Challenges with downloaded databases remain

ctb commented 8 years ago

See #21 for prev.

With 0.0.8, after a

dammit databases --database-dir=/dammit-db

I get:

--- Checking for database prep (dir: /dammit-db)

          [x] download_and_gunzip:Pfam-A.hmm

          [ ] hmmpress:Pfam-A.hmm

          [x] download_and_gunzip:Rfam.cm

          [ ] cmpress:Rfam.cm

          [x] download_and_gunzip:aa_seq_euk.fasta

          [x] lastdb:aa_seq_euk.fasta.db

          [x] download_and_gunzip:ODB8_EukOGs_genes_ALL_levels.txt

          [x] download_and_untar:dammit-db-metazoa

despite:

# ls /dammit-db
ODB8_EukOGs_genes_ALL_levels.txt  aa_seq_euk.fasta
Pfam-A.hmm                        aa_seq_euk.fasta.db.bck
Pfam-A.hmm.h3f                    aa_seq_euk.fasta.db.des
Pfam-A.hmm.h3i                    aa_seq_euk.fasta.db.prj
Pfam-A.hmm.h3m                    aa_seq_euk.fasta.db.sds
Pfam-A.hmm.h3p                    aa_seq_euk.fasta.db.ssp
Rfam.cm                           aa_seq_euk.fasta.db.suf
Rfam.cm.i1f                       aa_seq_euk.fasta.db.tis
Rfam.cm.i1i                       buscodb
Rfam.cm.i1m                       databases.doit.db
Rfam.cm.i1p

ctb commented 8 years ago

Actually, maybe not. I was running the wrong version :). Let me try...

camillescott commented 8 years ago

It might be necessary to remove the old doit db from the db directory On Nov 19, 2015 7:24 PM, "C. Titus Brown" notifications@github.com wrote:

Actually, maybe not. I was running the wrong version :). Let me try...

— Reply to this email directly or view it on GitHub https://github.com/camillescott/dammit/issues/24#issuecomment-158268191.

ctb commented 8 years ago

Mostly my fault. all good now.

dib-lab / dammit

Challenges with downloaded databases remain #24