SPeW | Automatic Packaging and Distribution of Bioinformatics
kandi X-RAY | SPeW Summary
kandi X-RAY | SPeW Summary
This repo was created as part of an NCBI-hackathon @ Univerisity of Pittsburgh in September of 2017. During this 3 day event, several disucssions occured about the best option to accomplish our goal of creating a method to take a NextGen Seq pipeline into a flexible format that can be easily shared. This is a summary of those discussions, edited by those who were present. Most Seq pipelines are inherently a string of pre-made programs linked together by the creator according to their personal preferences or prior experience, including comfort of specific programming languages, knowledge of what algorithms exist, and word of mouth about what is "best" option to use. This typically limits sharing the pipeline to another user who may want to make small modifications, or requires installing new software in order to run. In addition, many users may choose to run their pipeline on a local machine, cloud computing or a HPC. Thus, putting a pipeline into a format or framework that manages the pipeline and allows for easy modifications for future users as well as ability to share, would be of tremendous use to many beginner or intermediate bioinformatics users.
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Top functions reviewed by kandi - BETA
- Main function .
- Run Biopython pipeline .
- trim two fastq files
- Get the name of the adapter .
- Get the path to the output folder .
- Run bowtie2 .
- aligns the hatsat2
- Combine the fpkm files .
- Determine sample name .
- Return the name of the genome .
SPeW Key Features
SPeW Examples and Code Snippets
Lines of Code : 56License : Permissive (MIT)
Copycurl -fsSL get.nextflow.io | bash
mkdir -p bin
mv *.sh bin
chmod +x *.sh
#!/usr/bin/env nextflow
/*
* input parameters for the pipeline
*/
params.in = "$baseDir/data/*.fastq.gz"
inFiles = file(params.in)
process trimming{
input:
file reads fr Community Discussions
Trending Discussions on SPeW
QUESTION
I've installed PyAudio and it's working exactly as I want it to, both for playing and recording audio. However, every time I initialise a PyAudio object, it barfs a whole bunch of warnings and error into STDERR and it's making it difficult to sort through my own application's logs. Here's a sample out of an ipython session:
ANSWER
Answered 2021-Jun-13 at 20:51The problem was that PyAudio loads a bunch of non-Python stuff whenever it's envoked, and it's that's stuff that's printing to STDOUT so it has to be silenced directly. The cleanest way to do this is to wrap it in a context manager that silences STDOUT for the shortest amount of time possible:
QUESTION
I'm building a little k8s controller based on the sample-controller.
I'm listening for ServiceAccount events with the following event handler:
...ANSWER
Answered 2021-May-27 at 17:35SampleController is not the most easy code to deal with. They have example on how they cast objects to a known resource type. And they also have example on how they lookup the resource from a lister.
Unless you have specific needs, I would recommend to also consider using kubebuilder and follow the kubebuilder book that has intuitive explanations of making controllers.
QUESTION
I have small code which reads 100 MB file from Google cloud storage and then return output.
Code works fine for 1MB file but fails for 100 mb file.
Below is the code which is not working
...ANSWER
Answered 2021-May-19 at 02:39io.copy was trying to copy the details but OS was not allowing it. it was throwing error as (*net.OpError)(0xc0003302d0)(write tcp [::1]:80->[::1]:63014: wsasend: An established connection was aborted by the software in your host machine
QUESTION
I have a springboot application where I authenticate a user and if he is logged in I redirect him to the index.html. However, this index page just loads the plain .html and no js or css at all. I don't see any error in the server error logs nor in the browser's console. I have tried disabling spring security on my css files to no effect.
Here is my project structure:
- resources
- static
- css_general
- css_page_specific
- login.html
- index.html
- commons.js
- static
Here is my application.properties config. I have pointed thymeleaf's default path to static folder so that I can at least get this running first.
...ANSWER
Answered 2021-May-13 at 16:35The reason this happens is because you are storing your templates in /static (which lets you access those files without running them through the regular parsing and rendering processes of Thymeleaf). Accessing /index.html returns the file as static html. In order to fix this you need to:
Create another controller (or add another method to your login controller) that serves
index.htmlthrough the Thymeleaf renderer.
QUESTION
I am trying to run a website using gunicorn on my synology ds214se nas. When i run gunicorn through ssh(Putty) it works flawlessly but when i try to run it with the Synology Task Scheduler it doens't seem to work no matter what I try. Errorlog found below:
...ANSWER
Answered 2021-Apr-21 at 19:44I had a similar problem and went troubleshooting. I created a startfile with two lines:
QUESTION
I have a camera in my scene, which I am currently moving on the x y and z axis using WASD. However, I would want it to move according to the direction it is facing. For better illustration of what I mean, I am using snippets from the program blender to demonstrate the idea.
