read only file system for fasta, and mkdir errors - with fix

[colindaven]

Hi,

thanks for this tool.

I've downloaded a singularity version - see below and tried it in a nextflow process using singularity.

It looks like it is trying to write to the system root read only rather than $PWD - the current workflow directory.

Is there an env variable to set the directory to write to ? Or is my container incorrect/misconfigured?

edit - I worked it out

1. the fasta must be on a non-read only file system, so I copied it to the local dir
2. the output dir must exist, so mkdir -poutput was run

thanks

## container

sudo singularity build earlgrey.sif docker://tobybaril/earlgrey_dfam3.7

## command
    cp $fasta ${prefix}_earlgrey.fasta
    mkdir -p $params.outdir
    earlGrey -g ${prefix}_earlgrey.fasta -s arabidopsis -o $params.outdir -t $task.cpus

# errors 

work/1f/f9943cbd9e566f208402ee82400aae$ cat .command.err 
INFO:    fuse2fs not found, will not be able to mount EXT3 filesystems
INFO:    gocryptfs not found, will not be able to use gocryptfs
WARNING: While bind mounting '/mnt:/mnt': destination is already in the mount point list
realpath: output: No such file or directory
mkdir: can't create directory '/arabidopsis_EarlGrey/': Read-only file system
mkdir: can't create directory '/arabidopsis_Database/': Read-only file system
mkdir: can't create directory '/arabidopsis_RepeatModeler/': Read-only file system
mkdir: can't create directory '/arabidopsis_strainer/': Read-only file system
mkdir: can't create directory '/arabidopsis_Curated_Library/': Read-only file system
mkdir: can't create directory '/arabidopsis_RepeatMasker_Against_Custom_Library/': Read-only file system
mkdir: can't create directory '/arabidopsis_RepeatLandscape/': Read-only file system
mkdir: can't create directory '/arabidopsis_mergedRepeats/': Read-only file system
mkdir: can't create directory '/arabidopsis_summaryFiles/': Read-only file system
mkdir: can't create directory '/arabidopsis_heliano/': Read-only file system
tee: /arabidopsisEarlGrey.log: Read-only file system

[TobyBaril]

Hi @colindaven , thanks for raising this - I'm guessing from the edit all is working now?

Thanks!

Toby

[colindaven]

Hi @TobyBaril yes and no, I still haven't got output yet but will raise another issue with details. I just thought I'd leave this here to help people with similar issues.