bwa_index seems to contain a symbolic link

[ialbert]

After performing a

refgenie pull hg19/bwa_index

bwa did not map any reads. I started troubleshooting, and I believe the bwa_index tarfile contains a soft link. Here is what I see:

ls -l /Users/ialbert/refs/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/bwa_index/default/

prints:

lrwxr-xr-x 1 ialbert staff 172B Aug 10 13:05 baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c.fa -> /project/shefflab/deploy/rg.databio.org_full/genomes/data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/fasta/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c.fa

Note that it links to a file location:

/project/shefflab/deploy/rg.databio.org_full/genomes/data/...

[martinaryee]

I ran into the same issue and temporarily fixed it by manually overwriting the symlink with a new one that points to the local FASTA from the hg19/fasta resource:

cd ~/refgenie/alias/hg19/bwa_index/default/
ln -sf ../../../../data/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c/fasta/default/baa91c8f6e2780cfd8fd1040ff37f51c379947a2a4820d6c.fa .

My concern is that I've now significantly reduced some of the reproducibility benefits...