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fix: issues with mouse db and db module list #28

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fix: issues with mouse db and db module list #28

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20c5aea
fix: issues with mouse db and db module list
dcdanko Feb 7, 2022
37b7f87
chore: add jpeg to aptitude install
dcdanko Feb 7, 2022
ec77c05
fix: more aptitude installs to support pillow
dcdanko Feb 7, 2022
4d22f95
fix: add -y
dcdanko Feb 7, 2022
eb8a1f0
fix: safe load yaml
dcdanko Feb 7, 2022
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2 changes: 2 additions & 0 deletions .circleci/config.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,8 @@ jobs:
command: |
apt update
apt install -y wget
apt-get install -y libjpeg-dev zlib1g-dev
apt-get install -y build-essential libssl-dev libffi-dev libxml2-dev libxslt1-dev zlib1g-dev
cd $HOME
wget "https://repo.anaconda.com/miniconda/Miniconda3-4.7.10-Linux-x86_64.sh" -O miniconda.sh
printf '%s' "8a324adcc9eaf1c09e22a992bb6234d91a94146840ee6b11c114ecadafc68121 miniconda.sh" | sha256sum -c
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3 changes: 2 additions & 1 deletion cap2/pipeline/databases/__init__.py
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Expand Up @@ -4,12 +4,13 @@
from .hmp_db import HmpDB
from .uniref import Uniref90
from .kraken2_db import Kraken2DB, BrakenKraken2DB

from .fast_kraken2_db import FastKraken2DB

MODULES = [
HumanRemovalDB,
HmpDB,
Uniref90,
Kraken2DB,
BrakenKraken2DB,
FastKraken2DB,
]
15 changes: 8 additions & 7 deletions cap2/pipeline/databases/mouse_removal_db.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@

import luigi
from os.path import join, dirname
from os.path import join, dirname, isfile
from glob import glob
import subprocess
from os import makedirs
Expand Down Expand Up @@ -36,13 +36,14 @@ def __init__(self, *args, **kwargs):
def download_mouse_genome(self):
local_dir = join(self.config.db_dir, 'GRCm39')
makedirs(local_dir, exist_ok=True)
cmd = (
'wget '
f'--directory-prefix={local_dir} '
f'{MOUSE_GENOME_URL} '
)
self.run_cmd(cmd)
local_path = join(local_dir, 'GCA_000001635.9_GRCm39_genomic.fna.gz')
if not isfile(local_path):
cmd = (
'wget '
f'--directory-prefix={local_dir} '
f'{MOUSE_GENOME_URL} '
)
self.run_cmd(cmd)
return local_path

@property
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4 changes: 2 additions & 2 deletions cap2/pipeline/preprocessing/error_correct_reads.py
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Expand Up @@ -2,7 +2,7 @@
import luigi
import subprocess
from os.path import join, dirname, basename
from yaml import load
from yaml import safe_load
from shutil import rmtree

from ..config import PipelineConfig
Expand Down Expand Up @@ -93,7 +93,7 @@ def _run_paired(self):
cmd += f' -t {self.cores} -o {outdir}'
self.run_cmd(cmd) # runs error correction but leaves output in a dir
config_path = f'{self.sample_name}.error_correction_out/corrected/corrected.yaml'
spades_out = load(open(config_path).read())
spades_out = safe_load(open(config_path).read())
ec_r1 = spades_out[0]['left reads']
assert len(ec_r1) == 1
ec_r2 = spades_out[0]['right reads']
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