galaxyproject / galaxyproject/idc
Complexity of STAR indices
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Description
Hi there,
The tools `rna_star` and `rna_starsolo` use indices produced by the data manager `rna_star_index_builder_data_manager`.
Currently the last version of STAR is 2.7.10b and the earlier version of STAR which makes compatible indices is 2.7.4a released in 2018:
https://github.com/alexdobin/STAR/blob/56c9fd59d0cbddd630f9ed2a656dd3a963a1b6b4/source/parametersDefault#L1-L3
This corresponds to `rna_star_index_builder_data_manager` revision [9:c520a52b5174](https://toolshed.g2.bx.psu.edu/repository/view_changelog?id=60543b5d862da792) version 2.7.4a and [11:d63c1442407f](https://toolshed.g2.bx.psu.edu/repository/view_changelog?id=60543b5d862da792) version 2.7.4a+galaxy1.
Currently, in [data_manager.yml](https://github.com/galaxyproject/idc/blob/main/data_managers.yml) we have:
https://github.com/galaxyproject/idc/blob/4aee221c69daebd09e602159d7a6a2911d339d1f/data_managers.yml#L34
which were generating a table called `rnastar_index2.loc` (the new version of the table is `rnastar_index2x_versioned.loc`):
```
$ head /data/galaxy/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_star_index_builder/6ef6520f14fc/data_manager_star_index_builder/data_manager/rna_star_index_builder.xml
builder
macros.xml
#
#The column should be 1 or 0, indicating whether the index was made
#with an annotation (i.e., --sjdbGTFfile and --sjdbOverhang were used) or not,
#respecively.
#
#Note that STAR indices can become quite large. Consequently, it is only
#advisable to create indices with annotations if it's known ahead of time that
#(A) the annotations won't be frequently updated and (B) the read lengths used
#will also rarely vary. If either of these is not the case, it's advisable to
#create indices without annotations and then specify an annotation file and
#maximum read length (minus 1) when running STAR.
#
#hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0
#hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1
$ cat /data/galaxy/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_star_index_builder/6ef6520f14fc/data_manager_star_index_builder/tool_data_table_conf.xml.sample
value, dbkey, name, path
value, dbkey, name, path, with-gtf
```
However, when I check in the [cvmfs cache](http://datacache.galaxyproject.org/idc/config/), I have a table named `rnastar_index2x_versioned.loc` and the version inside is `2.7.4a`.
:upside_down_face:
After this big introduction, I have 2 questions:
- Do you know why the data on cvmfs does not corresponds to the version of the data manager listed in the data_manager.yml?
- Should IDC support old STAR indices version or only the one from now?
Thank you so much.
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