Error after loading up bebatut MetaPhlAn2 to our local Galaxy instance

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Error after loading up bebatut MetaPhlAn2 to our local Galaxy instance

Dooley, Damion
After loading up MetaPhlAn2 (8991e05c44e4) from toolshed and attaching
db_v20, I tried running a few fasta files on it, including the tool's
test-data/input_sequences.fasta file, but after about a minute of churning
I keep getting this error:

Fatal error: Exit code 1 ()

Traceback (most recent call last):
  File
"/usr/local/galaxy/shared/tool_dependency/metaphlan2/2.5.0/bebatut/package_
metaphlan2_2_5_0/43a80f92815f/metaphlan2.py", line 1172, in <module>
    tree = TaxTree( mpa_pkl, ignore_markers )
  File
"/usr/local/galaxy/shared/tool_dependency/metaphlan2/2.5.0/bebatut/package_
metaphlan2_2_5_0/43a80f92815f/metaphlan2.py", line 857, in __init__
    clades_txt = ((l.strip().split("|"),n) for l,n in
mpa_pkl['taxonomy'].items())
AttributeError: 'list' object has no attribute 'items'

I believe the database is connected properly, but would the tool run for a
while even if it wasn't?  It seems like the mpa_pkl file data is loaded
via the --mpa_pkl attribute as in tool command line:

which bowtie2 || exit 200) && metaphlan2.py
/galaxy_data/production1/files/013/dataset_13546.dat -o
/galaxy_data/production1/files/013/dataset_13547.dat --input_type fasta
--bowtie2_exe `which bowtie2` --bowtie2db
/usr/local/packages/metaphlan2/db_v20/mpa_v20_m200 --mpa_pkl
/usr/local/packages/metaphlan2/db_v20/mpa_v20_m200".pkl" --no_map -t
rel_ab --tax_lev a --min_cu_len 2000 --min_alignment_len 0 --stat_q 0.1 -s
/galaxy_data/production1/files/013/dataset_13548.dat

Tool's xml file does a touch of funny business with the mpa_v20_m200".pkl"
file name parameter, but I guess that works if no one else has a problem
with it.

Thx for any info,

Damion
 

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