Unable to install Kmergenie

Question

[juliana.calderon]

Hello there, I'm trying to install KmerGenie following the README file. I downloaded the kmergeni-1.6892.tar.gz, unzipped it and did make under the folder, but it didn't work. It shows like the following

julibio@DESKTOP-OTF949V ~/curso-bio/kmergenie/kmergenie-1.7051/kmergenie-1.7051
$ make
cd ntCard && ./configure && make
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
./configure: line 3043: test: syntax error: `-std=c++17' unexpected
checking for gawk... (cached) gawk
checking for x86_64-conda-linux-gnu-gcc... /home/julibio/miniconda3/envs/kmergenie/bin/x86_64-conda-linux-gnu-cc
checking whether the C compiler works... no
configure: error: in `/home/julibio/curso-bio/kmergenie/kmergenie-1.7051/kmergenie-1.7051/ntCard':
configure: error: C compiler cannot create executables
See `config.log' for more details
make: *** [makefile:75: ntCard/ntcard] Error 77

Please helpp, how do I install Kmergenie? :(((

[rpolicastro]

It looks like you have some sort of kmergenie conda environment with gcc that make is trying to use. Theoretically you could just install kmergenie in its entirety using conda without dealing with building from source. If there's no particular reason conda doesn't work for this use case I would just go that route.

conda create --dry-run -n kmergenie_clean -c conda-forge -c bioconda kmergenie==1.7051

Remove --dry-run if everything looks good and you want to actually create the environment.

You can then active the environment and start using it when you're ready.

conda activate kmergenie_clean

If you have docker installed it's also available as a docker container from biocontainers. Here's a little example command that will download the container and run kmergenie --help.

docker run --rm quay.io/biocontainers/kmergenie:1.7051--py39r42h4e691d4_7 kmergenie --help

[juliana.calderon]

Hi, I have tried the command you recommended but I keep getting other errors when I try to use Kmergenie

$ kmergenie R1.fastq
/home/julibio/miniconda3/envs/kmergenie_clean/bin/kmergenie:29: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  import pkg_resources
running histogram estimation
Traceback (most recent call last):
  File "/home/julibio/miniconda3/envs/kmergenie_clean/bin/kmergenie", line 303, in <module>
    best_k = execute_once(arguments_passed_list, first_pass=first_pass)
  File "/home/julibio/miniconda3/envs/kmergenie_clean/bin/kmergenie", line 279, in execute_once
    ntcard_wrapper(k_interval)
  File "/home/julibio/miniconda3/envs/kmergenie_clean/bin/kmergenie", line 221, in ntcard_wrapper
    max_read_length = get_read_length(read_file_list)
  File "/home/julibio/miniconda3/envs/kmergenie_clean/bin/kmergenie", line 147, in get_read_length
    from readfq import readfq
ModuleNotFoundError: No module named 'readfq'

What should I do? :(

Answer 1

[rpolicastro]

I tried with the docker container and got the same error, so the bioconda version appears to be broken. Installing from source (and using conda to install R and Python) worked for me though.

Install the required system dependencies.

sudo apt-get update
sudo apt-get install make zlib1g-dev g++ curl

Install Python and R through conda. Remove --dry-run if everything looks correct.

conda create --dry-run -n kmergenie_dependencies -c conda-forge -c bioconda python==3.12.0 r-base==4.3.1 
conda activate kmergenie_dependencies

Now download and compile kmergenie.

curl "http://kmergenie.bx.psu.edu/kmergenie-1.7051.tar.gz" | tar -xzvf -
cd kmergenie-1.7051/
make
cd ..

# Add the kmergenie directory to your path.
export PATH=${PATH}:${PWD}/kmergenie-1.7051

[juliana.calderon]

Thank you so much!! it worked!!! <3