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dib-lab / dammit

just annotate it, dammit!
http://dib-lab.github.io/dammit/
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--full not working to download uniref90 #36

Closed macmanes closed 8 years ago

macmanes commented 8 years ago

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 commented 8 years ago

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

— Reply to this email directly or view it on GitHub https://github.com/camillescott/dammit/issues/36.

Camille Scott

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

camille.scott.w@gmail.com