conda installation issue

[ntromas]

Hi,

Thanks for this pipeline! I met that issue during the installation and I wonder if that could impact the installation.

_conda env create -f PopCOGenT.yml Collecting package metadata (repodata.json): done Solving environment: done

Downloading and Extracting Packages _openmp_mutex-4.5 | 22 KB | ##################################### | 100% Preparing transaction: done Verifying transaction: \ SafetyError: The package for r-base located at /home/nico/miniconda3/pkgs/r-base-3.3.2-0 appears to be corrupted. The path 'lib/R/doc/html/packages.html' has an incorrect size. reported size: 2946 bytes actual size: 11567 bytes

ClobberError: This transaction has incompatible packages due to a shared path. packages: defaults/linux-64::libgfortran-3.0.0-1, defaults/linux-64::libgcc-7.2.0-h69d50b8_2 path: 'lib/libgfortran.so.3'

ClobberError: This transaction has incompatible packages due to a shared path. packages: defaults/linux-64::libgfortran-3.0.0-1, defaults/linux-64::libgcc-7.2.0-h69d50b8_2 path: 'lib/libgfortran.so.3.0.0'

ClobberError: This transaction has incompatible packages due to a shared path. packages: defaults/linux-64::openblas-0.2.19-0, defaults/linux-64::libopenblas-0.3.6-h5a2b251_2 path: 'lib/libopenblas.so'

ClobberError: This transaction has incompatible packages due to a shared path. packages: defaults/linux-64::openblas-0.2.19-0, defaults/linux-64::libopenblas-0.3.6-h5a2b251_2 path: 'lib/libopenblas.so.0'

ClobberError: This transaction has incompatible packages due to a shared path. packages: defaults/linux-64::libopenblas-0.3.6-h5a2b251_2, conda-forge/linux-64::libblas-3.8.0-11_openblas path: 'lib/libblas.so'

ClobberError: This transaction has incompatible packages due to a shared path. packages: defaults/linux-64::libopenblas-0.3.6-h5a2b251_2, conda-forge/linux-64::libcblas-3.8.0-11_openblas path: 'lib/libcblas.so'

ClobberError: This transaction has incompatible packages due to a shared path. packages: defaults/linux-64::libopenblas-0.3.6-h5a2b251_2, conda-forge/linux-64::liblapack-3.8.0-11_openblas path: 'lib/liblapack.so'

done Executing transaction: done #

To activate this environment, use

#

$ conda activate PopCOGenT

#

To deactivate an active environment, use

#

$ conda deactivate_

When I run the program, I got this:

sh PopCOGenT.sh PopCOGenT.sh: 4: source: not found PopCOGenT.sh: 5: source: not found PopCOGenT.sh: 6: source: not found usage: get_alignment_and_length_bias.py [-h] [--genome_dir GENOME_DIR] [--genome_ext GENOME_EXT] [--alignment_dir ALIGNMENT_DIR] [--mugsy_path MUGSY_PATH] [--mugsy_env MUGSY_ENV] [--base_name BASE_NAME] [--final_output_dir FINAL_OUTPUT_DIR] [--num_threads NUM_THREADS] [--keep_alignments] [--slurm] [--script_dir SCRIPT_DIR] [--source_path SOURCE_PATH] get_alignment_and_length_bias.py: error: argument --genome_dir: expected one argument usage: cluster.py [-h] [--base_name BASE_NAME] [--length_bias_file LENGTH_BIAS_FILE] [--clonal_cutoff CLONAL_CUTOFF] [--output_directory OUTPUT_DIRECTORY] [--infomap_args INFOMAP_ARGS] [--infomap_path INFOMAP_PATH] [--single_cell] cluster.py: error: argument --base_name: expected one argument

Here is the config file:

Base name for final output files ust a prefix to identify your outputs.

base_name='TARApop'

Output directory for the final output files.

This will create the directory if it does not already exist.

final_output_dir=/home/nico/programmes/PopCOGenT-master/output/ mkdir -p ${ [--final_output_dir FINAL_OUTPUT_DIR] [--num_threads NUM_THREADS] [--keep_alignments] [--slurm] [--script_dir SCRIPT_DIR] [--source_path SOURCE_PATH] get_alignment_and_length_bias.py: error: argument --genome_dir: expected one argument usage: cluster.py [-h] [--base_name BASE_NAME] [--length_bias_file LENGTH_BIAS_FILE] [--clonal_cutoff CLONAL_CUTOFF] [--output_directory OUTPUT_DIRECTORY] [--infomap_args INFOMAP_ARGS] [--infomap_path INFOMAP_PATH] [--single_cell] cluster.py: error: argument --base_name: expected one argument

Here is the config file:

_Base name for final output files ust a prefix to identify your outputs. base_name='MAGspop'

Output directory for the final output files.

This will create the directory if it does not already exist.

final_output_dir=/home/nico/programmes/PopCOGenT-master/output/ mkdir -p ${final_output_dir}

Path to mugsy and mugsyenv.sh. Please provide absolute path.

mugsy_path=/home/nico/miniconda3/envs/PopCOGenT/bin/mugsy mugsy_env=/home/nico/miniconda3/envs/PopCOGenT/bin/mugsyenv.sh

Path to infomap executable. Please provide absolute path.

infomap_path=/home/nico/programmes/PopCOGenT-master/Infomap

Path to genome files.

genome_dir=/media/nico/MyBook/test/

Genome file filename extension.

genome_ext=.fasta

Are you running on a single machine? Please specify the number of threads to run.

This can, at maximum, be the number of logical cores your machine has.

num_threads=10

Whether to keep alignments after length bias is calculated.

Alignment files can be 10MB each and thus a run on 100 genomes can take up on the order of 50 GB of space if alignment files are not discarded.

If you want to keep alignments, set to --keep_alignments. Otherwise leave as ''.

keep_alignments=--keep_alignments

Directory for output alignments. Must provide absolute path.

alignment_dir=/home/nico/programmes/PopCOGenT-master/output/proc/ mkdir -p ${alignment_dir}

Are your genomes single-cell genomes? If so, this should equal --single_cell. Otherwise leave as ''.

single_cell=''

Are you using a slurm environment? Then this should equal --slurm, otherwise, leave as empty quotes.

slurm_str=''

If using slurm, please specify the output directory for the runscripts and source scripts. Absolute paths required.

script_dir='' sourcepath=''

I probably have done something wrong, not sure where...

Thanks for your help!