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Hi, I am trying to use GROBID on my organization's HPC cluster. I have tried to use it on my own laptop (ARM Macbook), but I keep having trouble running the docker image. Our cluster does not support …
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From the step of `rnaseqc_call`, 8 bam files returned with an error message indicating `BAM file shares no contigs with GTF`
and this error message is preventing moving forward to the next step for…
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Hi,
This seems to be related to issue #399 which had been closed, but I'm unsure what the solution was as I continue to get errors.
I installed kallisto from conda which installed kallisto versi…
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Hello! I am trying to install BRAKER using the singularity image provided on a HPC cluster. I follow the instructions in the website provided (https://hub.docker.com/r/teambraker/braker3), but am unab…
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**Describe the bug**
Mamba not detected in snakemake when hybracter is run on the cluster via slurm. hybracterENV installed with miniforge3.
**To Reproduce**
1. conda activate hybracterENV in …
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### Description of the bug
The process NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE starts the FluteMLE command using the data of the gene_summary.txt file. It downloads several pathway files…
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I am trying to use AnnotSV on my Illumina Manta vcf outputs specifically the diploid vcfs. However, I cannot seem to make it work with a HPO in Singularity.
There are 2 input variables:
- `singu…
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Hi,
I am trying to run Ubermag on an HPC via a Jupyter-Notebook container pulled from the docker-hub using Singularity.
I followed the Conda installation procedure written on the Ubermag website an…
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Because the website could not recognize our input data,
[gene_information.txt](https://github.com/OceaneCsn/DIANE/files/12167445/gene_information.txt)
[design.txt](https://github.com/OceaneCsn/DIAN…
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For each user, we create a persistent folder at a location other than scratch (configurable in json), folder name could be @.
This per-user folder will be mounted into each container at the same loc…