atlas | ATLAS - Three commands to start analyzing your metagenome data | Genomics library
kandi X-RAY | atlas Summary
kandi X-RAY | atlas Summary
Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, to Annotation.
Support
Quality
Security
License
Reuse
Top functions reviewed by kandi - BETA
- Return a setuptools command class
- Get the project root directory
- Split a fasta file into subsets
- Extract the version information
- Create a configuration object from a root
- Create plots for the quality plot
- Draws the average quality score plot
- Convert a pandas DataFrame to a table
- Generate a plot for read quality reads
- Create a FASTA file for each bin
- Convert a Pandas DataFrame into a table
- Run predict_genes
- Reads a bbplit coverage file
- Get sruntable from given identifiers
- Run download
- Get SRA URL from a run accession
- Parse comments from a file
- Combine coverage files into a single dataframe
- Scan the contents of setup py py py
- Splits a FASTA file into subsets
- Create the versioneer config file
- Extract version information from VCS
- Run a snakemake workflow
- Return a dictionary of sample files
- Prepare the sample table for writing
- Validate the merged runinfo table
- Parse arguments from terminal
atlas Key Features
atlas Examples and Code Snippets
Community Discussions
Trending Discussions on atlas
QUESTION
I would like to connect to my Atlas cluster only once per instance running Cloud Functions.
Here is my code for an instance :
...ANSWER
Answered 2022-Mar-25 at 16:08You can store your database client as a global variable. From the documentation,
Cloud Functions often recycles the execution environment of a previous invocation. If you declare a variable in global scope, its value can be reused in subsequent invocations without having to be recomputed.
Try refactoring the code as shown below:
QUESTION
I tried to add a spritesheet to my Phaser game the same way I've done it a few times before, however this time it seems to not load the images correctly, causing it to display a black & green square instead and causing it to throw an error when trying to play an animation.
Can anyone tell what is causing this issue?
(Warning: Playing the Code here seems to freeze up your browser for a few seconds, alternatively view on JSFiddle: https://jsfiddle.net/cak3goru/4/ )
...ANSWER
Answered 2022-Feb-23 at 05:57The problem is, that you are using the wrong function, you should use this.anims.generateFrameNames
, and not this.anims.generateFrameNumbers
.
And set the correct key clean
for the sprite.
the line should be:
QUESTION
There has been other questions on the subject, but nothing seems working for me.
I have a functional CURL, but I want to translate to JS (with Node).
ANSWER
Answered 2022-Feb-19 at 13:04You need to specify that it's a digest:
QUESTION
I'm trying to connect a nodejs with mongodb using mongo db compass and im getting the following error:
...ANSWER
Answered 2021-Nov-21 at 14:18For first, you have double quotes in the connection
variable. Secondly: it seems to me that mongoUri should include the username and password in the query string, right?
QUESTION
I am using MongoDB(Mongo Atlas) in my Django app. All was working fine till yesterday. But today, when I ran the server, it is showing me the following error on console
...ANSWER
Answered 2021-Oct-03 at 05:57This is because of a root CA Let’s Encrypt uses (and Mongo Atals uses Let's Encrypt) has expired on 2020-09-30 - namely the "IdentTrust DST Root CA X3" one.
The fix is to manually install in the Windows certificate store the "ISRG Root X1" and "ISRG Root X2" root certificates, and the "Let’s Encrypt R3" intermediate one - link to their official site - https://letsencrypt.org/certificates/
Copy from the comments: download the .der field from the 1st category, download, double click and follow the wizard to install it.
QUESTION
I have a documents in MongoDB Atlas with this structure:
...ANSWER
Answered 2022-Jan-21 at 20:00Try this one:
QUESTION
I usually create a copy of a database in the same cluster in the same account like this:
- DUMP THE ORIGINAL DATABASE
mongodump --uri 'mongodb+srv://ACC_USER_NAME:ACC_USER_PASSWORD@cluster0.fklgt.mongodb.net/ORIGINAL_DATABASE_NAME' --archive="DUMP_FILE_NAME" --forceTableScan
- RESTORE THE DATABASE FROM THE DUMP FILE
mongorestore --uri 'mongodb+srv://ACC_USER_NAME:ACC_USER_PASSWORD@cluster0.fklgt.mongodb.net/ORIGINAL_DATABASE_NAME' --archive="DUMP_FILE_NAME" --nsFrom='ORIGINAL_DATABASE_NAME.' --nsTo='NEW_DATABASE_NAME.'
