minion | Server wrapper that turns command line tools | Runtime Evironment library
kandi X-RAY | minion Summary
kandi X-RAY | minion Summary
Minion is the server side code that powers all iobio web services. It wraps a command line program and hooks the input files/streams and stdout streams to websocket streams, enabling multiple web services to be piped together. It also handles converting the URL into a command and error handling. If you are wanting run a particular iobio webservice see the minion-services repo.
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Community Discussions
Trending Discussions on minion
QUESTION
I am writing a snakemake pipeline to eventually identify corona virus variants.
Below is a minimal example with three steps:
...ANSWER
Answered 2021-Jun-10 at 07:54I think the problem is that rule catFasta
doesn't contain the wildcard barcode
. If you think about it, what job name would you expect in {wildcards.barcode}.{rule}.{jobid}
?
Maybe a solution could be to add to each rule a jobname
parameter that could be {barcode}
for guppyplex
and minion
and 'all_barcodes'
for catFasta
. Then use --jobname "{params.jobname}.{rule}.{jobid}"
QUESTION
I am writing a snakemake to produce Sars-Cov-2 variants from Nanopore sequencing. The pipeline that I am writing is based on the artic network, so I am using artic guppyplex
and artic minion
.
The snakemake that I wrote has the following steps:
- zip all the
fastq
files for all barcodes (rulezipFq
) - perform read filtering with
guppyplex
(ruleguppyplex
) - call the
artic minion
pipeline (ruleminion
) - move the stderr and stdout from qsub to a folder under the working directory (rule
mvQsubLogs
)
Below is the snakemake that I wrote so far, which works
...ANSWER
Answered 2021-Jun-08 at 15:40The rule that fails is rule guppyplex
, which looks for an input in the form of {FASTQ_PATH}/{{barcode}}
.
Looks like the wildcard {barcode}
is filled with barcode49/barcode49.consensus.fasta
, which happened because of two reasons I think:
First (and most important): The workflow does not find a better way to produce the final output. In rule catFasta
, you give an input file which is never described as an output in your workflow. The rule minion
has the directory as an output, but not the file, and it is not perfectly clear for the workflow where to produce this input file.
It therefore infers that the {barcode}
wildcard somehow has to contain this .consensus.fasta
that it has never seen before. This wildcard is then handed over to the top, where the workflow crashes since it cannot find a matching input file.
Second: This initialisation of the wildcard with sth. you don't want is only possible since you did not constrain the wildcard properly. You can for example forbid the wildcard to contain a .
(see wildcard_constraints
here)
However, the main problem is that catFasta
does not find the desired input. I'd suggest changing the output of minion
to "nanopolish/{barcode}/{barcode}.consensus.fasta"
, since the you already take the OUTDIR from the params, that should not hurt your rule here.
Edit: Dummy test example:
QUESTION
I'm making a calculator for a game I play and whenever I run it, it just returns "NaN" for two values, only one of the values actually returns as it should. The two values that return NaN are the ones that run through switch statements and I found that the values you get from the switch statements are undefined so I think that's where it goes wrong. I tried looking for other questions like this on StackOverflow and I found some but their answers didn't work for me.
...ANSWER
Answered 2021-May-08 at 14:49The main problem is to use strings from input. The further effect is to get no values from the switch
statements, because the value is a string and in all cases, you have numbers. The comparison is here strict, like ===
.
For unknown values, you could return the function and omit calculation with not given values.
QUESTION
So, lately, I was making this game on python Tkinter where the computer gives me a random word and I have to type out the words and letters I see in the word give to me, so the problem here is that, "ans" is an entry widget and I want it to work like once I am done typing the word or letter I see in the given word I should press the enter key and when I press the enter key the computer should see whatever is written inside the widget and take it inside a variable so that I can type that variable as the text of the label present on the right side (a1-a18) of the screen, and on pressing enter it should do all that and also delete everything that was previously written inside the entry widget
...ANSWER
Answered 2021-Apr-22 at 19:52To bind the return/enter key, use entry.bind("", func)
:
QUESTION
I apologise is the title isn't correctly worded, I'm fairly new to Programming.
I have an object, for this example lets say its the following
...ANSWER
Answered 2021-Apr-13 at 10:40As pointed out by @VLAZ interfaces cannot be instantiated, they just prescribe a "shape" for a class implementing them. So in your example DefinedPeople.CategoryA[0].name
doesn't make sense, because you cannot access the property CategoryA
on an interface (which is not an object).
