[BUG] Docker container (v.5.5.4) lacks dependencies

[huangnengCSU]

Is there an existing issue for this?

• I have searched the existing issues

Have you loaded the SQANTI3.env conda environment?

• I have loaded the SQANTI3.env conda environment

Are you running SQANTI3 on its latest release?

• I have SQANTI3 updated to the latest release

Problem description

Hi,

I used docker image version 5.5.4. I ran sqanti3_qc.py successfully but encountered the error about "RColorConesa" when I ran sqanti3_filter.py rules.

Due to the setting of cluster, I can not install SQANTI3 with conda successfully, I have to use docker container. I built two versions but meet the same issue. Here shows my commands,

singularity build sqanti3.sif docker://anaconesalab/sqanti3

singularity pull docker://anaconesalab/sqanti3:v5.5.4

Code sample

#!/bin/bash
module load singularity/3.4.2

ref=""
anno=""

# QC
isoform=""
outdir=""
mkdir -p ${outdir}
singularity run sqanti3_v5.5.4.sif sqanti3_qc.py \
--isoforms ${isoform} \
--refGTF ${anno} \
--refFasta ${ref} \
--dir ${outdir} \
--cpus 32

# filter
classification_file=""
singularity run sqanti3_v5.5.4.sif sqanti3_filter.py rules \
--sqanti_class ${classification_file} \
--cpus 32 \
--dir ${outdir}

Error

ERROR:
Details: Command '/conda/miniconda3/envs/sqanti3/bin/Rscript /opt2/sqanti3/5.5.4/SQANTI3-5.5.4/src/utilities/report_filter/SQANTI3_filter_report.R -d gm24385_pb_masseq_primfilt_bambu_sqanti3 -o isoforms -u /opt2/sqanti3/5.5.4/SQANTI3-5.5.4/src/utilities -f rules' returned non-zero exit status 1.
INFO:

ERROR:

-------------------------------------------------

         SQANTI3 Rules filter report

--------------------------------------------------
Loading required package: magrittr

Reading Rules result classification table...
Warning message:
One or more parsing issues, call `problems()` on your data frame for details,
e.g.:
  dat <- vroom(...)
  problems(dat)
Loading required package: ggplot2
Warning in install.packages("RColorConesa") :
  'lib = "/conda/miniconda3/envs/sqanti3/lib/R/library"' is not writable
Error in install.packages("RColorConesa") : unable to install packages
Calls: suppressMessages -> withCallingHandlers -> install.packages
Execution halted

Anything else?

No response

[pabloati]

Hi,

That is an issue that might happen on some systems, due to that package not being supported anymore. I have eliminated it from the scripts, as it was no longer needed, and the changes will be available with the release 6.0 (which will be set as pre-release today). I will update this thread once the changes have been made permanent