Add pyqtl to qtl/Dockerfile so eqtl_prepare_expression.py runs smoothly

[dampierch]

Intro

Thank you for maintaining this code. I encountered an error this morning when I tried to use the latest eqtl_prepare_expression.py script. I think I identified where the problem comes from, and I propose a simple solution that I think will solve it.

Observed Error

singularity exec ${cont_dir}${sif} bash -c "
    ${src}eqtl_prepare_expression.py ${tpm_gct} ${reads_gct} ${gtf} \
    ${sample_participant_lookup} ${vcf_chr_list} ${prefix} \
        --tpm_threshold 0.1 \
        --count_threshold 6 \
        --sample_frac_threshold 0.2 \
        --normalization_method tmm
"
Traceback (most recent call last):
  File "gtex-pipeline/qtl/src/eqtl_prepare_expression.py", line 11, in <module>
    import qtl.io
ImportError: No module named 'qtl'

Likely Problem

• eqtl_prepare_expression.py imports pyqtl since Feb 3 2021
• qtl/Dockerfile does not install pyqtl

Proposed Solution

• Add "qtl" at the end of line 82 in qtl/Dockerfile

[francois-a]

Thanks, fixed.