For the same reason you can't use your Person
interface to initialise an instance variable like you're trying to do in DefinedPeople
.
In order to get what you want, your DefinedPeople
interface should look like this:
QUESTION
The problem I'm having is that this set of code NEEDS to happen in order. It is all packaged inside a component that is updating every second.
Here is what I want to happen when the component mounts:
Step 1: On load, retrieve the last known timestamp stored in local storage and subtract it by new Date() /1000
then console log the answer.
Step 2: retrieve all data from local storage and update state (this includes the timestamp), continuing this process every second.
As it stands in my code, step 2 is happening first.
Here's a video of the app I'm working with and the component that's updating every second to provide context to my issue. I highlight my console log being 0. This is the issue I want to fix. I need the console log to not give me 0, but the current timestamp - the previous timestamp. This is so if a user using my app goes offline and comes back, it counts the time they were gone.: https://www.youtube.com/watch?v=N0tOZhHfio4
Here's my current code:
...ANSWER
Answered 2021-Apr-03 at 00:42A few things. I don't know exactly what you are doing, but you have to know that Javascript is an asynchronous programming language. That means that stuff doesn't happen in order. If a function takes time, Javascript will go onto the next function. It won't wait for the first function to finish to then go to the second function. This makes Javascript very efficient but adds a little more difficulties to the user. There are a few ways to go around this. I have linked articles to three methods.
Callbacks: https://www.w3schools.com/js/js_callback.asp
Promises: https://www.w3schools.com/js/js_promise.asp
Async/Await: https://www.w3schools.com/js/js_async.asp
You can choose whichever you like depending on your circumstances. Also there is something wrong with your code on the last line.
Lockr.set('timeStamp', timeStamp());
You are passing in the timestamp function. When you do this remove the ()
from the timestamp
. Anyways, I hope this helped.
QUESTION
I'm using IBM Cloud Code Engine to build the source code from a private git repo. I have tried many times, and the buildrun always failed. Following are the steps I have done.
Add my public key (/root/.ssh/id_rsa.pub) to my private repo as a deploy key
Use IBM Cloud Code Engine CLI to create repo access credential
ibmcloud ce repo create --name ibmgithub --key-path /root/.ssh/id_rsa --host github.ibm.com
Use IBM Cloud Code Engine CLI to create a build and then submit a build run
ibmcloud ce build create --name minion --image us.icr.io/mynamespace/myimg --rs ce-default-icr-us-south --git-repo-secret ibmgithub --source https://github.ibm.com/myaccount/myrepo --strategy dockerfile --size medium
The build run always fails
ANSWER
Answered 2021-Apr-01 at 05:55Since you're using an ssh key, make sure the URL to your git repo starts with git@
instead of https://
. So it should be git@github.ibm.com/myaccount/myrepo in your case.
For further issues with failing builds, you can check the related troubleshooting buildruns section in the Code Engine docs.
QUESTION
I want to write a Makefile that will iterate through a string and print it word by word.
Here is what I did in the Makefile:
...ANSWER
Answered 2021-Mar-29 at 09:41Makefile variables do not use the same assignment syntax as shell variables. MINION="foo fou bar"
will assign the string "foo fou bar"
to the MINION
Makefile variable, which will then be substituted into the shell command line as for n in "foo fou bar"
.
Use instead
QUESTION
Trying to create an auto-clicker/idle game. So far the entire application works except for this loop. After the loop begins, if I update the counter, different values update in intervals. So my counter will display those different values, going back and forth between them depending on how many times I've tried to mess with the counter while its looping.
I've tried using while loops, if statements, and for loops. And for each of those loops I've tried both setInterval()
and setTimeout()
. They either lead to the problem above, or the browser crashing.
Here's a video of the issue: Youtube Link
Here's the relevant code I've got currently:
...ANSWER
Answered 2021-Mar-29 at 00:40If you're computing state based off of a previous state, you should use functional updates.
Try passing setCounter
a function that receives the previous state instead of using counter
directly (do this with any of your useState
hooks that depend on previous state):
QUESTION
How can I add a local image in the value of embed.add_field(name=f'Last Match ({status})', value=
ANSWER
Answered 2021-Mar-22 at 12:40We cannot add image in the value field of add_field
. Please refer to discord.Embed for all the functions of discord.Embed class.
We use set_image
to set image ( big in size ) and set_thumbnail
to set an image to the top right of the embed ( like a logo ).
Depending on your usage you can use anyone of them.
If you want to embed local images you can refer to this page on discord py api.
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