Installation on ABiMS platform
Some users at the Station Biologique de Roscoff plan to use Magneto in their process.
We exchanged with @chaffron-s and here is my state-of-the-art.
I still don"t know if it links to the installation or my usage or possibly a bug somewhere?
Thanks
My naive protocol:
# Virtual env
module load python/3.9
python -m venv ~/venv_magneto
. ~/venv_magneto/bin/activate
# Installation
cd ~/tmp/
git clone https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto.git
python3 -m pip install magneto/
# Test
cd ~/tmp/
mkdir magneto_test
tar -zxf magneto/test/dummy_dataset.tar.gz -C magneto_test/
cd magneto_test/dummy_dataset/
magneto init --wd .
magneto run all --dummy --rerun-incomplete --profile config/slurm/
The output
--config target=all samples=config/dummy_samples.yaml --rerun-incomplete --profile config/slurm/ --printshellcmds
NC_000964
dummy_dataset/NC_000964.fa.gz
NC_002971
dummy_dataset/NC_002971.fa.gz
[...]
NC_004668
dummy_dataset/NC_004668.fa.gz
NC_004842
dummy_dataset/NC_004842.fa.gz
Building DAG of jobs...
MissingInputException in rule fastP_SE in file /home/fr2424/sib/lecorguille/venv_magneto/lib/python3.9/site-packages/magneto/rules/QC.smk, line 376:
Missing input files for rule fastP_SE:
output: /home/fr2424/sib/lecorguille/tmp/magneto_test/dummy_dataset/tmp/NC_000964_NC_000964_QC_SE.fastq.gz, /home/fr2424/sib/lecorguille/tmp/magneto_test/dummy_dataset/reports/pre_processing/fastP/NC_000964_NC/NC_000964_NC_000964_fastp.json, /home/fr2424/sib/lecorguille/tmp/magneto_test/dummy_dataset/reports/pre_processing/fastP/NC_000964_NC/NC_000964_NC_000964_fastp.html
wildcards: SE=NC_000964_NC, run=000964
affected files:
dummy_dataset/NC_004668.fa.gz
dummy_dataset/NC_004369.fa.gz
dummy_dataset/NC_004842.fa.gz
dummy_dataset/NC_002971.fa.gz
dummy_dataset/NC_000964.fa.gz
Traceback (most recent call last):
File "/home/fr2424/sib/lecorguille/venv_magneto/bin/magneto", line 33, in <module>
sys.exit(load_entry_point('magneto==0.0.0', 'console_scripts', 'magneto')())
File "/home/fr2424/sib/lecorguille/venv_magneto/lib/python3.9/site-packages/click/core.py", line 1130, in __call__
return self.main(*args, **kwargs)
File "/home/fr2424/sib/lecorguille/venv_magneto/lib/python3.9/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/home/fr2424/sib/lecorguille/venv_magneto/lib/python3.9/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/fr2424/sib/lecorguille/venv_magneto/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/fr2424/sib/lecorguille/venv_magneto/lib/python3.9/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/home/fr2424/sib/lecorguille/venv_magneto/lib/python3.9/site-packages/magneto/magneto.py", line 185, in run
subprocess.check_call(cmd, shell=True)
File "/shared/software/miniconda/envs/python-pytorch-tensorflow-3.9-1.11.0-2.6.2/lib/python3.9/subprocess.py", line 373, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'snakemake --snakefile /home/fr2424/sib/lecorguille/venv_magneto/lib/python3.9/site-packages/magneto/Snakefile --configfile './config/config.yaml' --directory '.' --use-conda --config target=all samples=config/dummy_samples.yaml --rerun-incomplete --profile config/slurm/ --printshellcmds ' returned non-zero exit status 1.