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rsa-tools / rsat-code

This repo contains the code required to run a local version of the software suite Regulatory Sequence Analysis Tools (RSAT).
http://rsat.eu
GNU Affero General Public License v3.0
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problem with download-organism using docker #39

Closed roniweiss12 closed 6 months ago

roniweiss12 commented 6 months ago

hello, I'm following the RSAT docker tutorial. I launched the container with: docker run --rm -v $HOME/rsat_data:/packages/rsat/public_html/data/ -v $HOME/rsat_results:/home/rsat_user/rsat_results -it biocontainers/rsat:20230828_cv1 and then when i run download-organism -v 2 -org Prunus_persica.Prunus_persica_NCBIv2.38 -server https://rsat.eead.csic.es/plants i get the following output:

; INFO  Local genome directory  /packages/rsat/public_html/data/genomes/
; download-organism  -v 2 -org Prunus_persica.Prunus_persica_NCBIv2.38 -server https://rsat.eead.csic.es/plants
; Program version               1.32
; INFO  Downloading     1       organisms
;       1       Prunus_persica.Prunus_persica_NCBIv2.38
; 2024-02-22.102059     Getting information about supported organisms from server
; 2024-02-22.102100     Getting list of supported organisms from remote server
;       rsat supported-organisms-server -url https://rsat.eead.csic.es/plants -v 0 -return ID,last_update,source | grep -v '^#'
; INFO  0       supported organisms on server   https://rsat.eead.csic.es/plants
; 2024-02-22.102100     Downloading     genome  1/1     Prunus_persica.Prunus_persica_NCBIv2.38 RSAT server     https://rsat.eead.csic.es/plants
; 2024-02-22.102142     Updating organism       Prunus_persica.Prunus_persica_NCBIv2.38
; install-organism  -v 1 -task config,phylogeny -org Prunus_persica.Prunus_persica_NCBIv2.38 -date '<NA>' -source '<NA>'
;
; Tasks:
;       config
;       phylogeny
;
; Supported organism table:
;    RSAT config                /packages/rsat/public_html/data/supported_organisms.tab
; 2024-02-22.102142     Installing organism     1/1     Prunus_persica.Prunus_persica_NCBIv2.38
;
; Organism parameters:
;    ID                         Prunus_persica.Prunus_persica_NCBIv2.38
;    Name                     
;    Update date                2024-02-22.102142
;    Data source                <NA>
;
; Directories and files:
;    Refseq dir               
;    Installation directory     /packages/rsat/public_html/data/genomes/Prunus_persica.Prunus_persica_NCBIv2.38
;    Genome directory           /packages/rsat/public_html/data/genomes/Prunus_persica.Prunus_persica_NCBIv2.38/genome
;    genome sequence file       /packages/rsat/public_html/data/genomes/Prunus_persica.Prunus_persica_NCBIv2.38/genome/contigs.txt
;    feature table              /packages/rsat/public_html/data/genomes/Prunus_persica.Prunus_persica_NCBIv2.38/genome/feature.tab
;    synonyms                   /packages/rsat/public_html/data/genomes/Prunus_persica.Prunus_persica_NCBIv2.38/genome/feature_names.tab
genome folder 
variants folder/packages/rsat/public_html/data/genomes/Prunus_persica.Prunus_persica_NCBIv2.38/variations
Error
        Cannot write output file >/packages/rsat/public_html/data//supported_organisms_tmp_2024-02-22.102143_oBfQ0I
; 2024-02-22.102143     Updating config and phylogeny
        install-organism -v 1 -task config,phylogeny -org Prunus_persica.Prunus_persica_NCBIv2.38 -date "<NA>" -source "<NA>"
; Host name     0c2802e935b5
; Job started   2024-02-22.102059
; Job done      2024-02-22.102143
; Seconds       0.06
;       user    0.06
;       system  0.01
;       cuser   0.84
;       csystem 0.32

The error is: Cannot write output file >/packages/rsat/public_html/data//supported_organisms_tmp_2024-02-22.102143_oBfQ0I I suspect the problem is the double slash (...data//supported...). I also tried to launch the container with no slash after data: docker run --rm -v $HOME/rsat_data:/packages/rsat/public_html/data -v $HOME/rsat_results:/home/rsat_user/rsat_results -it biocontainers/rsat:20230828_cv1 but it didn't help. How can I solve this? or, could the probelm be something else? I would appreciate any help!

Roni

eead-csic-compbio commented 6 months ago

Hi @roniweiss12 , can you please make sure your local folder $HOME/rsat_data is writable by all? Should be drwxrwxrwx

roniweiss12 commented 6 months ago

Thanks for the fast reply! I changed it and it worked indeed. I just want to metion that the tutorial says to use chmod -R a+w rsat_data/genomes rsat_results and doesn't mention the rsat_data folder itself...

Thanks again anyway!

eead-csic-compbio commented 6 months ago

I will change it in the tutorial, thanks for your feedback, Bruno

PS: https://github.com/rsa-tools/installing-RSAT/commit/21db76ed2cd5ce470d5280063866faba4f2d5cc5