Unable to add expression matrix using singularity/docker #14
Description
Hello and thanks so much for the great tool!
I've been struggling to add custom expression matrices to sandy -- specifically, I'm encountering an error at what appears to be the SQLITE DB insertion step:
:: Inserting new_exp_mat1 from temp_mini.tsv ...
:: Checking if there is already an expression-matrix 'new_exp_mat1' ...
:: expression-matrix 'new_exp_mat1' not found
:: Indexing 'temp_mini.tsv' ...
:: Converting data to bytes ...
:: Compressing bytes ...
:: Storing expression-matrix 'new_exp_mat1'...
sandy expression add: DBIx::Class::Storage::DBI::_dbh_execute(): DBI Exception: DBD::SQLite::st execute failed: attempt to write a readonly database [for Statement "INSERT INTO expression_matrix ( is_user_provided, matrix, name, source) VALUES ( ?, ?, ?, ? )" with ParamValues: 1=1, 2='.�..q#¤g..e�1.Ã0..5!iHá¯.B.< .ç.o�.N2ÍÍìÍ-¯7µÖ..égn.ýøÊ. .â§A1.Ã.dÒì3W±*&«.¸u.~�´l-2Æ9@¿q.SéM...Èsþ..w¦.e á#.rá"¥2~.W
Fù...', 3='new_exp_mat1', 4='not defined'] at /usr/local/lib/perl5/vendor_perl/5.36.0/x86_64-linux-gnu/App/Sandy/DB/Handle/Expression.pm line 39
I'm wondering if this is related to the fact that I have to use the docker image via singularity (due to permissions in my compute environment). I've also struggled to install Sandy via cpanm. I've included the call to singularity exec below (with the --bind path replaced with a standin), and the mini expression matrix I'm using below that. Any advice on resolving this issue would be greatly appreciated -- thank you!
$ singularity \
exec \
--bind /path/to/input/data/ \
docker://galantelab/sandy:latest \
sandy expression add \
--verbose \
--expression-matrix new_exp_mat1 \
new_exp_mat_1.tsv
$ cat new_exp_mat_1.tsv
ENST00000009105 867
ENST00000010299 183
ENST00000054668 2616
ENST00000060969 84
ENST00000072644 2148
ENST00000207457 367
ENST00000234739 297
ENST00000234816 263
ENST00000234827 917
ENST00000234875 2192