BWA | Backdoored Web Application - a reference test | Hacking library

I have a table that looks as follows (data posted below):

I would like to exclude all iso3c (the three letter codes) for which var has not at least three values (i.e 0,1,2,3). As example, for AGO the only value is 0. So this one needs to go. The next one ALB can stay, because the value goes up to 3. I want to do something like, setDT(DT)[max(as.numeric(as.character(var))) <3, iso3c:=NA, by="iso3c"]. But that does not do anything to the data.

Any ideas?

i got a file formatted like that : (each space = tab separator)

i have this data in MongoDB:

I want to use the binaries bwa and samtools in IBM cloud functions. I've tried to include both in the .zip as explained here but both executables are missing some shared libraries. What would be a general approach to fix those sorts of problems? Do I have to create a docker image for that?

I align reads with bwa and call variants with gatk. gatk needs the creation of a dict for the reference genome, and bwa needs creation of indices. When I use touch for both of them I get this error:

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 and shell: command, here I've use conda wrappers which download these yaml files into the Singularity container (if I'm thinking correctly) so I thought should function the same - see the Note: at the end though...

I am trying to create a function that takes in two variables, the continent and the column that would like to be worked with from a dataframe. I am then trying to calculate the mean value of the column for that particular continent to replace the NAs that are in that column for that continent. However, I seem to be having trouble when it comes to the actual replacement of the values, I keep running into errors. I have tried multiple ways such as replace, replace_na and mutate but I keep getting errors that I cannot seem to get away from. This code works when it is not in a function, but the minute I add it to the function I seem to get this error.

I am trying to execute the workflow of the Snakemake's official tutorial via Tibanna on AWS.

As instructed here,

1. I have installed Tibanna and set up environment variables.
2. Then I deployed Tibanna Unicorn to a folder snakemake-tutorial in a specific S3 bucket specific-bucket.
3. I set up the default unicorn.
4. As a last step, I run the following command:

I'm creating a Snakemake workflow that will wrap up some of the tools in the nvidia clara parabricks pipelines. Because these tools run on GPU's, they typically can only handle one sample at a time, otherwise the GPU will run out of memory. However, Snakemake shoves all the samples through to Parabricks at one time - seemingly unaware of the GPU memory limits. One solution would be to tell Snakemake to process one sample at a time, thus the question:

How do I get Snakemake to process one sample at a time?

Because parabricks is a licensed product (and therefore not necessarily reproducible), I will show an example of the parabricks rule I am trying to run (pbrun fastq2bam), as well as a minimal reproducible example using open source software (fastqc) which we can work on/from

Snakefile: