--full not working to download uniref90

[macmanes]

using dammit 0.2.0

$ dammit databases --install --full --database-dir /mnt/harmonia/
========================================
dammit! a tool for easy de novo transcriptome annotation
Camille Scott 2015
========================================

submodule: databases

--- Checking PATH for dependencies

          [x] TransDecoder

          [x] LAST

          [x] HMMER

          [x] Infernal

          [x] crb-blast

          [x] BLAST+

          [x] BUSCO


--- Dependency results

          All dependencies satisfied!


--- Checking for database prep (dir: /mnt/harmonia)

          [ ] download_and_gunzip:Pfam-A.hmm

          [ ] hmmpress:Pfam-A.hmm

          [ ] download_and_gunzip:Rfam.cm

          [ ] cmpress:Rfam.cm

          [ ] download_and_gunzip:aa_seq_euk.fasta

          [ ] lastdb:aa_seq_euk.fasta.db

          [ ] download_and_gunzip:ODB8_EukOGs_genes_ALL_levels.txt

          [ ] download_and_untar:harmonia-metazoa

--- Database results

          Database prep incomplete

[camillescott]

Yeah, this is a purposeful regression in 0.2.0, as --full wasn't being run
in the annotation stage anyhow. I'll be putting together a list of known
issues today and adding this, though it will be reactivated in an upcoming
version.

On Thu, Dec 10, 2015 at 4:02 AM, Matt MacManes notifications@github.com
wrote:

using dammit 0.2.0

$ dammit databases --install --full --database-dir /mnt/harmonia/

dammit! a tool for easy de novo transcriptome annotation

Camille Scott 2015

submodule: databases

--- Checking PATH for dependencies

      [x] TransDecoder

      [x] LAST

      [x] HMMER

      [x] Infernal

      [x] crb-blast

      [x] BLAST+

      [x] BUSCO

--- Dependency results

      All dependencies satisfied!

--- Checking for database prep (dir: /mnt/harmonia)

      [ ] download_and_gunzip:Pfam-A.hmm

      [ ] hmmpress:Pfam-A.hmm

      [ ] download_and_gunzip:Rfam.cm

      [ ] cmpress:Rfam.cm

      [ ] download_and_gunzip:aa_seq_euk.fasta

      [ ] lastdb:aa_seq_euk.fasta.db

      [ ] download_and_gunzip:ODB8_EukOGs_genes_ALL_levels.txt

      [ ] download_and_untar:harmonia-metazoa

--- Database results

      Database prep incomplete

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Camille Scott

Department of Computer Science
Lab for Data Intensive Biology
University of California, Davis

camille.scott.w@gmail.com