How do you install? Is the guide outdated?

[Rohcode]

Hi Hope you're well! Are the install instructions out of date? How does one get Yleaf running?

From: https://github.com/genid/Yleaf

The easiest way to get Yleaf up and running is by using a conda environment.

first clone this repository to get the environment_yleaf.yaml

git clone https://github.com/genid/Yleaf.git cd Yleaf

create the conda environment from the .yaml the environment will be called yleaf

conda env create --file environment_yleaf.yaml

activate the environment

conda activate yleaf

pip install the cloned yleaf into your environment. Using the -e flag allows you to modify the config file in your cloned folder

pip install -e .

verify that Yleaf is installed correctly. You can call this command from any directory on your system

Yleaf -h

Debian 12 VM. Installed git, miniconda then followed the instructions above. Step "conda env create --file environment_yleaf.yaml" failed/fails with the message:

@192:~/Yleaf$ conda env create --file environment_yleaf.yaml
Channels:
 - anaconda
 - defaults
 - conda-forge
 - bioconda
Platform: linux-aarch64
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - atk-1.0==2.36.0=ha1a6a79_0

Current channels:

  - https://conda.anaconda.org/anaconda
  - https://repo.anaconda.com/pkgs/main
  - https://repo.anaconda.com/pkgs/r
  - https://conda.anaconda.org/conda-forge
  - https://conda.anaconda.org/bioconda

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

Maybe a server was down so I tried again a few hours later to no avail. The response message lead me to https://anaconda.org/bioconda/yleaf which offered instructions so I tried: conda install bioconda::yleaf That installed fine and says can call/run Yleaf from anywhere! But apparently not:

@192:~$ Yleaf -h
Traceback (most recent call last):
  File "/home/c/miniconda3/bin/Yleaf", line 6, in <module>
    from yleaf.Yleaf import main
  File "/home/c/miniconda3/lib/python3.13/site-packages/yleaf/Yleaf.py", line 34, in <module>
    from yleaf import yleaf_constants, download_reference
  File "/home/c/miniconda3/lib/python3.13/site-packages/yleaf/yleaf_constants.py", line 55, in <module>
    name, value = line.strip().split('=')
    ^^^^^^^^^^^
ValueError: too many values to unpack (expected 2)

Hmm... perhaps the manual install is the way to go!

or manually install everything

install python and libraries

apt-get install python3.6 pip3 install pandas pip3 install numpy

install Burrows-Wheeler Aligner for FASTQ files

sudo apt-get install minimap2

install SAMtools

wget https://github.com/samtools/samtools/releases/download/1.4.1/ samtools-1.4.1.tar.bz2 -O samtools.tar.bz2 tar -xjvf samtools.tar.bz2 cd samtools-1.4.1/ ./configure make make install

clone the yleaf repository

git clone https://github.com/genid/Yleaf.git

pip install the yleaf repository

cd Yleaf pip install -e .

verify that Yleaf is installed correctly. You can call this command from any directory on your system

Yleaf -h

This was going well until step "wget https://github.com/samtools/samtools/releases/download/1.4.1/" because https://github.com/samtools/samtools/releases/download/1.4.1/ is now 404 because of a bug apparently fixed in 1.20 https://github.com/samtools/samtools/releases/tag/1.20

Hmm. perhaps none of the APIs are broken and Yleaf still works with samtools 1.21?

So I substitute: "wget https://github.com/samtools/samtools/releases/download/1.21/ " "samtools-1.21.tar.bz2 -O samtools.tar.bz2" returns "bash: samtools-1.21.tar.bz2: command not found".. however "tar -xjvf samtools-1.21.tar.bz2" seems to work so I cd in with cd samtools-1.21 and try "./configure make" which fails with:

@192:~/samtools-1.21$ ./configure make
configure: WARNING: you should use --build, --host, --target
checking for gawk... no
checking for mawk... mawk
checking for make-gcc... no
checking for gcc... no
checking for make-cc... no
checking for cc... no
checking for make-cl.exe... no
checking for cl.exe... no
checking for make-clang... no
checking for clang... no
configure: error: in '/home/c/samtools-1.21':
configure: error: no acceptable C compiler found in $PATH
See 'config.log' for more details

As a novice travelling from the comfort of macOS, Windows and Docker to Linux, this seemed like a good moment to ask for help😆 Thank you