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oushujun / EDTA

Extensive de-novo TE Annotator
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
GNU General Public License v3.0
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singularity install not working #476

Closed tallnuttrbgv closed 2 months ago

tallnuttrbgv commented 2 months ago

System as follows (different system from previous issue):

cat /etc/os-release NAME="CentOS Linux" VERSION="8" ID="centos" ID_LIKE="rhel fedora" VERSION_ID="8" PLATFORM_ID="platform:el8" PRETTY_NAME="CentOS Linux 8" ANSI_COLOR="0;31" CPE_NAME="cpe:/o:centos:centos:8" HOME_URL="https://centos.org/" BUG_REPORT_URL="https://bugs.centos.org/" CENTOS_MANTISBT_PROJECT="CentOS-8" CENTOS_MANTISBT_PROJECT_VERSION="8"

Pulled sif with:

singularity pull EDTA.sif docker://quay.io/biocontainers/edta:1.9.6--1

and it seemed to complete ok.

Then get error:

singularity exec /media/storage/bin/EDTA.sif EDTA.pl --genome /home/tallnutt/d/r12.24_themeda/themeda_scaf_norpts.fasta --species Maize --cds /home/tallnutt/d/r12.24_themeda/cds_from_genomic.fna --anno 1 --threads 10 WARNING: Skipping mount /usr/local/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LANG = "en_US.UTF-8" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C").

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Extensive de-novo TE Annotator (EDTA) v1.9.6
Shujun Ou (shujun.ou.1@gmail.com)

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At least 1 parameter is required: 1) Input fasta file: --genome

This is the Extensive de-novo TE Annotator that generates a high-quality structure-based TE library. Usage:

tallnuttrbgv commented 2 months ago

I notice in another comment dev has said only the mamba yml install method works - have now done this on a VM.