In Image 1, it is quite easy. Moving forward will simply move on the x (red) axis, moving to the sides will be on the y (green) axis. The problems arise when the camera is rotated, thereby changing it's position relative to the axes, as Image 2 shows from the top view:
If I now try to move forward (direction of the red arrow), I need the movement to accommodate for the rotation, and adjust the x and y coordinates so that the camera moves forward from it's perspective.
Is there a way of doing this? I have tried many calculations involving sine and cosine, and quite a few google searches, but it led to no result. Google mostly showed unsolved questions or solutions using OpenGL, and my math equations simply spewed out incorrect results.
I hope I explained the problem clearly, if not I will be happy to provide additional information. Thank you for your time!
...ANSWER
Answered 2021-Apr-20 at 16:08I know im like 3 months late but I think I know what you mean.
In JavaFX you have a group called world (Everything 3d except the camera). If you want to rotate the camera to the left (example around the y axis) you don't touch the camera but the world and rotate that around the y axis.
I'll be honest I don't 100% understand why it works but it does for me (I'm working on a game so I had to go through it).
I hope this answers your question :D
EDIT 1: Sample code
QUESTION
So here is the problem: I want to call a rust compiler on a piece of code. Instead of spewing warnings though stderr, it outputs a help page on stdout and exits. What is wrong with this?
...ANSWER
Answered 2021-Apr-16 at 11:43You don't need a specific crate to launch a process, the standard process::Command contains what you need.
You seem to want to launch rustc then inherit stdin and/or stdout.
That would be this:
QUESTION
As I understand it, logs do not get garbage collected in node.js, so an app which is doing a lot of logging can potentially lead to memory exhaustion.
Does the logging facility of pm2 however alter that? ie, If I'm running a node.js script under pm2 spewing out tons of console.log(messages), does pm2 'intercept' them, presumably freeing it from memory and writing it to a file, or does it simply observe stdout & stderr and copy new lines into their respective out/error .pm2/logs file?
...ANSWER
Answered 2021-Mar-22 at 16:51Yes, you're right at the point pm2 just capture stdout and stderr to the logs files. But it also has some options to control the logs. You can disable writing common logs by the ecosystem.config.json like this:
QUESTION
I've updated Vuetify from version 2.2.x to version 2.4.6 by running npm uninstall --save vuetify and then npm run install --save vuetify@latest. It's previously installed using vue add vuetify Now serving the project spews out these error messages
ANSWER
Answered 2021-Mar-14 at 16:32You should have a package.lock.json file. Delete that, and also delete the node_modules folder. Re-run npm install and try building again
QUESTION
I have a problem on some Android devices with the particle system's rendering (weirdly enough the problem seems occur on devices with higher capabilities). The problem occurs when mesh based particles (Renderer/Renderer Mode/Mesh) are being rendered. It seems like the meshes that are being spewed out and slowly shrunk with time are being reduced ("reverse-tessellated") which results in a nasty visual effect. Does anyone know what might be the cause of this?
UPDATE: One thing that I've noticed is that with time - the longer the gameplay - this problem is getting worse.
UPDATE: What I've tried is to make one particle system bigger (around x5 times) in order to check if it will have any effect on it's rasterization. Normally particles are sized down from 1 to 0 based on their life-time. What I've noticed, after sizing them up, is that the problem does not occur anymore.
UPDATE: Visualisation of the problem:
Properly rendered:
Improperly rendered:
...ANSWER
Answered 2021-Feb-16 at 07:57I was able to track the issue down. It turned out to be a problem within a toon shader I wrote while a go. All the things I've noticed are valid but unfortunately it took some time to put me on the right track.
Taken from Unity's documentation
The half and fixed types only become relevant when targeting mobile GPUs, where these types primarily exist for power (and sometimes performance) constraints. Keep in mind that you need to test your shaders on mobile to see whether or not you are running into precision/numerical issues.
Unfortunately for me, as it cost me quite some time, I've used half3/4 values with POSITION semantics which caused some numerical precision issues on some Android devices (in this case the particles were getting smaller and smaller - size 0 to be exact). As a general rule, from what I've read in Unity's documentation, float3/4 should always be preferred in conjunction with POSITION semantics.
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