svndigest - svndigest

Rev	Date	Author	Line
6677	14 Apr 22	nicklas	1	This folder contain Singularity definition files for the creating containers
6677	14 Apr 22	nicklas	2	with all software that is needed to re-create the SCAN-B analysis pipeline as
6677	14 Apr 22	nicklas	3	it has been implemented in Reggie. The 'def' folder contain the definition
6677	14 Apr 22	nicklas	4	files. In most cases a single container is used for a single step in the
6677	14 Apr 22	nicklas	5	pipeline, but some containers are re-used in some steps. For example, the
6677	14 Apr 22	nicklas	6	container for demuxing is also used in the FASTQ import step since they
6677	14 Apr 22	nicklas	7	use the same software.
6677	14 Apr 22	nicklas	8
6677	14 Apr 22	nicklas	9	Use the build *.sh scripts to build the containers and save them in the
6677	14 Apr 22	nicklas	10	'sif' folder.
6677	14 Apr 22	nicklas	11
6677	14 Apr 22	nicklas	12	The SIF files are named according to the Reggie step they are used in,
6677	14 Apr 22	nicklas	13	followed by the pipeline version number (eg. the version number that is
6677	14 Apr 22	nicklas	14	used on the Software items), followed by the nameanv version of the main
6677	14 Apr 22	nicklas	15	software component that is used. For example, the current Hisat alignment
6677	14 Apr 22	nicklas	16	container is version 5 in the SCAN-B pipeline and uses Hisat version 2.2.1:
6677	14 Apr 22	nicklas	17
6677	14 Apr 22	nicklas	18	hisat-v5-hisat2.2.1.sif