picard | Easily declare large spaces of neural networks | Machine Learning library
kandi X-RAY | picard Summary
kandi X-RAY | picard Summary
The format for a picard configuration looks something like this.
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Top functions reviewed by kandi - BETA
- Return a graph representation of a model specification
- Draw networkx graph
- Get the nodes from the edges
- Get an operator image
- Get the next state from the given operator
- Get an operator by name
- Return the cleaned op name
picard Key Features
picard Examples and Code Snippets
Community Discussions
Trending Discussions on picard
QUESTION
I have a text string that contains several instances of numbers, example of the data is below.
I am trying to extract the number of keys (the number that is followed by the text -keys). I tried several REGEXP_EXTRACT
patterns without luck.
...{38-keys,fit-out,closed,eddy-tamy,datechange-feb2025,staff-onboard,sandy-brighton,open-dec2020}
{same-year,budgeted,signature-done,mark-picard,hotel,5-keys}
{active,building,itsa-signed,2322-keys,pending-signature,next-year-(construction),opening-feb2024}
ANSWER
Answered 2021-Apr-01 at 09:27- Use #1 OR #2 OR #3 below (added two additional suggestions as the author received an error with #1 and then #2 in regards to the
CAST
function which may be a result of spacing, Data Source (PostgreSQL) specific or another issue).
CAST
It can be achieved by using the Calculated Field below (where Field
represents the respective field name) which extracts all digits immediately preceding -keys
; the CAST
function was added to ensure that the field Type is Number (the default field Type of REGEXP_EXTRACT
values are Text); also, for future reference, the Raw Input Literal R
was used so that \d
represents the sequence for a digit vs the default (without R
) in Google Data Studio, which requires two back slashes (\\d
):
QUESTION
I need to return an array of nodes sorted from high to low. At the moment I am trying to implement an inorder traversal which gives me the exact opposite of what I'm looking for.
The tree looks like:
...ANSWER
Answered 2021-Apr-04 at 18:34You should just swap the two if
statements where you make a recursive call, so that you first visit rightReport
and then later leftReport
.
QUESTION
I need to traverse a binary search tree and return an array of the leaf nodes. At the moment I am traversing through the entire tree and returning one node at a time.
My tree looks like:
...ANSWER
Answered 2021-Apr-03 at 07:22findOfficersWithNoDirectReports() {
// If this is a leaf node, return the officer name
if (!this.leftReport && !this.rightReport) {
return [this.officerName]
}
// Otherwise, combine the left and right results
val result = []
if (this.leftReport) {
result = result.concat(this.leftReport.findOfficersWithNoDirectReports());
}
if (this.rightReport) {
result = result.concat(this.rightReport.findOfficersWithNoDirectReports());
}
return result;
}
QUESTION
Is it possible for a function to return a specific Data Type based on the parameter entered?
Here's an example of what I'm trying to do:
I've defined different datatypes that will hold data from an API call
...ANSWER
Answered 2021-Mar-06 at 17:13You can use protocols:
Create protocol with given fields, and make all DataType1,2 etc classes conform to it:
QUESTION
I am trying to do a findOneAndUpdate() to Find a document and update it in one atomic operation
...ANSWER
Answered 2021-Feb-26 at 23:16Try this, probably will work:
QUESTION
I have tables for users, tags, and join table taggings.
I'm currently using scope
to filter users through different variables, for example:
ANSWER
Answered 2020-Nov-09 at 16:53You can get a count and use having to stipulate that the user must have one or more tags:
QUESTION
I am trying to create a docker image for BBMAP
(https://sourceforge.net/projects/bbmap/files/latest/download) shell script suite available online along with samtools and picard.jar. I was able to run samtools and picard, but for some reason I am not able to add bbmap
below. Can someone please let me know what I am missing here?
I am trying to add shell scripts to bin to run them as executables. In my docker file below, this is where I need help:
...ANSWER
Answered 2020-Nov-06 at 00:24Earlier in your script, you run:
QUESTION
I am trying to run this docker image, but not sure why I am getting this error:
...ANSWER
Answered 2020-Nov-03 at 06:11Exit status 127
means no command found.
This is due to the java
command in openjdk:8-jre
not located in /usr/bin/java
, see next:
QUESTION
After running the variant calling, I would like to merge only specific outputs as shown in d
.
This is giving me an error of missing input files
. How to solve this?
ANSWER
Answered 2020-Oct-21 at 15:30The output of varcall
is
QUESTION
TLDR I'm getting the following error:
The 'conda' command is not available inside your singularity container image. Snakemake mounts your conda installation into singularity. Sometimes, this can fail because of shell restrictions. It has been tested to work with docker://ubuntu, but it e.g. fails with docker://bash
I had created a Snakemake
workflow and converted the shell:
commands to rule-based package management via Snakemake wrappers:
.
However, I ran into issues running this on HPC and one of the HPC support staff strongly recommended against using conda
on any HPC system as:
"if the builder [of wrapper] is not super careful, dynamic libraries present in the conda environment that relies on the host libs (there are always a couple present because builder are most of the time carefree) will break. I think that relying on
Singularity
for your pipeline would make for a more robust system." - Anon
I did some reading over the weekend and according to this document, it's possible to combine containers with conda-based package management; by defining a global conda
docker container and per-rule yaml
files.
Note: In contrast to the example in the link above (Figure 5.4), which uses a predefined
yaml
andshell:
command, here I've use conda wrappers which download theseyaml
files into theSingularity
container (if I'm thinking correctly) so I thought should function the same - see the Note: at the end though...
Snakefile
, config.yaml
and samples.txt
Snakefile
...ANSWER
Answered 2020-Sep-22 at 15:02TLDR:
fastqc singularity container used in qc rule likely doesn't have conda
available in it, and this doesn't satisfy what snakemake's--use-conda
expects.
Explanation:
You have singularity containers defined at two different levels - 1. global level that will be used for all rules, unless they are overridden at rule level; 2. per-rule level that will be used at the rule level.
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