Raoul J.P. Bonnal
Raoul J.P. Bonnal
I can get the usual information from the below GSE but I can not find a way to read the `series_table` where the authors keep track of each single cell...
Now only a few high level functionalities are tested by biogem. I'd like to write more tests for all options supported by biogem, this will be useful during the switch...
The database created is distributed with the gem. Using db/database.yml, path to db depends by where the gem is installed. If the user need to establish a connection can't know...
Task in biongs which make the mapping using tophat, has the parameter fastq. The procedure can not handle smoothly if the user has fastq.gz file but must importantly generic names...
If the user reinstalls the gem binaries installed in common are wiped out. Provide an option to avoid this behavior '--do-not-reinstall'
the REQUIREMENTS section (including dependency on gnuplot) should be moved to the top of README
Probably, file/dir name conventions should only be applied to biongs project types. To clarify, 'biongs tasks' and 'types of projects' should be described differently. Tasks are the minimum unit of...
I succeeded to run "biongs quality:fastq_stats" and "biongs quality:boxplot" but it seems that these doesn't depend on the "biongs project:new" directory structure. This is useful.
If we don't rely on the gnuplot in the near future, it would be also nice (already in TODO).
Software must be installed on your local machine, biongs can not download it.