Re: "med.bio" under Ubuntu-MATE 18.04 LTS
On 27/05/18 23:13, Tony Travis wrote:
> [...]
>> File "/usr/share/metaphlan2/_metaphlan2.py", line 22
>> print("Command: {}".format(' '.join(cmd)), end='\n\n')
>> ^
>> SyntaxError: invalid syntax
Hi,
The problem is that "_metaphlan2.py" uses Python3 syntax but the Debian
"postinst" script runs "pycompile" on it, which defaults to Python2.
Here is a patch, with the print function included from the future and
function annotations removed.
HTH,
Tony.
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--- _metaphlan2.py.orig 2018-02-07 10:43:00.000000000 +0000
+++ _metaphlan2.py 2018-05-28 01:27:41.168280522 +0100
@@ -3,7 +3,7 @@
# This module defines the functions which run MetaPhlAn2 on
# single and paired fastq data.
-
+from __future__ import print_function
import subprocess as sb
from q2_types.per_sample_sequences import SingleLanePerSampleSingleEndFastqDirFmt
from q2_types.per_sample_sequences import SingleLanePerSamplePairedEndFastqDirFmt
@@ -11,7 +11,6 @@
import biom
import os
-
def metaphlan2_helper(raw_data, nproc, input_type, output_file, verbose=True):
cmd = ['metaphlan2.py', str(raw_data), '--input_type', str(input_type),
'--biom', str(output_file), '--nproc', str(nproc)]
@@ -24,8 +23,7 @@
sb.run(cmd, check=True)
-def profile_single_fastq(raw_data: SingleLanePerSampleSingleEndFastqDirFmt,
- nproc: int=1) -> biom.Table:
+def profile_single_fastq(raw_data, nproc=1):
output_biom = None
with tempfile.TemporaryDirectory() as tmp_dir:
@@ -36,8 +34,7 @@
return output_biom
-def profile_paired_fastq(raw_data: SingleLanePerSamplePairedEndFastqDirFmt,
- nproc: int=1) -> biom.Table:
+def profile_paired_fastq(raw_data, nproc=1):
output_biom = None
with tempfile.TemporaryDirectory() as tmp_dir:
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