And that works perfectly.
Now, I created a new MongoDB atlas account, and I am trying to copy the original database into the new account.
So the first step is similar:
- DUMP THE ORIGINAL DATABASE
mongodump --uri 'mongodb+srv://ORIGINAL_ACC_USER_NAME:ORIGINAL_ACC_USER_PASSWORD@cluster0.fklgt.mongodb.net/ORIGINAL_DATABASE_NAME' --archive="DUMP_FILE_NAME" --forceTableScan
- RESTORE THE DATABASE FROM THE DUMP FILE
Here I could not find which params to use.
In the first example, in the second step, the URI is like this:
mongodb+srv://ACC_USER_NAME:ACC_USER_PASSWORD@cluster0.fklgt.mongodb.net/ORIGINAL_DATABASE_NAME
So I obviously should replace
ACC_USER_NAME:ACC_USER_PASSWORD
with
NEW_ACC_USER_NAME:NEW_ACC_USER_PASSWORD
But, what about the ORIGINAL_DATABASE_NAME
, I could not find an equivalent to put there.
The rest of the params:
--archive="DUMP_FILE_NAME" --nsFrom='ORIGINAL_DATABASE_NAME.' --nsTo='NEW_DATABASE_NAME.'
should remain the same.
...ANSWER
Answered 2022-Jan-22 at 21:25First, you should do mongodump
. You already did that correctly.
QUESTION
ANSWER
Answered 2021-Dec-01 at 07:57I don't think it's possible to manipulate the configuration file during the build/deployment that happens within the Oryx-container. What you could do is to manipulate the file during the pipeline run by, for example, tokenizing the environment-specific configuration values and replacing the tokens during the pipeline run. To achieve this with single json-file (ie. having just a file with the localhost-value stored in version control) you could use tokenizer- and replace tokens -task from Colin's ALM Corner extension collection (https://marketplace.visualstudio.com/items?itemName=colinsalmcorner.colinsalmcorner-buildtasks). Another option would be to have multiple environment-specific configuration files in version control and just copying a specific one over the appsettings.json during the pipeline run.
Not sure if Static Web App environment variables could be utilized here, but adding it here if someone using GitHub Actions is looking for this - they are not yet supported by Azure Pipelines.
QUESTION
I am using d3 to plot a route on a map:
...ANSWER
Answered 2021-Dec-04 at 07:31A clipping function won't achieve the correct effect as it will cut your features not coerce them to follow that line.
Instead, we can combine your projection with a geotransform to force the line to adhere to rules within the projected space:
QUESTION
After the release of Python 3.10, I reinstalled my modules for the newest version and I'm getting some trouble. First of all I tried to pip Numpy as it's the required one for matplotlib. But I got this problem:
...ANSWER
Answered 2021-Nov-06 at 23:20As others have stated, Python 3.10 is not currently compatible with Matplotlib. You need to install and use Python 3.9 until it is supported. Until then you have a few options:
WindowsYou can use the Python Launcher for Windows (py.exe) script to choose which Python version to run like so:
py.exe script help:
py -h
List all installed versions
py -0
Use a specified version
py -3.9
e.g. 1
Create a virtual environment using python 3.9
py -3.9 venv .venv
e.g. 2
install matplotlib with pip using python 3.9
py -3.9 -m pip install matplotlib
On Linux you can run whatever Python version you like like so:
python3.9
You can set up a local (your working directory and all sub-directories) virtual environment that will use your specified version like so:
python3.9 -m venv .venv
Which will set the version of python used to 3.9 while in the local directory, and allow you to type python
instead of python3.9
each time you need it.
Another relevant and helpful post by Rotareti here.
Please note that I have not described how to activate and use Python Virtual Environments here in detail, for more information on using them read the python docs.
Reference this answer if you're interested in installing a matplotlib release candidate.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install atlas
You can use atlas like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.
Support
Reuse Trending Solutions
Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items
Find more librariesStay Updated
Subscribe to our newsletter for trending solutions and developer bootcamps
Share this Page