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icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
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Error executing process > 'install_IEDB (Install IEDB)' #77

Open Xiao-Zhong opened 2 weeks ago

Xiao-Zhong commented 2 weeks ago

Hi, Sorry for bothering you again! First, thanks!

I'm slowly pushing forward in running your pipeline, and have encountered the issues below: 1, as posted, the pipeline failed to install IEDB, due to cd /opt/iedb/. Here the directory is unavailable in our HPC.

Command error: .command.sh: line 5: cd: /opt/iedb/: No such file or directory

See the details in: nextflow.log

2, can I ask how does the pipeline install GATK4 via conda profile? In the 'profiles.config' file, I only can see GATK3-related code. withLabel: GATK3 { conda = 'bioconda::gatk=3.8' params.gatk3_conda_url = "https://anaconda.org/bioconda/gatk/3.8/download/noarch/gatk-3.8-hdfd78af_11.tar.bz2" }

I've manually installed the latest GATK 4 (gatk-4.5.0.0), and looks working, however I'm unsure if the version is compatible with your pipeline.

Regards, Xiao

riederd commented 2 weeks ago

we recommend to run the pipeline using singularity -profile singularity, did you try this? With conda or local installation of the tools we see such problems.

Xiao-Zhong commented 2 weeks ago

Thank you! I would like to try singularity, however it's unavailable on the HPC I'm using and I haven't managed to install singularity without root permission.

I've installed a few dependencies manually after repeatedly running your pipeline and finding errors, but got stuck at 'Install IEDB'.

OK. I've asked IT team if they're happy to install singularity, will try to work around the issues via checking your code or will test your pipeline on a virtual machine with root permission. Hopefully either way will work!

Regards, Xiao

Xiao-Zhong commented 1 week ago

Hi, Just let you know nextNEOpi ran almost without error with -profile singularity,cluster, after I installed singularity by conda. I haven't seen Sequenza result and am checking what's going on. Thanks!