lmtani

version development


workflow MinibuscoWorkflow {
    input {
        Array[String] accessions
        String busco_lineage
    }

    call MinibuscoDownload {

lmtani

from typing import Dict

import factory
import flask
import flask_sqlalchemy
import pydantic
import pytest

# Conforme: https://flask-sqlalchemy.palletsprojects.com/en/2.x/api/?highlight=init_app#flask_sqlalchemy.SQLAlchemy.init_app
db = flask_sqlalchemy.SQLAlchemy()

lmtani

Inputs

• Sample 1 g.vcf
• Sample 2 g.vcf
• Human reference genome (gs://genomics-public-data/references/hg38/v0/Homo_sapiens_assembly38.fasta)

g.vcf files and produced databases available in Google Drive: https://drive.google.com/file/d/1rq5p5YpDYY6n0OqTL05IaDAl8vlMhxNv/view?usp=sharing

Using locally (works)

lmtani

"""
Script para gerar todas as CDSs de determinada assembly do genoma humano.

Essas coordenadas são usadas para o calculo de cobertura das regiões alvo
do exoma.
"""
from pyensembl import EnsemblRelease

CHROMOSOMES = list(map(str, list(range(1, 24)))) + ["X", "Y", "MT"]

lmtani

import requests
import os
import hashlib

# url = "http://sandbox.thesubdb.com"
url = "http://api.thesubdb.com"
user_agent = "SubDB/1.0 (Pyrrot/0.1; http://github.com/jrhames/pyrrot-cli)"


def hash_thesubdb(video_path):

lmtani

FROM continuumio/miniconda:4.6.14

ENV DEBIAN_FRONTEND=noninteractive

RUN apt-get update && apt-get install -y build-essential postgresql postgresql-contrib

RUN conda config --add channels bioconda/label/cf201901 \
    && conda config --add channels conda-forge/label/cf201901 \
    && conda install augustus rmblast maker hisat2 braker busco=3.0.2 blast pfam_scan \
    && pip install biopython bcbio-gff networkx markdown2 matplotlib \

lmtani

Keybase proof

I hereby claim:

• I am lmtani on github.
• I am taniguti (https://keybase.io/taniguti) on keybase.
• I have a public key ASCll6gURTY8PtotQhknqBVuFMwZPzt3MJJztYC3rseT4wo

To claim this, I am signing this object: