Public Databases

/n/shared_db

We started using /n/shared_db for public databases with the launch of the O2 cluster. The databases are organized in this folder structure:

Genome/software/Version/database

For example:

mm10/rsem/1.3.0/mm10

Exceptions:

Some databases were assembled by developers and their original folder structure was kept, as in:
- ```
igenome/03032016/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome
```
bcbio databases are maintained by the Harvard Chan Bioinformatics Core , and installed this way:
- ```
bcbio/biodata/genomes/Hsapiens
```

/n/groups/shared_databases

This folder was created for an earlier cluster (Orchestra), but is still in use. The structure is like this:

software/genomeVersion/database

Exceptions:

There are some exceptions to the structure, such as: ignome and blastdb

A quick way to find the desired databases:

We have create a text file containing all the database names and paths. You can directly search the species and software:

$ grep bowtie2  /n/shared_db/allDatabases.no.bcbio.singularity.rcbio.txt | grep hg19 | less

You should see (uk means unknown here):

/n/groups/shared_databases/rsem_indexes_bowtie2/hg19.ump
/n/groups/shared_databases/rsem_indexes_bowtie2/hg19.chrlist
/n/groups/shared_databases/rsem_indexes_bowtie2/hg19.rev.2.bt2
/n/groups/shared_databases/rsem_indexes_bowtie2/hg19.fa
/n/groups/shared_databases/rsem_indexes_bowtie2/hg19.n2g.idx.fa
/n/groups/shared_databases/rsem_indexes_bowtie2/hg19.3.bt2
/n/groups/shared_databases/rsem_indexes_bowtie2/hg19.transcripts.fa.fai
...
/n/groups/shared_databases/bowtie2_indexes/hg19.rev.2.bt2
/n/groups/shared_databases/bowtie2_indexes/hg19.fa
/n/groups/shared_databases/bowtie2_indexes/hg19.3.bt2
...
/n/groups/shared_databases/bowtie2_indexes/hg19.1.bt2
/n/groups/shared_databases/bowtie2_indexes/hg19.fai
/n/shared_db/hg19/uk/bowtie2
/n/shared_db/hg19/uk/bowtie2/2.2.9
/n/shared_db/hg19/uk/bowtie2/2.2.9/chrUn_gl000233.fa
...
/n/shared_db/hg19/uk/bowtie2/2.2.9/chr9_gl000198_random.fa
/n/shared_db/hg19/uk/bowtie2/2.2.9/chr6_apd_hap1.fa
/n/shared_db/hg19/uk/bowtie2/2.2.9/chr3.fa
/n/shared_db/hg19/uk/bowtie2/2.2.9/chr2.fa

...