Closed SuhasSrinivasan closed 4 months ago
Could you install newest orfik from GitHub and try again ?
remotes::install_github("Roleren/ORFik") # Then restart R
Thank you for reviewing the issue.
I uninstalled the Bioconductor version and installed from GitHub. The version number appears to be the same 1.23.10.
The GitHub version still has the issue.
> config = config(config_csv)
> config
fastq bam ref exp
"~/hyerim/riboseq/fastq" "~/hyerim/riboseq/bam" "~/hyerim/riboseq/reference" "~/Bio_data/ORFik_experiments/"
> config_inf = config.exper(experiment = 'chx',
+ assembly = 'hs_assembly',
+ type = c('Ribo-seq'))
/home/user1/.cache/R/BiocFileCache
does not exist, create directory? (yes/no): yes
--------------------------------
Setting up config file for ORFik
This config defines where to save:
fastq, bam files, references and experiments
Saving to: /home/user1/.cache/R/BiocFileCache/fa8a388fb8_fa8a388fb8.csv
ORFik now uses BiocFileCache for config, moving your old config
> config_inf
fastq Ribo-seq bam Ribo-seq ref
"~/Bio_data/raw_data/Ribo-seq/chx/" "~/Bio_data/processed_data/Ribo-seq/chx/" "~/Bio_data/references/hs_assembly/"
exp Ribo-seq
"chx_Ribo-seq"
Hm, will take a look at this
Hm, can you restart R and try again, I do not get this on my end:
# -> directories are correct
> config()
fastq bam ref
"/media/roler/S/data/Bio_data/raw_data" "/media/roler/S/data/Bio_data/processed_data" "/media/roler/S/data/Bio_data/references"
exp
"~/Bio_data/ORFik_experiments/"
> config.exper(experiment = 'chx', assembly = 'hs_assembly',type = c('Ribo-seq'))
fastq Ribo-seq bam Ribo-seq
"/media/roler/S/data/Bio_data/raw_data/Ribo-seq/chx/" "/media/roler/S/data/Bio_data/processed_data/Ribo-seq/chx/"
ref exp Ribo-seq
"/media/roler/S/data/Bio_data/references/hs_assembly/"
Related to #170 so now resolved
Hi,
I noticed this issue since the first time of trying the vignette, but as there were important issues, waited to bring this to your attention.
Issue 1
Following this particular step
There was difficulty to set custom configuration, and it always defaults to
~/Bio_data/
Seems like
config()
expects a path argument, after supplying that:But now it is observed that
exp
is predefined inconfig.save()
Issue 2
config.exper()
seems to use the same default path~/Bio_data/
Load config and verify the information.
Define the experiment, but it is again going back to
~/Bio_data/