target assemblies.
#
# If migrating annotations from assembly A to assembly B, A is the source
# and B is the target. Source and target assemblies are specified as path
# to the corresponding FASTA files (must end in .fa).
:source_fa: 'data/CA0.2_contigs.fasta'
:target_fa: 'data/hybrid_CA0.2.fasta'

# Number of processes that will be used to parallelise flo. Ideally, this
# will be the number of CPU cores you have.
:processes: '24'

# Parameters to run BLAT with.
#
# In addition to the options specified here, -noHead option is set by flo.
# -noHead simply causes the output BLAT output files to not have a header.
# It doesn't impact accuracy of results.
#
# Empty string is equivalent to:
#
#   -t=dna -q=dna -tileSize=11 -stepSize=11 -oneOff=0 -minMatch=2
#   -minScore=30 -minIdentity=90 -maxGap=2 -maxIntron=75000
#
# The default string defined below is a suitable trade-off between running
# time and sensitivity.
#:blat_opts: '-fastMap -tileSize=12 -minIdentity=98'
:blat_opts: 'blat -noHead -fastMap -ooc=data/11.ooc -minScore=100 -minIdentity=98'

# Path to the GFF files containing annotations on the source assembly that
# will be lifted to the target assembly.
:lift:
  - 'data/CA0.2_gene_models_noseq.gff3'

[splaisan]

this is a submission error, can be deleted, sorry!